Contacts of the strand formed by residues 31 - 37 (chain C) in PDB entry 5J12
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 GLN 31 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C VAL* 1.3 72.7 - - - +
32C ILE* 1.4 58.8 + - - +
46C TRP* 3.2 6.9 - - - +
47C ASN* 3.0 52.0 + - - +
305C NAG 4.3 18.3 - - - +
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Residues in contact with ILE 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C VAL* 3.9 4.6 + - + -
31C GLN* 1.4 77.0 - - - +
33C GLN* 1.3 63.8 + - - +
34C ILE* 4.1 22.9 - - + -
44C VAL* 4.1 14.6 - - + -
45C THR 3.3 4.9 - - - +
46C TRP* 3.6 16.2 - - + -
97C PHE* 4.3 10.1 - - + -
99C ILE* 3.4 32.5 - - + -
107C PHE* 3.8 32.8 - - + -
305C NAG 3.9 8.0 - - - +
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Residues in contact with GLN 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ILE* 1.3 75.4 - - - +
34C ILE* 1.3 64.6 + - - +
35C ILE* 3.7 25.0 - - + +
43C GLN* 3.6 1.7 - - - +
44C VAL* 3.3 4.9 - - - +
45C THR* 2.8 48.9 + - - +
199C TYR* 3.6 28.0 + - - +
305C NAG 3.5 21.1 + - + +
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Residues in contact with ILE 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ILE* 4.1 12.8 - - + -
33C GLN* 1.3 78.7 - - - +
35C ILE* 1.3 64.3 + - - +
42C VAL* 4.2 19.7 - - + -
43C GLN 3.4 7.6 - - - +
44C VAL* 4.2 10.3 - - + -
95C LEU* 5.5 3.4 - - + -
97C PHE* 3.9 26.9 - - + -
111C ARG* 4.5 10.5 - - + -
113C MET* 5.4 5.8 - - + +
116C TYR* 3.3 54.5 - - + +
199C TYR* 2.8 23.5 + - - -
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Residues in contact with ILE 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C GLN* 3.7 24.2 - - + +
34C ILE* 1.3 82.0 - - - +
36C TYR* 1.3 61.6 - - - +
37C PHE* 3.6 43.4 - - + -
41C THR 3.5 2.1 - - - +
42C VAL* 3.4 2.1 - - - +
43C GLN* 2.8 47.3 + - - +
116C TYR 3.5 5.4 - - - +
118C LYS* 3.9 27.1 - - + -
199C TYR* 3.8 17.7 - - + +
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Residues in contact with TYR 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ILE* 5.9 0.7 - - + -
35C ILE* 1.3 71.7 - - - +
37C PHE* 1.3 64.2 + - - +
38C ASN 3.2 1.2 + - - -
39C LEU* 3.3 50.7 + - + +
40C GLU 3.5 4.3 - - - -
41C THR 3.4 5.6 - - - -
42C VAL* 3.6 14.4 - - + +
88C ALA* 3.3 27.4 - - + +
91C ARG 2.7 41.3 + - - -
113C MET* 3.4 44.9 - - + +
114C VAL* 3.7 8.7 - - + -
116C TYR* 2.9 14.8 + - - +
117C LEU* 3.4 6.3 - - + +
118C LYS 2.9 23.2 + - - -
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Residues in contact with PHE 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ILE* 3.9 38.1 - - + -
36C TYR* 1.3 69.7 - - - +
38C ASN* 1.4 58.0 + - + +
40C GLU* 2.7 30.4 + - + +
41C THR* 2.8 37.5 + - + +
43C GLN* 3.7 39.9 - - + -
85C LEU* 5.3 2.0 - - + -
118C LYS* 3.9 20.0 - - + -
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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