Contacts of the helix formed by residues 511 - 537 (chain A) in PDB entry 4C48
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 511 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A LYS 3.5 2.7 + - - +
510A LYS* 1.3 69.4 - - - +
512A PHE* 1.3 65.8 - - - -
513A PHE* 2.8 8.0 + - - -
514A GLY* 2.9 14.9 + - - -
515A TRP* 3.7 4.1 + - - +
518A ARG* 5.1 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU* 4.4 27.4 - - + -
360A GLN* 5.3 0.9 - - - -
511A GLY* 1.3 69.4 - - - -
513A PHE* 1.3 95.5 + + + +
515A TRP* 3.1 53.5 + + + +
516A PHE* 3.0 41.4 + + + +
16C PRO* 6.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A TYR* 3.6 39.0 - + - -
357A LEU* 5.6 3.4 - - - -
360A GLN* 3.1 44.1 + - + +
509A LYS* 4.3 12.1 - - + -
510A LYS 4.0 17.3 - - - +
511A GLY* 2.8 1.9 + - - -
512A PHE* 1.3 103.4 - + + +
514A GLY* 1.3 53.7 + - - +
516A PHE* 3.4 1.5 + - - +
517A ASN* 2.4 38.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A GLY 4.4 5.8 - - - -
507A GLU 4.0 14.4 - - - -
509A LYS* 4.0 10.4 + - - +
511A GLY 2.9 8.6 + - - -
513A PHE* 1.3 76.1 - - - +
515A TRP* 1.3 65.1 + - - +
517A ASN* 3.1 5.4 + - - +
518A ARG* 2.9 44.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A GLY 3.7 3.6 + - - +
512A PHE* 3.1 54.7 + + + +
514A GLY* 1.3 74.0 - - - +
516A PHE* 1.3 66.9 + + - +
518A ARG* 3.1 16.7 + - + +
519A MET* 2.8 67.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU* 3.2 43.5 - - + -
358A PHE* 4.0 20.6 - + - -
360A GLN* 3.9 12.8 - - - +
512A PHE* 3.0 32.8 + + + +
513A PHE 3.4 8.7 - - - +
514A GLY 3.2 0.2 - - - -
515A TRP* 1.3 84.0 - + - +
517A ASN* 1.3 63.1 + - - +
519A MET* 3.2 2.6 + - + +
520A PHE* 2.8 48.6 + + + +
19C MET* 3.6 30.5 - - + -
23C LEU* 5.3 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A PHE 5.3 3.3 - - - +
360A GLN* 2.7 33.8 + - - +
505A HIS* 3.4 24.1 - - + +
506A GLY* 4.0 20.4 + - - +
507A GLU* 4.7 5.2 - - + -
513A PHE 2.4 31.7 + - - +
514A GLY 3.1 6.7 + - - +
516A PHE* 1.3 80.9 - - - +
518A ARG* 1.3 57.4 + - - +
520A PHE* 3.9 5.0 - - - +
521A GLU* 3.1 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A GLU* 2.9 48.0 + - + +
508A GLY* 4.8 2.6 - - - -
509A LYS 4.6 5.1 + - - -
511A GLY 5.1 1.0 + - - -
514A GLY* 2.9 38.7 + - - +
515A TRP* 3.2 15.2 - - - +
517A ASN* 1.3 77.2 - - - +
519A MET* 1.3 61.0 + - + +
521A GLU* 3.3 6.1 + - - +
522A LYS* 2.8 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A TRP* 2.8 52.9 + - + +
516A PHE* 4.1 3.1 - - + +
518A ARG* 1.3 76.7 - - + +
520A PHE* 1.3 55.4 + - - +
522A LYS* 3.5 34.8 - - + +
523A SER* 2.5 36.1 + - - -
23C LEU* 6.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A PHE* 3.7 22.0 - + - -
505A HIS* 6.1 2.9 - + - -
516A PHE* 2.8 34.8 + + + +
517A ASN* 3.9 5.4 - - - +
519A MET* 1.3 75.8 - - - +
521A GLU* 1.3 57.9 + - + +
523A SER* 2.9 9.7 + - - -
524A THR* 2.7 48.3 + - + -
972A LEU* 4.4 5.8 - - + -
973A ARG* 3.4 56.8 - - + -
