Contacts of the strand formed by residues 92 - 99 (chain A) in PDB entry 4S10
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 ALA 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ARG* 4.1 8.7 - - + +
39A GLN 3.1 32.5 - - - +
40A ALA* 3.6 5.2 - - + +
41A PRO* 4.9 3.1 - - - -
90A ASP 3.2 5.4 + - - +
91A THR* 1.3 77.2 - - - +
93A VAL* 1.3 61.2 + - - +
94A TYR* 3.3 18.8 - - + -
122A GLN* 3.2 10.0 + - - +
123A VAL 2.8 31.2 + - - +
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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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38A ARG* 3.3 2.1 - - - -
39A GLN* 2.8 36.2 + - + +
92A ALA* 1.3 73.1 - - - +
94A TYR* 1.3 60.8 + - - +
95A TYR* 3.8 32.4 - - + +
119A GLN 4.4 2.5 - - - +
120A GLY* 4.0 6.3 - - - -
121A THR* 3.2 28.3 - - - +
122A GLN* 3.1 19.1 - - + +
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Residues in contact with TYR 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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6A GLU* 4.0 3.6 - - - +
20A LEU* 3.5 32.1 - - + -
36A TRP* 4.3 5.4 - + + -
37A PHE 3.4 7.4 - - - +
38A ARG* 2.7 47.1 + - + -
48A VAL* 4.2 12.3 - - + -
81A LEU* 5.1 4.5 - - + -
83A MET* 3.8 21.5 - - - -
90A ASP* 2.3 38.6 + - - +
92A ALA* 3.3 18.6 - - + -
93A VAL* 1.3 73.7 - - - +
95A TYR* 1.3 61.4 + - - +
120A GLY* 3.1 3.6 - - - -
121A THR* 2.7 38.6 + - + +
123A VAL* 3.5 25.3 - - + +
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Residues in contact with TYR 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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6A GLU* 3.8 1.1 - - - -
36A TRP* 3.3 12.0 - - - -
37A PHE* 2.7 37.2 + - + +
38A ARG* 4.6 1.1 - - - -
39A GLN* 3.9 27.3 + - + +
45A ARG* 3.4 45.6 + - + -
93A VAL* 3.8 34.1 - - + +
94A TYR* 1.3 73.7 - - - +
96A CYS* 1.3 62.3 + - - +
117A TRP* 4.0 20.4 - - + -
118A GLY 3.7 11.7 - - - -
119A GLN* 3.6 20.2 - - - -
120A GLY* 3.7 11.4 - - - -
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Residues in contact with CYS 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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4A LEU* 3.6 11.9 - - + -
6A GLU* 2.8 26.5 + - + +
22A CYS* 2.0 53.4 - - + -
34A MET* 3.6 11.2 - - - -
35A GLY 3.6 5.4 - - - -
36A TRP* 4.2 9.0 - - + -
79A VAL* 5.2 2.0 - - - -
95A TYR* 1.3 74.8 - - - +
97A ALA* 1.3 63.0 + - - +
117A TRP* 3.4 8.5 - - - -
118A GLY 3.2 20.8 + - - -
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Residues in contact with ALA 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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4A LEU* 3.6 5.0 - - - +
34A MET* 3.2 7.4 - - - +
35A GLY 2.7 42.3 + - - +
37A PHE* 4.1 3.4 - - + -
96A CYS* 1.3 77.2 - - - +
98A ALA* 1.3 60.9 + - - +
114A TYR* 3.4 22.0 - - + -
116A THR 3.2 8.7 - - - +
117A TRP* 3.6 28.3 - - + -
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Residues in contact with ALA 98 (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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2A VAL* 5.8 0.2 - - + -
4A LEU* 4.0 14.6 - - + -
32A PHE* 4.1 13.0 - - + -
33A VAL 3.4 9.2 - - - +
34A MET* 4.5 1.8 - - + -
97A ALA* 1.3 76.9 - - - +
99A ASP* 1.3 59.5 + - - +
100A LEU* 3.6 22.0 - - + -
114A TYR* 3.7 4.5 - - - -
115A ASP* 3.1 27.5 + - - +
116A THR* 2.8 21.9 + - - +
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Residues in contact with ASP 99 (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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32A PHE* 4.1 0.5 - - - +
33A VAL* 2.9 46.9 + - + +
98A ALA* 1.3 70.1 - - - +
100A LEU* 1.3 61.5 + - - +
101A HIS* 3.1 22.0 + - - +
102A ARG* 3.2 26.3 + - - +
107A GLY* 5.2 2.6 - - - -
108A SER 5.5 0.2 + - - -
113A ASP* 2.9 24.2 - - - +
114A TYR* 3.8 9.8 - - + -
115A ASP* 3.4 4.3 - - - +
230C ARG* 2.6 27.5 + - - -
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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