Contacts of the helix formed by residues 491 - 504 (chain B) in PDB entry 3GJN
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 SER 491 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489B PHE* 3.5 0.6 - - - +
490B LYS* 1.3 81.1 + - - +
492B PHE* 1.3 61.2 + - - +
493B ASP* 3.1 11.7 + - - +
494B ASP* 2.7 31.4 + - - +
495B PHE 3.3 14.2 + - - -
556B TYR* 3.1 23.2 + - - -
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Residues in contact with PHE 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491B SER* 1.3 73.1 - - - +
493B ASP* 1.3 58.1 + - - +
495B PHE* 3.5 28.2 - + - +
496B ARG* 3.1 24.1 + - + +
543B LEU* 4.4 32.8 - - + -
545B ALA* 4.8 18.2 - - + -
556B TYR* 3.3 31.4 + + + -
561B ILE* 3.9 22.4 - - + -
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Residues in contact with ASP 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491B SER* 3.1 10.0 + - - +
492B PHE* 1.3 76.9 - - - +
494B ASP* 1.3 64.9 + - - +
495B PHE 3.0 1.3 - - - -
496B ARG* 2.8 40.6 + - - +
497B LYS* 3.0 35.5 + - - +
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Residues in contact with ASP 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488B GLU 4.5 0.5 - - - +
489B PHE* 3.6 8.1 - - - -
490B LYS* 2.9 55.4 + - + +
491B SER* 2.7 18.4 + - - +
493B ASP* 1.3 76.3 - - - +
495B PHE* 1.3 62.3 + - - +
497B LYS* 3.5 15.4 + - - +
498B LYS* 3.2 50.6 + - - +
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Residues in contact with PHE 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B ALA* 4.0 18.6 - - + -
476B VAL* 5.5 1.1 - - + -
484B LEU* 3.6 29.4 - - + -
489B PHE* 3.9 31.2 - + + +
491B SER 3.3 12.1 + - - +
492B PHE* 3.5 31.0 - + - +
493B ASP 3.0 0.6 - - - -
494B ASP* 1.3 80.7 - - - +
496B ARG* 1.3 66.7 + - - +
498B LYS* 3.3 1.9 + - - +
499B PHE* 3.0 30.3 + + + +
543B LEU* 4.4 11.9 - - + -
556B TYR* 4.1 16.6 - + + -
558B MET* 4.0 17.9 - - + -
561B ILE* 4.0 26.0 - - + -
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Residues in contact with ARG 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492B PHE* 3.1 14.2 + - + +
493B ASP* 2.8 37.5 + - - +
495B PHE* 1.3 77.4 - - - +
497B LYS* 1.3 88.2 + - - +
499B PHE* 3.4 2.6 + - - +
500B TRP* 3.1 45.7 + - - +
524B GLY 2.3 35.8 + - - -
525B LYS* 3.8 8.5 - - - +
526B ALA* 4.3 9.0 - - - +
543B LEU* 3.4 35.2 - - + +
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Residues in contact with LYS 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493B ASP* 3.0 23.3 + - - +
494B ASP* 3.5 20.9 - - - +
496B ARG* 1.3 102.7 - - - +
498B LYS* 1.4 58.1 + - + +
500B TRP* 3.1 2.9 + - - -
501B GLU* 3.0 34.6 + - - +
523B VAL 4.7 10.4 + - - +
524B GLY* 3.6 26.4 - - - +
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Residues in contact with LYS 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484B LEU* 4.0 7.0 - - + -
487B LYS* 4.4 16.8 - - + +
488B GLU 4.9 6.8 + - - +
489B PHE* 3.9 25.8 - - + -
490B LYS* 5.5 2.0 - - - +
494B ASP* 3.2 41.9 + - - +
495B PHE 3.3 0.6 + - - +
497B LYS* 1.4 72.8 - - - +
499B PHE* 1.3 65.8 + - - +
500B TRP 3.2 0.4 - - - -
501B GLU* 3.5 24.4 - - + +
502B GLU* 3.1 29.5 + - - +