976A LEU* 3.8 25.4 - - + -
19C MET* 5.4 0.2 - - + -
23C LEU* 4.4 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A HIS* 3.6 36.1 + - + +
507A GLU* 4.1 19.1 - - - +
517A ASN 3.1 18.4 + - - +
518A ARG* 3.7 4.7 - - - +
520A PHE* 1.3 82.3 - - + +
522A LYS* 1.3 57.6 + - - +
524A THR* 3.3 15.2 - - - +
525A HIS* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A ARG* 2.8 16.3 + - - +
519A MET* 3.5 42.2 - - + +
521A GLU* 1.3 72.2 - - - +
523A SER* 1.3 68.0 + - - +
524A THR 2.9 2.9 + - - -
525A HIS* 3.0 7.9 + - - +
526A HIS* 3.0 25.0 + - + +
27C TYR* 6.4 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A MET 2.5 22.4 + - - -
520A PHE* 2.9 17.7 + - - -
522A LYS* 1.3 74.4 - - - +
524A THR* 1.3 55.2 + - - +
526A HIS* 3.7 7.5 - - - +
527A TYR* 3.0 29.1 + - - +
972A LEU* 5.5 2.0 - - - +
23C LEU* 4.3 30.8 - - - +
26C ILE* 5.3 7.2 - - - +
27C TYR* 6.1 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A PHE* 2.7 30.5 + - + -
521A GLU* 3.3 21.3 - - - +
522A LYS 2.9 0.6 + - - -
523A SER* 1.3 74.7 - - - +
525A HIS* 1.3 62.5 + - - +
527A TYR* 3.1 7.1 + - - +
528A THR* 2.7 37.4 + - - +
969A ARG* 3.9 26.9 - - + +
972A LEU* 4.3 21.5 - - + +
973A ARG* 5.7 0.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A GLU* 3.0 12.3 + - - +
522A LYS* 3.0 10.3 + - - +
524A THR* 1.3 73.8 - - - +
526A HIS* 1.3 64.8 + - - +
528A THR* 3.1 7.5 + - - -
529A ASP* 2.5 35.3 + - + +
969A ARG* 6.2 1.1 - - - +
2040A NI 2.0 41.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A LYS* 3.0 14.1 + - + +
523A SER* 3.7 12.3 - - - +
525A HIS* 1.3 77.0 - - - +
527A TYR* 1.3 58.6 + - - +
529A ASP* 3.8 5.0 - - - +
530A SER* 2.9 40.8 + - - -
26C ILE 5.4 0.4 + - - -
27C TYR* 3.4 48.2 - + + -
30C GLY* 4.2 5.7 - - - -
31C GLU* 3.7 26.3 + - + +
34C ASN* 4.2 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A SER 3.0 16.4 + - - +
524A THR* 3.1 4.9 + - - +
526A HIS* 1.3 81.7 + - - +
528A THR* 1.3 63.8 + - - +
530A SER* 3.2 7.7 + - - -
531A VAL* 2.9 39.8 + - + +
968A VAL* 3.1 36.0 - - + +
972A LEU* 3.5 31.4 - - + -
1019A ILE* 2.3 58.0 + - + +
1020A PHE* 3.4 39.0 - + - -
26C ILE* 5.2 11.0 - - + +
30C GLY* 6.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A THR* 2.7 25.6 + - - +
525A HIS* 3.6 6.9 - - - -
527A TYR* 1.3 78.5 - - - +
529A ASP* 1.3 62.6 + - - +
530A SER 3.0 1.3 - - - -
531A VAL* 3.0 6.1 + - - +
532A GLY 3.0 24.4 + - - -
965A LEU* 3.4 32.6 - - + +
968A VAL* 4.9 2.5 - - + -
969A ARG* 3.6 49.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A HIS* 2.5 28.5 + - + +
526A HIS* 3.8 4.9 - - - +
528A THR* 1.3 73.6 - - - +
530A SER* 1.3 58.8 + - - +
532A GLY* 3.6 3.6 + - - +
533A GLY* 3.6 14.0 + - - -
965A LEU* 5.6 0.2 - - - -
2040A NI 1.8 47.2 - - - +
34C ASN* 4.9 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A HIS* 2.9 37.8 + - - -
527A TYR* 3.3 13.5 - - - -
528A THR 3.0 0.2 - - - -
529A ASP* 1.3 75.2 - - - +
531A VAL* 1.3 64.0 + - - +
