Contacts of the strand formed by residues 57 - 65 (chain C) in PDB entry 1GQT
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 ASN 57 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C ALA* 3.0 38.1 + - - +
5C GLY 3.7 7.8 + - - +
6C SER* 3.5 9.7 - - - -
7C LEU 2.8 26.0 + - - +
55C GLY 4.6 5.2 + - - +
56C ALA* 1.3 74.6 - - - +
58C ILE* 1.3 56.7 + - - +
81C ASN 5.8 0.2 - - - -
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Residues in contact with ILE 58 (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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7C LEU* 3.3 20.2 - - + +
9C VAL* 3.8 26.9 - - + -
48C ALA* 4.1 19.1 - - + -
51C ALA* 4.4 2.5 - - + -
52C GLY* 3.9 22.2 - - - +
56C ALA* 3.5 12.0 + - + +
57C ASN* 1.3 75.0 - - - +
59C ALA* 1.3 81.1 + - - +
60C PHE* 4.0 2.0 - - + +
81C ASN 3.7 18.7 + - - +
82C ILE* 3.7 10.2 - - + -
83C ASP* 3.0 26.0 + - - +
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Residues in contact with ALA 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU 3.0 8.9 + - - +
8C VAL* 3.4 7.7 - - + +
9C VAL 2.9 25.5 + - - +
58C ILE* 1.3 78.9 - - - +
60C PHE* 1.3 59.3 + - - +
61C ILE 4.2 0.2 - - - -
83C ASP* 3.4 18.2 - - + +
86C PRO* 4.5 0.9 - - + -
131C ARG* 3.6 39.5 - - + +
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Residues in contact with PHE 60 (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 VAL* 3.4 13.9 - - + -
11C GLY 3.7 20.4 - - - -
13C ILE* 3.6 23.6 - - + -
44C GLY 3.7 14.6 - - - -
45C ALA* 3.5 37.7 - - + -
48C ALA* 4.0 13.7 - - + -
58C ILE* 4.4 4.0 - - + -
59C ALA* 1.3 73.1 - - - +
61C ILE* 1.3 64.5 + - - +
62C ALA* 3.6 14.4 - - + -
77C LEU* 3.9 17.0 - - + -
82C ILE* 3.6 22.0 - - + -
83C ASP 3.1 7.8 + - - +
86C PRO* 3.5 23.1 - - - +
87C VAL* 3.5 17.6 - - + +
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Residues in contact with ILE 61 (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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8C VAL* 3.7 26.7 - - + -
9C VAL 2.7 13.0 + - - +
10C LEU* 3.3 22.0 - - + -
11C GLY 3.2 24.9 + - - -
60C PHE* 1.3 70.9 - - - +
62C ALA* 1.3 63.8 - - - +
86C PRO* 3.6 26.9 - - + +
120C LEU* 3.7 14.7 - - + +
124C LEU* 5.2 7.6 - - + +
125C VAL* 5.7 1.6 - - - +
128C GLN* 3.6 35.4 - - + +
131C ARG* 4.6 3.4 - - - -
132C ILE* 4.0 15.9 - - + -
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Residues in contact with ALA 62 (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 GLY 3.2 22.4 - - - +
12C SER 5.2 0.2 - - - -
13C ILE* 3.5 26.7 - - + -
60C PHE* 3.6 15.0 + - + -
61C ILE* 1.3 75.4 - - - +
63C CYS* 1.3 62.6 + - - +
86C PRO 3.3 6.6 + - - +
87C VAL* 3.2 4.7 - - + +
88C SER* 2.7 31.6 + - - -
120C LEU* 4.0 7.6 - - - -
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Residues in contact with CYS 63 (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 GLY 4.9 0.4 + - - -
13C ILE* 4.4 7.7 - - - +
62C ALA* 1.3 80.7 - - - +
64C THR* 1.3 63.0 + - - +
87C VAL* 4.6 0.2 - - - -
88C SER* 3.1 9.4 - - - +
90C ILE* 3.6 25.6 - - + -
95C THR* 5.9 0.2 - - - +
116C ALA* 3.8 14.2 - - - +
117C ASN* 3.7 20.1 + - - +
119C ALA 4.1 1.3 - - - -
120C LEU* 3.5 43.4 - - - +
124C LEU* 4.1 16.4 - - - -
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Residues in contact with THR 64 (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 ILE* 3.8 20.9 - - + -
63C CYS* 1.3 73.0 - - - +
65C GLY* 1.3 68.6 + - - +
70C GLY* 3.8 4.0 - - - -
73C VAL* 3.8 28.7 - - + -
74C ARG* 3.0 37.3 + - + -
87C VAL* 4.2 1.5 - - + +
88C SER 2.9 8.5 + - - -
89C VAL* 4.1 1.9 - - - +
90C ILE* 3.0 24.8 + - - +
95C THR* 3.7 12.1 - - - +
116C ALA* 3.4 11.6 - - - +
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Residues in contact with GLY 65 (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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64C THR* 1.3 87.2 + - - +
66C ASP* 1.3 58.0 + - - -
67C ASP* 3.1 14.8 + - - +
70C GLY* 4.1 3.5 - - - -
74C ARG* 4.7 1.6 + - - -
89C VAL* 3.8 5.5 - - - +
90C ILE 3.8 5.6 - - - -
93C GLU 3.1 17.7 - - - -
95C THR* 3.0 23.3 + - - -
116C ALA* 3.6 8.0 - - - +
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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