Contacts of the strand formed by residues 55 - 60 (chain A) in PDB entry 3GJ9
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 ILE 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ILE* 4.0 24.5 - - + -
34A GLY 3.6 2.2 - - - +
35A GLY* 3.7 9.0 - - - +
36A GLY* 3.7 27.8 - - - +
54A GLY* 1.3 73.6 - - - -
56A TYR* 1.3 63.6 + - - +
76A LYS* 3.2 11.1 - - - +
77A ILE* 2.9 56.3 + - + +
85A MET* 3.6 24.8 + - + +
88A VAL* 4.2 3.6 - - + +
89A THR 4.5 4.9 - - - +
90A HIS* 4.7 2.7 - - - +
93A ALA* 3.6 28.0 - - + -
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Residues in contact with TYR 56 (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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33A ILE* 3.2 7.4 - - - +
34A GLY 2.9 36.4 + - - +
44A ASN* 2.9 25.6 - - - +
46A PHE* 4.0 29.4 - - + -
47A SER* 3.0 23.1 - - - -
52A ASP* 2.9 32.7 + - - -
54A GLY 3.7 14.1 - - - -
55A ILE* 1.3 80.7 - - - +
57A VAL* 1.3 65.1 + - - +
58A THR* 3.4 3.3 + - + -
74A GLY 3.4 23.8 - - - -
75A ASP 3.2 7.2 - - - -
76A LYS* 3.6 29.0 - - + +
440C ARG* 5.7 0.7 - - - +
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Residues in contact with VAL 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 4.0 3.4 - - + -
32A SER 3.4 6.7 - - - +
33A ILE* 4.7 0.7 - - - +
46A PHE* 4.3 2.4 - - - -
56A TYR* 1.3 72.4 - - - +
58A THR* 1.3 58.9 + - - +
59A ARG 3.5 23.1 - - - +
60A VAL* 3.5 20.0 - - + -
71A LEU* 3.6 37.7 - - + -
72A GLN 3.7 12.1 - - - +
73A ILE* 3.6 0.7 - - - +
74A GLY* 2.6 31.0 + - - -
75A ASP* 2.8 22.6 + - + +
77A ILE* 4.2 18.8 - - + -
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Residues in contact with THR 58 (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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32A SER* 2.8 14.2 + - - -
34A GLY* 3.7 17.3 - - - +
46A PHE* 4.3 19.6 - - + -
56A TYR* 3.9 4.9 - - + +
57A VAL* 1.3 75.4 - - - +
59A ARG* 1.3 69.3 + - - +
73A ILE* 3.6 17.1 - - - +
102B GLU* 5.7 0.7 - - - +
440C ARG* 3.6 22.2 - - - +
442C GLU* 2.6 42.3 + - - +
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Residues in contact with ARG 59 (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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31A PHE* 3.1 8.8 - - - +
32A SER* 2.8 44.8 + - - +
57A VAL* 3.5 3.0 - - - +
58A THR* 1.3 91.4 + - - +
60A VAL* 1.3 67.0 + - - +
61A SER* 4.2 1.3 - - - +
73A ILE* 4.4 6.5 - - + -
101B SER* 4.2 23.0 + - - -
102B GLU* 5.6 8.9 + - - +
442C GLU* 2.6 32.2 + - - +
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Residues in contact with VAL 60 (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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30A GLY 3.7 6.3 - - - +
31A PHE* 4.4 3.1 - - + -
57A VAL* 3.5 19.1 - - + -
59A ARG* 1.3 82.2 - - - +
61A SER* 1.3 59.2 + - - +
66A ALA* 4.3 2.9 - - + -
67A GLU* 3.6 43.5 - - + +
71A LEU* 3.9 14.1 - - + +
72A GLN 4.0 3.8 - - - -
73A ILE* 3.8 26.8 - - + +
127A CL 4.4 1.6 - - + -
106B ARG* 2.2 41.7 + - - +
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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