Contacts of the helix formed by residues 508 - 525 (chain A) in PDB entry 4Z4Q
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 ASP 508 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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433A GLU* 4.4 1.4 - - - +
506A ASP* 2.8 39.4 + - + +
507A ALA* 1.3 79.6 - - - +
509A THR* 1.3 65.1 + - - +
510A ASP* 3.4 12.9 + - - +
511A GLY 2.9 30.3 + - - -
512A ALA* 3.1 19.6 + - - +
581A LYS 3.7 15.5 - - - +
1076A HIS* 6.2 0.6 - - - -
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Residues in contact with THR 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A ASP* 1.3 76.6 - - - +
510A ASP* 1.3 70.4 + - - +
512A ALA* 2.9 27.9 - - - +
513A HIS 2.9 7.1 + - - -
1019A ARG* 4.5 10.3 - - + +
1020A TYR* 3.6 19.7 - - - +
1023A TYR* 3.4 55.4 - - + -
1028A ARG* 4.4 0.5 + - - -
1076A HIS* 5.6 0.3 - - - -
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Residues in contact with ASP 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A GLU* 4.6 7.2 - - - +
458A LYS* 3.1 32.6 + - + +
508A ASP* 3.4 11.2 + - - +
509A THR* 1.3 83.7 + - - +
511A GLY* 1.3 60.2 + - - +
513A HIS* 3.3 5.0 + - - +
514A ILE* 3.0 34.9 + - + +
1020A TYR* 3.8 4.7 - - - -
1028A ARG* 3.0 31.2 + - - -
1076A HIS* 4.3 12.8 + - - -
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Residues in contact with GLY 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A GLU* 3.7 17.9 + - - -
505A THR* 3.5 21.6 + - - -
506A ASP 3.7 4.9 - - - -
508A ASP* 2.9 15.3 + - - -
509A THR 3.2 0.2 - - - -
510A ASP* 1.3 73.4 - - - +
512A ALA* 1.3 67.0 + - - +
514A ILE* 3.0 5.2 + - - +
515A GLN* 2.9 27.6 + - - +
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Residues in contact with ALA 512 (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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506A ASP 4.7 0.2 + - - -
508A ASP 3.1 12.4 + - - +
509A THR* 2.9 17.2 + - - +
511A GLY* 1.3 76.8 - - - +
513A HIS* 1.3 62.2 + - - +
515A GLN* 3.3 9.7 + - - +
516A THR* 3.1 20.6 + - - -
1016A ARG* 3.7 39.9 - - + +
1019A ARG* 4.6 8.7 - - + -
1020A TYR* 4.7 1.1 - - + -
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Residues in contact with HIS 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A LYS* 2.8 32.1 + - + +
509A THR 2.9 5.7 + - - -
510A ASP 3.5 7.4 - - - +
512A ALA* 1.3 76.1 - - - +
514A ILE* 1.3 57.9 + - - +
516A THR* 2.9 40.3 + - + -
517A LEU* 3.0 35.2 + - + +
622A MET* 5.0 2.2 - - - +
1016A ARG 5.3 0.2 - - - -
1017A PHE* 4.9 7.9 - + - -
1020A TYR* 3.2 58.8 - + + +
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Residues in contact with ILE 514 (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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433A GLU* 3.7 34.8 - - + +
455A LEU* 4.5 11.9 - - + +
457A GLY 4.8 6.3 - - - +
458A LYS* 4.3 34.5 - - + +
459A VAL* 4.5 8.0 - - + +
505A THR* 3.6 20.4 - - + -
510A ASP* 3.0 19.8 + - + +
511A GLY 3.0 6.3 + - - +
513A HIS* 1.3 75.4 - - - +
515A GLN* 1.3 64.1 + - - +
517A LEU* 3.2 10.3 + - + +
518A LEU* 3.1 35.9 + - + +
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Residues in contact with GLN 515 (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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503A ILE* 4.5 13.0 + - + -
505A THR* 3.0 30.4 + - + +
506A ASP 4.7 2.8 + - - -
507A ALA* 6.2 0.4 - - - +
511A GLY 2.9 18.9 + - - +
512A ALA* 3.6 6.1 - - - +
514A ILE* 1.3 72.7 - - - +
516A THR* 1.3 55.2 + - - +
518A LEU* 3.0 7.8 + - - +
519A LEU* 2.8 41.9 + - + +
537A ILE* 3.5 41.9 - - + +
538A ALA 5.6 1.8 + - - -
1016A ARG* 3.2 35.5 + - + +
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Residues in contact with THR 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A ALA 3.1 5.0 + - - -
513A HIS* 2.9 19.7 + - + +
515A GLN* 1.3 79.4 - - - +
517A LEU* 1.3 58.4 + - - +
519A LEU* 4.6 1.8 - - - -
520A THR* 3.0 31.5 + - - +
622A MET* 3.0 40.8 - - + -
1013A MET* 3.7 18.0 + - - +
1016A ARG* 3.6 23.5 - - - +
1017A PHE* 3.9 22.1 + - + +
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Residues in contact with LEU 517 (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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458A LYS* 4.8 4.0 - - + -
459A VAL* 3.4 44.4 - - + +
460A ILE 4.4 6.3 - - - +
461A ASN* 3.9 24.7 - - + +
462A THR* 4.6 0.2 + - - -
513A HIS* 3.0 46.7 + - + +
514A ILE* 3.2 16.3 + - + +
516A THR* 1.3 74.1 - - - +