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Residues in contact with PHE 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B TRP* 4.1 8.3 - + - -
476B VAL* 4.1 26.0 - - + -
477B PRO* 4.3 3.1 - - + -
480B ILE* 3.7 25.5 - - + +
484B LEU* 3.9 19.9 - - + +
495B PHE* 3.0 29.1 + + + +
496B ARG* 3.5 6.5 - - - +
498B LYS* 1.3 78.9 - - - +
500B TRP* 1.3 98.0 + + - +
502B GLU* 3.4 2.6 + - - +
503B VAL* 3.1 39.9 + - + +
543B LEU* 3.7 26.7 - - + -
561B ILE* 6.1 0.2 - - + -
563B VAL* 4.0 16.6 - - + -
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Residues in contact with TRP 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B TRP* 3.8 21.5 - + - -
465B LEU* 4.7 2.0 - - + -
496B ARG* 3.1 45.8 + - - +
497B LYS 3.1 3.8 + - - +
499B PHE* 1.3 103.6 - + - +
501B GLU* 1.3 60.3 + - - +
503B VAL* 3.0 24.9 + - + +
504B SER 3.0 8.8 + - - -
513B PHE* 4.7 0.9 - + - -
521B MET* 3.4 28.4 - - + +
524B GLY 4.1 4.7 - - - +
525B LYS 3.9 13.5 - - - +
526B ALA* 3.5 24.2 - - + +
527B PRO* 3.5 37.7 - - + -
541B PHE* 4.1 13.6 + - + -
543B LEU* 4.3 9.0 - - + +
563B VAL* 3.7 31.9 - - + -
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Residues in contact with GLU 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497B LYS* 3.0 19.5 + - - +
498B LYS* 3.5 39.5 + - - +
500B TRP* 1.3 72.5 - - - +
502B GLU* 1.3 60.5 + - + +
504B SER* 2.8 18.9 + - - -
505B LYS* 3.0 28.7 - - - +
521B MET 3.4 12.1 + - - +
522B LYS* 3.4 26.0 - - - +
523B VAL* 4.0 11.3 - - - +
524B GLY* 4.3 1.6 - - - -
522C LYS* 6.5 0.4 - - + -
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Residues in contact with GLU 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480B ILE* 3.8 19.0 - - + +
483B LYS* 3.2 26.5 - - + +
484B LEU* 4.0 15.0 - - + -
487B LYS* 3.2 20.9 + - - -
498B LYS 3.1 20.2 + - - +
499B PHE 3.9 3.6 - - - +
500B TRP 3.2 0.2 - - - -
501B GLU* 1.3 73.3 - - + +
503B VAL* 1.3 69.4 + - - +
504B SER 2.8 2.8 + - - -
505B LYS* 3.1 12.0 + - - +
506B ASP* 3.1 24.1 + - - +
515C ARG* 2.8 40.0 + - - -
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Residues in contact with VAL 503 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B TRP* 3.7 30.1 - - + -
480B ILE* 3.8 25.8 - - + -
499B PHE* 3.1 43.3 + - + +
500B TRP* 3.0 12.8 + - + +
502B GLU* 1.3 77.8 - - - +
504B SER* 1.3 61.6 + - - +
506B ASP 3.4 4.0 + - - -
509B LEU* 3.6 11.8 - - + +
510B SER 3.4 18.0 + - - -
513B PHE* 4.0 9.0 - - + -
521B MET* 4.0 17.9 - - - -
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Residues in contact with SER 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B TRP 3.0 2.6 + - - -
501B GLU 2.8 17.5 + - - -
502B GLU 2.8 1.2 - - - -
503B VAL* 1.3 81.5 - - - +
505B LYS* 1.3 55.2 + - - +
506B ASP 3.5 0.4 - - - -
510B SER* 3.1 22.3 + - - -
518B ASN* 4.0 16.4 + - - +
521B MET* 3.5 26.0 - - - -
522B LYS* 3.5 12.2 + - - -
504C SER 4.1 5.9 - - - +
510C SER* 5.0 0.2 - - - -
518C ASN* 4.8 1.2 - - - +
522C LYS* 3.5 28.1 + - - -
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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
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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