Contacts of the helix formed by residues 528 - 545 (chain A) in PDB entry 3S95
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 GLU 528 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452A HIS* 3.2 50.4 - - + +
457A ILE* 3.8 18.3 - - + +
485A MET* 3.6 26.7 - - + +
527A ASP* 1.3 86.3 - - - +
529A LYS* 1.3 88.6 + - + +
530A VAL 3.1 0.2 - - - -
531A ASP* 3.0 14.6 + - - +
532A VAL 4.0 0.2 + - - -
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Residues in contact with LYS 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A ASP* 2.9 20.8 + - - +
528A GLU* 1.3 93.7 - - + +
530A VAL* 1.3 65.4 + - - +
531A ASP 3.1 0.4 - - - -
532A VAL* 2.9 31.4 + - + +
533A PHE 3.3 3.5 + - - -
591A PRO* 3.0 42.0 + - + +
592A GLU* 3.9 11.3 + - - +
594A ARG* 2.8 44.7 + - + +
596A SER* 4.1 20.6 - - - +
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Residues in contact with VAL 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A ILE* 3.6 22.2 - - + -
459A ARG* 4.7 1.8 - - + -
517A ALA* 3.7 24.3 + - + +
519A GLU* 3.5 18.1 + - + +
520A MET* 4.0 24.7 - - + -
526A TYR* 3.5 28.9 - - + -
527A ASP 3.1 18.3 + - - +
528A GLU 3.1 1.0 + - - -
529A LYS* 1.3 75.7 - - - +
531A ASP* 1.3 68.1 - - - +
533A PHE* 3.3 6.4 + - - +
534A SER* 3.2 22.6 + - - -
594A ARG* 4.0 0.2 - - - +
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Residues in contact with ASP 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A MET* 3.3 13.4 - - + +
452A HIS* 2.8 26.1 + - - +
457A ILE* 3.4 9.7 - - - +
458A HIS* 2.9 23.8 + - - +
459A ARG* 2.8 31.1 + - - -
460A ASP 4.6 0.3 + - - -
461A LEU* 3.8 6.6 + - + +
528A GLU 3.0 9.0 + - - +
530A VAL* 1.3 79.9 - - - +
532A VAL* 1.3 59.2 + - - +
534A SER* 3.3 9.4 + - - -
535A PHE* 3.0 22.9 + - - +
597A PHE* 3.5 17.0 - - + -
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Residues in contact with VAL 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A HIS* 4.8 1.8 - - + +
528A GLU 4.5 1.3 - - - +
529A LYS* 2.9 26.0 + - + +
531A ASP* 1.3 73.9 - - - +
533A PHE* 1.3 65.3 + - - +
535A PHE* 3.3 2.1 + - - +
536A GLY 2.9 18.7 + - - -
586A CYS* 3.6 26.8 - - + +
594A ARG* 3.8 20.6 - - + -
595A PRO 3.4 27.4 - - - +
596A SER* 4.8 0.4 - - - -
597A PHE* 3.6 33.7 - - + +
600A LEU* 3.9 5.2 - - + -
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Residues in contact with PHE 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A TRP 3.8 5.2 - - - -
516A MET 3.5 16.8 - - - -
517A ALA* 3.6 15.7 - - + -
518A PRO* 3.5 23.8 - - + -
529A LYS 3.3 5.7 + - - -
530A VAL 3.6 8.5 - - - +
531A ASP 3.2 0.4 - - - -
532A VAL* 1.3 76.5 - - - +
534A SER* 1.3 63.5 + - - +
536A GLY* 3.0 11.6 + - - -
537A ILE* 3.0 33.0 + - + +
555A ARG* 3.5 14.4 - - - -
559A PHE 3.5 22.0 - - - -
560A GLY* 4.6 4.9 - - - -
586A CYS 3.4 8.1 + - - -
587A CYS* 3.4 40.5 - - + -
588A ASP 4.7 0.2 - - - -
594A ARG* 3.8 22.9 - - - +
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Residues in contact with SER 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A ARG 5.6 3.3 + - - -
461A LEU* 3.3 33.3 + - - +
515A TRP* 2.7 31.5 + - - +
516A MET* 4.6 2.3 - - - -
517A ALA 4.6 0.2 + - - -
530A VAL 3.2 12.3 + - - -
531A ASP* 3.6 11.9 + - - -
533A PHE* 1.3 76.7 - - - +
535A PHE* 1.3 62.1 + - - +
537A ILE* 3.2 6.3 + - - +
538A VAL* 3.0 25.4 + - - +
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Residues in contact with PHE 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A ALA* 3.5 30.1 - - - -
444A ILE* 3.7 32.3 - - + -
445A ALA* 4.1 7.0 - - + -
461A LEU* 4.0 6.8 - - + +
531A ASP 3.0 13.2 + - - +
532A VAL 3.4 7.0 - - - +
534A SER* 1.3 74.1 - - - +
536A GLY* 1.3 58.8 + - - +
538A VAL* 3.1 12.2 + - + +
539A LEU* 2.9 58.2 + - + +
586A CYS* 3.9 6.3 - - - -
597A PHE* 3.6 15.9 - + + -
600A LEU* 3.9 31.0 - - + -
604A LEU* 3.7 18.4 - - + -
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Residues in contact with GLY 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532A VAL 2.9 11.1 + - - -
533A PHE 3.0 5.3 + - - -
535A PHE* 1.3 74.4 - - - +
537A ILE* 1.3 55.9 + - - +
539A LEU* 3.2 9.7 + - - +
540A CYS* 3.0 30.1 + - - -
583A THR* 3.5 4.0 - - - +
586A CYS* 3.6 23.7 - - - +
587A CYS* 3.6 14.8 - - - -
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Residues in contact with ILE 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514A TYR 3.8 11.9 - - - +