518A LEU* 1.3 64.0 + - - +
520A THR* 3.1 18.6 + - - -
521A PHE* 3.3 9.9 + - - +
622A MET* 3.6 20.0 - - + -
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Residues in contact with LEU 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A LEU* 4.2 3.8 - - + -
455A LEU* 3.5 32.8 - - + -
459A VAL* 4.3 17.0 - - + -
476A ILE* 6.4 0.7 - - + -
479A MET* 4.0 32.1 - - + -
503A ILE* 3.5 45.5 - - + -
514A ILE* 3.1 20.2 + - + +
515A GLN 3.0 5.5 + - - +
517A LEU* 1.3 75.1 - - - +
519A LEU* 1.3 62.6 + - - +
521A PHE* 2.9 24.1 + - + +
522A PHE* 3.0 20.1 + - + -
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Residues in contact with LEU 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A ILE* 4.4 9.2 - - + -
515A GLN* 2.8 22.3 + - + +
516A THR* 4.0 4.7 - - - +
518A LEU* 1.3 77.4 - - - +
520A THR* 1.3 55.5 + - - +
522A PHE* 3.0 7.8 + - + +
523A TYR* 2.8 31.0 + - - +
530A VAL* 6.2 1.3 - - + -
535A VAL* 4.1 19.5 - - + -
537A ILE* 4.3 15.3 - - + -
606A VAL* 3.8 29.2 - - + -
618A VAL* 6.2 0.2 - - - -
1009A LEU* 4.4 16.9 - - + +
1012A ILE* 4.1 26.9 - - + -
1013A MET* 4.2 15.0 - - + +
1016A ARG* 6.1 2.5 - - + -
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Residues in contact with THR 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ASN* 4.4 10.4 + - - -
462A THR* 3.7 10.8 + - - -
463A ALA* 5.1 3.3 + - - -
516A THR 3.0 17.8 + - - +
517A LEU* 3.1 17.5 + - - -
518A LEU 3.2 0.2 - - - -
519A LEU* 1.3 75.5 - - - +
521A PHE* 1.3 61.0 + - - +
523A TYR* 4.1 6.2 - - - +
524A ARG* 3.2 30.3 + - - +
618A VAL* 3.9 14.6 - - + -
622A MET* 3.3 34.2 - - + +
1013A MET* 3.6 15.3 - - + -
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Residues in contact with PHE 521 (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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459A VAL* 5.9 1.1 - - + -
460A ILE 5.7 0.2 - - - +
462A THR* 3.4 24.2 - - + +
476A ILE* 3.3 54.1 - - + -
479A MET* 4.6 15.0 - - + -
480A ILE* 5.3 8.5 - - + -
487A VAL* 5.8 3.8 - - + -
517A LEU 3.3 7.5 + - - +
518A LEU* 2.9 15.7 + - + +
520A THR* 1.3 84.3 + - - +
522A PHE* 1.3 86.6 + + - +
524A ARG* 4.8 0.7 - - - -
525A TYR* 3.0 48.8 + + + +
526A MET* 4.0 16.8 + - + -
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Residues in contact with PHE 522 (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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431A LEU* 3.9 19.3 - - + -
479A MET* 3.0 30.3 - - + -
483A ILE* 4.4 5.4 - - + -
501A ILE* 4.3 14.4 - - + -
503A ILE* 4.3 11.2 - - + -
518A LEU* 3.0 27.9 + - + -
519A LEU* 3.0 8.9 + - + +
521A PHE* 1.3 91.4 - + - +
523A TYR* 1.3 59.4 + - - +
524A ARG 3.4 0.2 - - - -
526A MET* 3.2 58.9 - - + +
527A ARG* 3.5 3.5 + - - -
529A LEU* 5.1 2.9 - - + -
530A VAL* 4.1 12.0 - - + +
535A VAL* 4.2 31.4 - - + -
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Residues in contact with TYR 523 (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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519A LEU 2.8 15.2 + - - +
520A THR* 4.3 4.3 - - - +
522A PHE* 1.3 79.3 - - - +
524A ARG* 1.3 73.6 + - + +
525A TYR 3.7 0.2 - - - -
527A ARG* 3.7 23.2 - - + +
530A VAL* 5.3 5.2 - - + -
611A LEU* 3.8 27.7 + - + +
614A ALA* 4.6 5.4 - - + -
615A GLU* 2.7 55.5 + - - +
618A VAL* 4.1 26.5 - - + -
1009A LEU* 3.7 31.9 - - + -
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Residues in contact with ARG 524 (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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462A THR* 2.7 28.4 + - - +
463A ALA* 3.6 32.2 + - + +
488A GLY* 5.2 2.3 - - - -
520A THR* 3.2 22.4 + - - +
523A TYR* 1.3 97.5 - - + +
525A TYR* 1.3 94.5 + - + +
526A MET 3.7 0.7 - - - -
527A ARG* 4.9 2.1 - - - +
615A GLU* 5.2 7.4 + - - -
618A VAL* 5.2 7.4 - - + +
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Residues in contact with TYR 525 (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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462A THR* 3.7 18.9 + - + -
467A MET* 4.1 28.2 - - + +
470A ILE* 5.3 7.5 - - + +
487A VAL* 3.9 8.4 - - + -
488A GLY* 3.0 44.1 + - - +
491A PHE* 4.5 1.2 - - - -
521A PHE* 3.0 41.4 + + + +
524A ARG* 1.3 117.7 + - + +
526A MET* 1.3 71.5 + - - +
527A ARG 3.9 0.4 - - - -
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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
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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