Contacts of the strand formed by residues 92 - 97 (chain A) in PDB entry 3WYR
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 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A CYS* 4.2 18.4 - - + +
11A SER* 3.7 38.1 - - - +
12A ALA* 3.9 7.6 - - + +
26A LEU* 3.7 42.2 - - + -
27A ARG 5.1 0.9 - - - +
39A LEU* 4.7 0.2 - - + -
71A THR* 4.9 0.2 - - - +
72A TYR* 2.9 58.1 + - + +
73A ARG* 5.0 1.1 - - - -
74A CYS* 4.2 18.6 - - - -
90A ASN 3.3 5.1 + - - +
91A PRO* 1.3 70.1 - - - +
93A VAL* 1.3 60.8 + - - +
94A ILE* 5.2 0.7 - - + -
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Residues in contact with VAL 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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12A ALA* 4.7 1.9 - - - +
16A ALA* 3.2 25.4 - - + +
70A GLY 3.5 4.7 - - - +
71A THR* 4.0 20.0 - - + -
91A PRO* 3.7 16.8 + - + +
92A LEU* 1.3 77.2 - - - +
94A ILE* 1.3 68.8 + - - +
95A MET* 3.7 23.1 - - + -
144A ARG* 5.4 1.3 - - - +
181A TYR* 3.4 35.0 - - + +
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Residues in contact with ILE 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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12A ALA* 4.0 15.5 - - + -
16A ALA 3.8 3.6 - - - +
18A VAL* 4.0 18.6 - - + -
24A VAL* 4.2 17.3 - - + -
26A LEU* 3.8 27.8 - - + -
61A ILE* 5.9 2.9 - - + -
64A VAL* 5.2 1.1 - - + -
68A HIS* 3.6 28.9 - - + +
69A ALA* 3.2 5.7 - - - +
70A GLY 2.9 35.9 + - - +
72A TYR* 3.8 22.0 - - + -
92A LEU* 4.6 1.8 - - + +
93A VAL* 1.3 84.0 - - - +
95A MET* 1.3 65.8 + - - +
96A VAL* 4.5 4.3 - - + -
181A TYR* 3.8 4.5 - - - +
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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 ALA* 3.0 41.3 + - + +
17A VAL* 3.7 10.7 - - + -
18A VAL* 2.9 30.9 + - - +
93A VAL* 3.7 19.5 - - + -
94A ILE* 1.3 74.8 - - - +
96A VAL* 1.3 62.4 + - - +
97A THR* 4.0 1.7 + - - +
142A GLU* 4.3 6.5 - - - +
144A ARG* 3.5 16.8 - - - -
181A TYR* 3.4 26.5 - - + +
183A TRP* 3.5 48.7 - - + +
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Residues in contact with VAL 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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18A VAL 3.3 3.4 - - - +
20A GLN* 3.7 34.5 - - + +
64A VAL* 3.7 17.3 - - + -
65A THR 3.6 18.8 - - - +
66A PRO* 4.3 13.7 - - + -
69A ALA* 3.8 25.4 - - + +
94A ILE* 4.5 4.0 - - + -
95A MET* 1.3 74.6 - - - +
97A THR* 1.3 59.0 + - - +
99A LEU* 4.0 13.2 - - + +
181A TYR 3.1 6.3 + - - -
182A GLU* 3.6 1.7 - - - -
183A TRP 2.7 34.4 + - - +
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Residues in contact with THR 97 (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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17A VAL* 3.7 23.4 - - + +
18A VAL 3.3 5.2 + - - +
19A PRO* 3.4 22.9 - - - +
20A GLN* 2.9 28.6 + - - +
95A MET 4.5 1.1 - - - +
96A VAL* 1.3 80.3 - - - +
98A GLY* 1.3 62.8 + - - +
99A LEU* 3.4 2.9 - - - -
173A PHE* 3.6 27.1 - - + -
183A TRP* 3.5 20.2 - - + -
184A SER 3.4 7.6 - - - -
185A ASP* 5.1 2.1 + - - -
186A ALA 5.3 0.4 - - - -
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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