Contacts of the strand formed by residues 10 - 15 (chain C) in PDB entry 5GT8
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 10 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C HIS* 4.0 9.4 - - + -
9C ARG* 1.3 75.4 - - - +
11C ARG* 1.3 73.4 + - - +
12C VAL* 4.8 1.6 - - + -
41C PHE* 3.8 24.5 - - + -
54C MET* 3.6 36.8 - - + -
55C VAL 3.5 9.4 - - - +
56C ASP 5.0 0.2 - - - +
75C THR* 3.7 0.2 - - - -
76C TRP* 2.8 53.4 + - + +
78C VAL* 3.8 25.8 - - + -
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Residues in contact with ARG 11 (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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9C ARG 4.6 4.9 - - - +
10C VAL* 1.3 83.2 - - - +
12C VAL* 1.3 62.7 + - - +
13C LEU* 4.1 3.6 - - + +
53C LEU 3.5 1.0 - - - +
54C MET* 3.2 6.4 - - - -
55C VAL 2.8 36.8 + - - +
57C GLU* 5.0 10.3 - - + -
60C PHE* 3.9 52.0 - - + -
71C VAL* 3.3 18.0 - - + +
72C ALA 2.9 22.2 + - - -
73C GLU* 3.9 13.3 + - - +
74C ALA 3.4 15.4 + - - -
75C THR* 4.0 18.2 + - - -
76C TRP* 4.4 0.9 - - - -
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Residues in contact with VAL 12 (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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10C VAL* 4.8 1.8 - - + -
11C ARG* 1.3 78.2 - - - +
13C LEU* 1.3 63.1 + - - +
52C THR* 4.3 17.0 - - + -
53C LEU 3.4 6.3 - - - +
54C MET* 4.0 16.4 - - + -
71C VAL* 3.6 4.2 - - - +
72C ALA* 2.8 49.8 + - + +
76C TRP* 3.6 25.0 - - + +
113C LEU* 3.6 26.2 - - + -
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Residues in contact with LEU 13 (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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11C ARG 4.1 7.4 - - - +
12C VAL* 1.3 78.3 - - - +
14C SER* 1.3 62.2 + - - +
15C VAL* 4.1 1.3 - - + -
52C THR* 3.3 11.8 - - - +
53C LEU* 2.8 48.5 + - + +
55C VAL* 3.8 28.7 - - + -
60C PHE* 3.8 24.0 - - + -
63C LEU* 4.1 17.9 - - + +
69C LEU* 3.6 31.9 - - + -
70C GLN 3.6 6.3 - - - +
71C VAL* 3.7 19.3 - - + +
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Residues in contact with SER 14 (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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13C LEU* 1.3 73.8 - - - +
15C VAL* 1.3 60.6 + - - +
16C ALA 3.8 0.4 + - - -
50C ASP* 2.5 36.6 + - - +
51C TYR 3.7 3.4 - - - -
52C THR* 4.6 3.3 + - - +
68C PHE 3.2 6.1 - - - +
69C LEU* 3.2 0.8 - - - -
70C GLN* 2.9 45.4 + - - +
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Residues in contact with VAL 15 (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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13C LEU* 5.0 3.1 - - + -
14C SER* 1.3 74.5 - - - +
16C ALA* 1.3 75.4 + - - +
19C GLY 4.1 0.9 - - - -
20C LEU* 3.8 20.2 - - + +
23C TYR* 3.8 33.9 - - + -
27C LEU* 6.0 1.1 - - + -
50C ASP* 3.4 2.0 - - - +
51C TYR* 2.9 40.7 + - + +
53C LEU* 3.5 24.5 - - + -
63C LEU* 6.0 1.8 - - + -
68C PHE* 3.1 5.6 - - + +
69C LEU* 4.1 24.2 - - + -
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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