532A GLY 3.2 0.2 - - - -
533A GLY* 3.2 3.6 + - - -
534A ILE* 3.1 28.8 + - - +
1020A PHE* 4.8 6.7 - - - -
30C GLY* 3.7 17.4 + - - -
33C PHE* 5.6 1.2 - - - +
34C ASN* 3.7 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A TYR* 2.9 57.2 + - + +
528A THR* 3.0 8.4 + - - +
530A SER* 1.3 72.8 - - - +
532A GLY* 1.3 65.6 + - - +
534A ILE* 3.8 9.4 - - + -
535A LEU* 2.9 30.8 + - + +
964A THR* 4.8 0.4 - - + -
965A LEU* 4.5 11.0 - - + -
968A VAL* 4.5 9.0 - - + -
1019A ILE 4.5 2.2 - - - +
1020A PHE* 4.2 11.0 - - + +
1023A PRO* 4.1 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 532 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A THR 3.0 13.3 + - - -
529A ASP* 3.6 6.5 + - - -
530A SER 3.2 0.4 - - - -
531A VAL* 1.3 76.1 - - - +
533A GLY* 1.3 60.0 + - - +
535A LEU* 3.2 6.7 + - - +
536A ARG* 3.1 21.5 + - - +
961A ILE* 6.3 0.9 - - - -
965A LEU* 3.8 15.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 533 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A ASP 3.6 8.5 + - - -
530A SER* 3.2 8.0 + - - -
532A GLY* 1.3 73.7 - - - +
534A ILE* 1.3 63.1 + - - +
535A LEU 3.3 0.5 + - - -
536A ARG* 3.3 15.4 + - - +
537A SER* 3.6 3.8 + - - -
33C PHE 5.7 0.7 - - - -
34C ASN* 5.5 4.3 - - - -
37C SER* 3.0 24.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 534 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A SER* 3.1 15.8 + - - +
531A VAL* 3.4 11.2 + - + +
533A GLY* 1.3 74.3 - - - +
535A LEU* 1.3 58.0 + - + +
537A SER 3.1 16.8 + - - -
538A THR* 3.9 2.1 + - - -
541A TYR* 3.4 49.8 + - + +
1020A PHE* 3.6 48.2 - - + +
1021A PHE* 6.5 0.2 - - + -
1023A PRO* 6.2 0.2 - - + -
1024A VAL* 3.7 26.3 - - + +
33C PHE* 3.9 23.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 535 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A VAL* 2.9 20.5 + - + +
532A GLY* 3.6 5.4 - - - +
534A ILE* 1.3 74.7 - - + +
536A ARG* 1.3 63.8 + - - +
537A SER 3.2 1.0 + - - -
538A THR* 4.0 6.9 + - - +
961A ILE* 4.1 20.6 - - + -
964A THR* 3.5 31.9 - - + -
965A LEU* 3.6 18.2 - - + -
1023A PRO* 3.9 20.2 - - + -
1024A VAL* 4.0 9.2 - - + +
1027A VAL* 3.6 39.2 - - + +
1031A ARG* 3.4 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 536 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A GLY 3.1 11.3 + - - +
533A GLY* 3.3 12.1 + - - +
535A LEU* 1.3 78.1 - - - +
537A SER* 1.3 59.6 + - - +
538A THR* 3.5 3.6 + - - +
1031A ARG* 4.8 10.9 + - - +
37C SER* 5.4 0.2 - - - +
38C GLY 4.6 1.4 - - - +
40C GLY* 5.6 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 537 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A GLY 3.6 0.7 + - - -
534A ILE 3.1 12.9 + - - -
536A ARG* 1.3 79.4 - - - +
538A THR* 1.3 64.5 + - - +
539A GLY 3.0 4.4 + - - -
540A ARG* 3.7 6.6 + - - +
541A TYR* 3.1 19.1 - - - -
37C SER* 2.7 25.9 + - - -
38C GLY 2.6 42.1 + - - -
39C VAL 4.7 2.2 - - - -
40C GLY* 5.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il