Contacts of the strand formed by residues 91 - 96 (chain A) in PDB entry 2GW5
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 LEU 91 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 3.6 48.9 - - + +
9A TRP* 3.9 10.5 - - + -
10A ALA* 4.0 13.2 - - + +
14A SER* 4.1 18.4 - - - -
24A LEU* 3.6 35.0 - - + -
71A GLY 3.6 2.1 - - - +
72A ARG* 4.6 0.4 - - - -
73A TYR* 2.9 37.4 + - + +
89A ASP 3.6 0.8 + - - -
90A PRO* 1.3 72.3 - - - +
92A VAL* 1.3 67.0 + - - +
93A LEU* 3.6 1.8 + - + +
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Residues in contact with VAL 92 (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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14A SER* 3.4 24.5 + - - +
15A VAL* 5.9 0.2 - - - +
71A GLY 3.7 3.6 - - - -
72A ARG* 4.4 21.8 - - + +
90A PRO* 4.2 7.6 + - + +
91A LEU* 1.3 74.6 - - - +
93A LEU* 1.3 57.7 + - - +
94A VAL* 3.8 13.2 + - + +
183A TYR* 3.5 35.4 - - + -
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Residues in contact with LEU 93 (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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14A SER* 3.5 27.1 - - - +
16A ILE* 4.1 18.4 - - + -
22A VAL* 4.5 4.9 - - + -
24A LEU* 4.3 20.2 - - + -
62A ILE* 3.8 26.0 - - + -
65A ILE* 3.9 17.0 - - + -
69A HIS 3.3 20.9 - - - +
70A THR* 3.2 8.5 - - - -
71A GLY 2.9 27.2 + - - +
73A TYR* 3.8 24.9 - - + -
91A LEU* 3.6 2.6 + - + +
92A VAL* 1.3 71.6 - - - +
94A VAL* 1.3 61.8 + - - +
183A TYR* 3.7 3.7 - - - +
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Residues in contact with VAL 94 (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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14A SER 2.8 13.5 + - - +
15A VAL* 4.1 14.6 - - + -
16A ILE* 2.9 29.1 + - - +
65A ILE* 4.2 2.8 - - - +
70A THR* 4.3 0.9 - - - -
92A VAL* 4.1 20.9 - - + +
93A LEU* 1.3 76.5 - - - +
95A MET* 1.3 67.8 + - - +
183A TYR* 3.2 20.4 - - + +
185A TRP* 3.4 59.9 - - + -
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Residues in contact with MET 95 (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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16A ILE 3.2 4.0 - - - +
18A GLN* 3.0 37.7 - - + +
19A GLY 3.6 0.4 - - - -
65A ILE* 2.6 42.2 - - + +
66A THR* 3.3 34.3 - - - -
67A TRP* 3.6 7.6 - - + +
70A THR* 3.5 15.5 - - + +
94A VAL* 1.3 76.7 - - - +
96A THR* 1.3 69.0 + - - +
98A ALA* 5.7 4.0 - - + -
183A TYR 3.0 6.9 + - - +
184A VAL* 3.5 14.7 - - + +
185A TRP 2.9 24.6 + - - +
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Residues in contact with THR 96 (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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15A VAL* 3.4 32.1 - - + -
16A ILE 2.9 8.1 + - - +
17A THR* 3.4 27.4 + - - +
18A GLN* 2.9 30.4 + - - +
95A MET* 1.3 76.1 - - - +
97A GLY* 1.3 61.4 + - - +
98A ALA* 3.7 1.1 + - - -
175A TYR* 3.6 25.8 - - + +
185A TRP* 3.6 18.2 - - + -
186A SER 3.7 7.0 - - - -
188A PRO* 4.6 6.8 - - - +
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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