Contacts of the strand formed by residues 2685 - 2688 (chain A) in PDB entry 4ERV
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 THR2685 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2680A LEU* 5.2 0.7 - - - -
2683A GLY 4.0 1.6 + - - -
2684A TRP* 1.3 73.4 - - - +
2686A VAL* 1.3 63.5 + - - +
2687A GLU* 4.3 17.9 - - + -
2797A ILE* 3.5 2.2 - - + +
2798A VAL* 3.2 8.7 - - - +
2799A SER* 2.9 47.7 + - - +
2800A ARG 4.5 6.6 + - - -
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Residues in contact with VAL2686 (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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2614A LEU* 3.7 34.2 - - + +
2676A LEU* 4.6 16.6 - - + +
2679A MET* 4.0 25.1 - - + -
2680A LEU* 4.0 25.2 - - + +
2684A TRP 4.1 1.5 + - - +
2685A THR* 1.3 79.7 - - - +
2687A GLU* 1.3 60.5 + - - +
2796A ILE* 3.8 21.3 - - + -
2797A ILE 3.7 2.9 - - - -
2798A VAL* 3.9 19.3 - - + -
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Residues in contact with GLU2687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2614A LEU* 5.6 0.9 - - - -
2685A THR* 4.3 15.9 - - + -
2686A VAL* 1.3 77.4 - - - +
2688A ARG* 1.3 65.6 + - - +
2796A ILE* 3.3 9.4 - - - -
2797A ILE* 2.8 47.3 + - + +
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Residues in contact with ARG2688 (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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2613A LYS* 6.5 1.6 - - + -
2614A LEU* 5.8 0.6 - - - +
2687A GLU* 1.3 79.9 - - - +
2689A THR* 1.3 66.7 + - - +
2690A LYS 4.2 0.2 + - - -
2693A GLU* 6.3 1.3 - - + -
2795A GLY 3.3 9.9 - - - +
2796A ILE* 4.1 10.3 - - + +
2797A ILE* 4.6 2.4 - - - +
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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
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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