Contacts of the strand formed by residues 477 - 481 (chain A) in PDB entry 2G56
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 ARG 477 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A GLU* 4.2 0.6 + - - +
208A THR* 2.8 35.2 + - - -
293A PHE* 3.2 51.6 - - - -
297A HIS* 2.9 39.6 + - - +
298A LEU* 4.3 10.5 - - + -
299A LYS 4.9 0.2 - - - +
300A GLN 3.7 6.5 - - - +
302A TYR* 2.8 28.9 + - + -
314A TYR 3.6 0.9 - - - +
315A VAL* 3.4 4.9 - - - -
316A THR* 2.9 48.4 + - - +
318A PRO* 4.7 2.7 - - - -
476A VAL* 1.3 77.6 - - - +
478A VAL* 1.3 63.9 + - - +
1020A DIO 3.2 22.1 + - - -
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Residues in contact with VAL 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A GLN 2.9 10.1 + - - +
301A LEU* 3.1 21.6 - - + -
302A TYR* 2.7 35.4 + - - -
313A LEU* 3.5 27.1 - - + -
314A TYR 3.4 2.7 - - - +
315A VAL* 4.7 3.4 - - + -
387A VAL* 4.8 1.8 - - + -
391A ILE* 3.7 25.1 - - + -
476A VAL* 4.2 15.0 - - + -
477A ARG* 1.3 79.7 - - - +
479A ALA* 1.3 56.8 + - - +
480A ILE* 4.4 2.9 - - + -
505A ILE* 3.9 20.2 - - + -
513A TRP* 4.5 2.2 - - + -
1020A DIO 5.3 0.4 - - - -
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Residues in contact with ALA 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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302A TYR* 3.2 9.0 - - + +
304A ILE* 4.0 12.6 - - + -
313A LEU* 3.4 4.2 - - - +
314A TYR* 2.7 49.2 + - + +
478A VAL* 1.3 76.6 - - - +
480A ILE* 1.3 63.9 + - - +
1020A DIO 3.6 38.6 - - - +
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Residues in contact with ILE 480 (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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301A LEU* 3.8 28.0 - - + -
302A TYR 2.7 10.5 + - - +
303A LYS* 4.8 3.1 - - + -
304A ILE* 2.8 27.7 + - - +
312A ASN 3.4 9.0 - - - +
313A LEU* 4.2 13.0 - - + -
379A LEU* 4.5 6.3 - - + -
384A LEU* 3.8 24.9 - - + -
387A VAL* 3.9 26.2 - - + -
478A VAL* 4.4 0.4 - - + -
479A ALA* 1.3 77.6 - - - +
481A VAL* 1.3 64.7 + - - +
485A PHE* 3.5 29.7 - - + -
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Residues in contact with VAL 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU* 4.2 13.5 - - + -
304A ILE* 3.4 28.7 - - + +
306A PRO* 3.3 36.8 - - + -
310A ILE* 4.2 12.8 - - + -
311A ARG* 3.3 5.5 - - - +
312A ASN* 2.8 38.8 + - + +
314A TYR* 3.6 28.3 - - + -
384A LEU* 5.2 0.2 - - - +
480A ILE* 1.3 77.5 - - - +
482A SER* 1.3 66.1 + - - +
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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