Contacts of the strand formed by residues 88 - 94 (chain A) in PDB entry 3R9X
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 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A TYR 3.3 2.6 + - - -
6A VAL* 3.3 16.3 - - + +
7A ALA 3.1 23.4 + - - -
86A ALA* 3.7 2.9 - - - +
87A ASP* 1.3 84.2 - - + +
89A ILE* 1.3 70.4 + - - +
90A LEU* 4.4 5.4 - - + -
116A LYS* 5.4 0.4 - - - -
117A PRO* 3.8 16.8 - - + +
119A ILE* 3.9 28.0 - - + -
169A ILE* 4.4 5.6 - - + +
172A TYR* 3.7 31.4 - - + +
173A LEU* 3.9 21.3 - - + +
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Residues in contact with ILE 89 (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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7A ALA* 3.8 2.9 - - + +
9A VAL* 4.1 17.7 - - + -
83A LEU* 3.4 29.2 - - + +
86A ALA* 4.4 9.4 - - + -
88A VAL* 1.3 76.7 - - - +
90A LEU* 1.3 73.3 + - - +
91A PHE* 3.8 4.5 - - + +
111A ILE* 4.1 30.1 - - + +
114A LEU* 4.3 15.3 - - + -
116A LYS* 4.5 19.5 - - + +
117A PRO 2.9 13.8 + - - +
118A VAL* 3.4 9.1 - - + -
119A ILE 2.8 31.5 + - - +
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Residues in contact with LEU 90 (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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6A VAL* 3.8 25.8 - - + -
7A ALA 2.8 14.6 + - - +
8A ILE* 3.5 23.3 - - + +
9A VAL* 2.9 27.9 + - - +
19A LEU* 4.2 15.7 - - + -
56A PHE* 4.1 6.7 - - + -
88A VAL* 4.4 1.1 - - + -
89A ILE* 1.3 77.7 - - - +
91A PHE* 1.3 61.4 + - - +
92A MET* 3.5 1.2 + - + -
119A ILE* 3.6 31.4 - - + -
121A VAL* 4.0 17.0 - - + -
165A LEU* 4.4 5.4 - - + -
169A ILE* 4.0 20.9 - - + -
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Residues in contact with PHE 91 (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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9A VAL* 3.6 9.6 - - - -
10A GLY* 3.9 13.9 - - - -
11A LYS 5.0 0.4 - - - -
89A ILE* 3.7 5.2 + - + -
90A LEU* 1.3 71.0 - - - +
92A MET* 1.3 65.3 + - - +
93A ILE* 3.6 9.8 + - + -
99A TRP* 3.6 36.1 - + - -
103A ASP* 3.5 35.4 - - + -
106A ILE* 3.7 23.3 - - + -
107A TYR* 4.1 13.0 - + + -
111A ILE* 3.6 26.0 - - + -
118A VAL* 4.5 10.3 - - + -
119A ILE 3.0 12.3 + - - +
120A VAL* 3.5 13.1 - - + +
121A VAL 3.0 21.3 + - - -
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Residues in contact with MET 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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8A ILE* 4.5 5.8 - - + -
9A VAL 2.8 17.2 + - - +
10A GLY* 3.7 16.5 - - - -
11A LYS 4.6 0.5 + - - -
14A VAL* 3.4 32.6 - - + +
15A GLY 3.5 31.4 - - - +
16A LYS* 3.5 7.2 - - + -
19A LEU* 3.3 38.8 - - + -
90A LEU* 3.5 3.6 + - + +
91A PHE* 1.3 73.1 - - - +
93A ILE* 1.3 69.4 + - - +
103A ASP* 4.8 1.2 - - - +
121A VAL* 3.3 27.1 - - + +
123A ASN* 3.9 10.8 - - + -
154A ILE* 4.5 2.0 - - + -
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Residues in contact with ILE 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 VAL* 4.5 3.1 - - - -
91A PHE* 4.1 26.5 - - + +
92A MET* 1.3 80.6 - - - +
94A ASP* 1.3 63.6 + - - +
98A GLY 4.3 13.0 - - - +
99A TRP* 4.2 11.7 - - + +
103A ASP* 3.9 21.1 - - - +
120A VAL* 4.3 6.7 - - + -
121A VAL 2.7 9.7 + - - +
122A ILE* 3.9 21.8 - - + -
123A ASN* 2.7 36.2 + - - +
137A LEU* 4.2 10.3 - - + -
141A ILE* 3.8 29.4 - - + -
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Residues in contact with ASP 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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11A LYS* 5.2 2.3 - - - +
13A ASN 4.6 1.6 - - - +
14A VAL* 4.0 20.7 - - + +
93A ILE* 1.3 76.5 - - - +
95A ALA* 1.3 54.9 + - - +
96A THR* 2.6 49.5 + - - +
97A GLU* 3.2 26.8 + - + +
98A GLY* 2.7 35.7 + - - +
103A ASP* 5.1 0.6 + - - -
123A ASN* 4.1 3.6 - - - -
124A LYS* 3.2 35.5 + - + +
127A LYS* 5.6 0.3 - - - -
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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