Contacts of the strand formed by residues 92 - 99 (chain A) in PDB entry 1JTO
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* 4.2 13.9 - - + -
39A GLN 3.6 15.9 - - - +
40A ALA* 3.7 13.7 - - + +
41A PRO* 5.3 1.8 - - - -
89A GLU 5.4 0.4 - - - +
90A ASP 3.2 5.2 + - - +
91A THR* 1.3 79.4 - - - +
93A ILE* 1.3 64.1 + - - +
94A TYR* 3.4 20.7 - - + -
128A GLN* 3.5 6.5 + - - +
129A VAL 3.0 32.1 + - - +
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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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38A ARG* 3.0 3.6 - - - -
39A GLN* 2.7 45.7 + - + +
92A ALA* 1.3 75.1 - - - +
94A TYR* 1.3 61.8 + - - +
95A TYR* 3.4 38.5 - - + +
126A GLY* 4.0 17.3 - - - -
127A THR 3.8 7.6 - - - +
128A GLN* 3.4 25.4 - - + +
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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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20A LEU* 3.8 29.8 - - + -
36A TRP* 4.4 7.5 - - + -
37A PHE 3.4 4.9 - - - -
38A ARG* 2.9 40.4 + - + -
48A VAL* 4.4 6.3 - - + -
68A PHE* 4.3 7.6 - + - -
81A LEU* 4.5 8.3 - - + -
83A MET* 3.3 27.7 - - + +
90A ASP* 2.8 29.1 + - - +
92A ALA* 3.4 24.2 - - + -
93A ILE* 1.3 74.8 - - - +
95A TYR* 1.3 60.8 + - - +
96A CYS 4.3 0.7 + - - -
125A GLN 4.4 1.0 - - - +
126A GLY* 3.4 2.3 - - - -
127A THR* 2.9 44.3 + - - +
129A VAL* 3.6 17.9 - - + -
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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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36A TRP* 3.1 10.1 - - - -
37A PHE* 2.6 47.1 + - + +
38A ARG 4.8 0.2 - - - -
39A GLN* 3.9 20.8 - - + +
45A ARG* 5.3 5.4 - - - -
93A ILE* 3.4 42.3 - - + +
94A TYR* 1.3 74.3 - - - +
96A CYS* 1.3 60.7 + - - +
97A ALA 4.0 0.2 + - - -
123A TRP* 3.8 35.0 - + + -
124A GLY 3.9 10.5 - - - +
125A GLN 5.3 0.2 - - - -
126A GLY* 3.5 30.3 - - - -
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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* 4.2 7.4 - - + -
6A ALA* 4.4 8.1 - - + -
22A CYS* 2.0 50.5 - - - -
34A MET* 3.9 13.2 - - - -
35A GLY 3.5 8.7 - - - -
36A TRP* 3.8 20.2 - - + -
79A VAL* 5.4 0.7 - - - -
94A TYR 4.3 0.4 + - - -
95A TYR* 1.3 75.0 - - - +
97A ALA* 1.3 65.7 + - - +
123A TRP* 3.6 2.9 - - - +
124A GLY* 3.1 32.1 + - - +
125A GLN 5.3 2.0 + - - -
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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* 3.9 3.4 - - - -
34A MET* 3.2 4.6 - - - +
35A GLY 2.8 33.5 + - - +
37A PHE* 3.9 22.4 - - + -
96A CYS* 1.3 79.8 - - - +
98A ALA* 1.3 60.3 + - - +
120A TYR* 3.7 18.9 - - + -
122A SER 3.3 11.0 - - - +
123A TRP* 4.0 17.7 - - + -
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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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4A LEU* 3.8 16.4 - - + +
27A TYR* 4.0 11.7 - - - +
31A PRO* 3.7 22.2 - - + -
33A CYS 3.0 12.3 - - - +
34A MET* 4.1 5.6 - - + -
97A ALA* 1.3 75.2 - - - +
99A ASP* 1.3 60.8 + - - +
100A SER 3.9 0.4 + - - -
120A TYR* 3.3 6.5 - - - -
121A ASP* 3.1 22.0 + - - +
122A SER* 3.0 16.1 + - - +
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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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31A PRO* 3.5 2.9 - - - +
32A TYR* 2.9 27.2 + - - +
33A CYS* 2.9 29.3 + - + -
98A ALA* 1.3 72.2 - - - +
100A SER* 1.3 59.3 + - - +
101A THR* 3.0 24.9 + - - -
103A TYR* 2.4 34.1 + - - -
107A TYR* 3.9 9.4 + - - -
118A TYR 4.8 0.3 - - - +
119A GLY* 3.1 30.9 - - - +
120A TYR* 4.3 5.3 - - + -
121A ASP* 4.0 0.2 - - - +
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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