Contacts of the strand formed by residues 34 - 38 (chain s) in PDB entry 5GJQ
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 VAL 34 (chain s).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14s VAL* 3.9 27.4 - - + +
15s ALA 4.6 0.2 - - - -
16s ALA* 3.9 22.4 - - + +
32s LYS* 4.2 11.1 + - - +
33s LYS* 1.3 79.8 - - - +
35s ILE* 1.3 61.6 + - - +
36s GLU* 3.6 3.5 + - - +
42s LEU* 3.9 26.7 - - + -
43s GLY 3.4 11.0 - - - +
44s THR* 4.4 2.9 - - + +
175s ASN* 5.3 2.9 - - + +
177s TYR* 3.7 49.6 + - + -
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Residues in contact with ILE 35 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32s LYS 4.8 1.6 - - - +
33s LYS 4.2 3.8 - - - +
34s VAL* 1.3 75.2 - - - +
36s GLU* 1.3 63.3 + - - +
37s ILE* 3.0 19.7 + - + +
42s LEU* 3.5 7.3 - - - +
43s GLY 2.7 36.1 + - - +
44s THR 3.6 26.5 - - - +
45s MET* 3.9 26.9 - - + -
52s CYS 4.2 14.1 - - - +
53s SER* 4.5 5.8 - - - +
56s GLU* 3.6 34.5 - - + +
57s ARG 5.7 0.2 - - - +
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Residues in contact with GLU 36 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32s LYS* 3.7 19.0 + - - +
34s VAL 3.6 3.1 + - - +
35s ILE* 1.3 73.3 - - - +
37s ILE* 1.3 67.9 + - - +
38s ASN 3.6 1.6 - - - -
42s LEU* 3.9 7.9 - - + -
177s TYR* 3.4 19.1 + - + +
184s TRP* 3.4 27.1 - - + -
186s ARG* 2.4 42.2 + - - -
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Residues in contact with ILE 37 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100l TRP* 5.3 4.3 - - - -
35s ILE* 3.0 17.9 + - + +
36s GLU* 1.3 76.3 - - - +
38s ASN* 1.3 72.3 + - - +
39s PRO* 4.6 1.4 - - - +
41s LEU* 3.2 27.7 + - + +
42s LEU 3.8 7.6 - - - +
43s GLY* 3.7 14.6 - - - +
56s GLU* 3.5 30.7 - - - +
59s LEU* 3.9 22.7 - - + +
60s ALA* 3.7 41.4 - - + +
63s CYS* 5.1 0.2 - - - -
101s ILE* 4.0 4.7 - - + -
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Residues in contact with ASN 38 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36s GLU 4.9 0.7 - - - -
37s ILE* 1.3 99.1 + - - +
39s PRO* 1.3 60.3 - - - +
40s TYR* 2.6 56.0 + - + -
41s LEU* 3.0 21.2 + - + +
60s ALA* 4.2 11.8 - - - +
63s CYS* 3.8 17.1 - - - +
64s ARG* 5.2 2.0 + - - +
67s GLU* 5.6 0.2 + - - -
184s TRP* 2.5 30.4 + - - -
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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