Contacts of the strand formed by residues 478 - 485 (chain A) in PDB entry 3GQL
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 LEU 478 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473A LEU* 4.0 6.7 - - + -
474A PRO 3.8 0.4 + - - -
475A ARG 3.6 17.8 + - - +
476A ASP* 3.2 3.7 - - - +
477A ARG* 1.3 78.4 - - - +
479A VAL* 1.3 61.9 + - - +
480A LEU* 3.6 15.2 + - + +
495A ALA* 4.5 2.7 - - + -
496A GLU 3.9 0.4 - - - +
497A ALA* 3.9 24.2 - - + +
511A VAL* 4.3 12.6 - - + -
513A VAL* 3.9 23.6 - - + -
551A CYS* 4.1 3.6 - - - -
558A TYR* 3.6 31.4 - - + -
560A ILE* 3.7 31.2 - - + -
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Residues in contact with VAL 479 (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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476A ASP 5.3 2.5 - - - +
477A ARG 5.1 0.4 - - - -
478A LEU* 1.3 72.5 - - - +
480A LEU* 1.3 71.1 + - - +
495A ALA* 3.2 3.1 - - - +
496A GLU* 2.9 50.4 + - + +
498A ILE* 4.1 25.4 - - + -
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Residues in contact with LEU 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A LEU* 3.6 29.5 + - + +
479A VAL* 1.3 82.4 - - - +
481A GLY* 1.3 60.0 + - - +
493A VAL* 4.1 20.6 - - + -
495A ALA* 3.7 8.7 - - + -
513A VAL* 4.4 6.5 - - + -
515A MET* 4.9 11.4 - - + -
558A TYR* 3.5 34.8 - - + +
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Residues in contact with GLY 481 (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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479A VAL 3.7 0.2 + - - -
480A LEU* 1.3 76.7 - - - +
482A LYS* 1.3 68.8 + - - +
483A PRO* 3.4 4.5 - - - +
493A VAL* 3.9 9.1 - - - +
494A LEU* 2.8 17.9 + - - +
495A ALA* 4.9 1.1 - - - -
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Residues in contact with LYS 482 (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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481A GLY* 1.3 69.7 - - - +
483A PRO* 1.3 67.4 - - + +
484A LEU* 6.0 1.6 - - + -
494A LEU* 2.6 53.1 + - + +
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Residues in contact with PRO 483 (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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481A GLY 3.9 4.0 - - - +
482A LYS* 1.3 86.1 - - + +
484A LEU* 1.3 60.1 + - - +
485A GLY* 3.1 13.8 + - - +
491A GLN* 5.3 5.6 - - - +
492A VAL 4.5 0.7 - - - +
493A VAL* 3.8 21.1 - - + -
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Residues in contact with LEU 484 (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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1A GQL 3.5 60.4 - - + +
482A LYS* 3.5 2.0 + - + +
483A PRO* 1.3 71.2 - - - +
485A GLY* 1.3 57.4 + - - +
492A VAL* 2.9 14.7 + - + +
493A VAL* 3.7 4.5 - - - +
494A LEU* 3.5 41.7 - - + +
512A ALA* 4.3 10.5 - - + -
563A TYR* 4.0 24.0 - - + +
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Residues in contact with GLY 485 (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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1A GQL 3.5 6.1 - - - -
483A PRO* 3.1 12.3 + - - +
484A LEU* 1.3 82.4 - - - +
486A GLU* 1.3 66.0 + - - +
491A GLN* 3.9 4.9 + - - +
492A VAL 3.0 17.7 + - - +
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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