515A TRP* 3.5 22.7 - - + -
533A PHE* 3.0 34.9 + - + +
534A SER 3.2 6.5 + - - +
536A GLY* 1.3 72.8 - - - +
538A VAL* 1.3 63.4 + - - +
540A CYS* 3.1 8.9 + - - +
541A GLU* 3.0 21.0 + - - +
548A ALA* 3.7 23.3 - - + -
553A LEU* 3.7 17.0 - - + -
555A ARG* 3.7 29.8 - - - +
561A LEU* 5.5 3.1 - - + -
587A CYS* 4.2 10.5 - - - -
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Residues in contact with VAL 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A LEU* 3.7 29.8 - - + -
444A ILE* 4.2 11.9 - - + -
461A LEU* 4.8 6.7 - - + -
462A ASN* 3.9 21.1 - - - +
463A SER* 4.8 1.3 - - - -
466A CYS* 5.6 0.7 - - - -
515A TRP* 3.8 17.9 - - + +
534A SER 3.0 20.5 + - - +
535A PHE* 3.1 15.5 + - + +
537A ILE* 1.3 76.6 - - - +
539A LEU* 1.3 62.0 + - + +
541A GLU* 3.1 15.7 + - - +
542A ILE* 2.9 29.4 + - + +
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Residues in contact with LEU 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A ALA* 3.5 31.9 - - + -
535A PHE* 2.9 49.0 + - + +
536A GLY* 3.2 8.3 + - - +
538A VAL* 1.3 73.3 - - + +
540A CYS* 1.3 57.0 + - - +
542A ILE* 3.2 9.1 + - + +
543A ILE* 2.9 35.0 + - + +
579A PHE* 3.8 18.6 - - + -
582A ILE* 4.1 15.7 - - + -
583A THR* 3.3 36.1 - - - +
586A CYS* 4.3 3.8 - - - -
604A LEU* 5.4 0.7 - - + -
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Residues in contact with CYS 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536A GLY 3.0 20.4 + - - -
537A ILE* 3.1 9.8 + - - +
539A LEU* 1.3 76.3 - - - +
541A GLU* 1.3 57.5 + - - +
543A ILE* 4.7 0.4 - - - -
544A GLY* 2.8 31.2 + - - -
546A VAL* 3.6 6.2 - - - +
553A LEU* 3.7 24.7 - - + -
561A LEU* 3.8 34.3 - - - -
566A PHE* 3.6 14.7 - - + -
580A PHE* 5.3 0.2 - - - -
583A THR* 3.5 16.8 - - - -
587A CYS* 4.5 2.7 - - - -
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Residues in contact with GLU 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ARG* 3.9 13.9 - - - -
425A ILE* 3.6 17.4 - - + +
463A SER* 2.6 34.1 + - - -
515A TRP* 2.8 37.4 + - - -
537A ILE* 3.0 13.9 + - + +
538A VAL* 3.1 15.0 + - - +
540A CYS* 1.3 77.3 - - - +
542A ILE* 1.3 57.4 + - - +
545A ARG* 2.8 31.0 + - - -
546A VAL* 3.4 26.3 + - + +
548A ALA* 4.1 14.4 + - + +
553A LEU* 5.2 0.7 - - + -
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Residues in contact with ILE 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A LEU* 4.1 13.2 - - + -
425A ILE* 3.9 23.1 - - + -
428A MET* 4.5 5.3 - - + +
437A ARG* 3.1 61.3 + - + +
440A PHE* 4.3 19.1 - - + -
441A ALA* 4.5 5.4 - - + +
444A ILE* 5.0 0.7 - - + -
538A VAL* 2.9 32.3 + - + +
539A LEU* 3.6 20.2 - - + +
541A GLU* 1.3 76.5 - - - +
543A ILE* 1.3 63.5 + - - +
545A ARG* 4.0 4.0 + - - +
579A PHE* 4.5 9.9 - - + -
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Residues in contact with ILE 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A TRP* 4.0 8.1 - - + -
437A ARG* 3.5 7.4 + - - -
539A LEU 2.9 18.0 + - - +
540A CYS 4.1 1.6 - - - +
542A ILE* 1.3 80.3 - - - +
544A GLY* 1.3 59.5 + - - +
545A ARG* 4.6 0.5 + - - +
566A PHE* 3.9 18.6 - - + -
571A CYS* 4.4 2.5 - - - -
572A PRO* 3.4 38.7 - - + +
575A CYS* 3.9 13.5 - - - -
579A PHE* 3.6 47.3 - - + +
580A PHE* 4.2 8.1 - - + -
583A THR* 3.2 31.4 - - + +
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Residues in contact with GLY 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GOL 3.2 16.8 + - - -
540A CYS 2.8 19.5 + - - -
543A ILE* 1.3 73.2 - - - +
545A ARG* 1.3 72.0 + - - +
546A VAL* 3.1 4.9 + - - -
566A PHE* 3.7 8.7 - - - -
570A TYR* 3.7 29.8 - - - +
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Residues in contact with ARG 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GOL 3.0 63.3 + - - +
422A ARG* 5.2 2.5 + - - -
425A ILE* 3.8 17.4 - - + +
428A MET* 3.0 47.8 + - + -
429A ASP* 3.6 18.6 - - - +
430A SER* 3.7 30.1 - - - +
437A ARG* 3.8 22.2 - - - +
541A GLU 2.8 14.0 + - - -
542A ILE 4.2 0.9 - - - +
543A ILE 3.4 1.0 + - - -
544A GLY* 1.3 76.9 + - - +
546A VAL* 1.3 57.5 + - - +
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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) + - + + + + + -
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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