Contacts of the strand formed by residues 121 - 128 (chain B) in PDB entry 1J7H
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 121 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ILE* 3.9 0.7 - - - +
35B PRO* 3.3 25.9 - - + +
47B ILE* 4.4 5.2 - - + +
50B GLN* 3.4 35.2 - - + +
51B ALA* 3.7 22.0 - - + +
54B SER* 3.3 30.5 - - - +
77B VAL* 4.9 7.2 - - + -
78B PHE 3.1 14.6 - - - +
79B VAL* 5.0 5.4 - - + -
88B VAL* 5.7 4.3 - - + -
115B LEU* 3.4 5.4 - - - +
119B VAL* 3.1 12.2 + - - +
120B GLY* 1.3 81.3 - - - +
122B GLU* 1.3 63.7 + - - +
123B ILE* 4.1 9.4 - - + -
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A SER* 5.8 0.2 - - - -
109A CYS 3.5 9.2 + - - +
110A VAL* 3.1 27.9 - - - +
32B GLY* 2.5 32.9 - - - +
33B GLN 3.2 9.8 - - - +
34B ILE* 3.4 10.7 - - + +
77B VAL* 2.7 35.5 - - - +
78B PHE* 3.0 14.2 + - + -
115B LEU* 3.5 14.8 - - + -
116B PRO* 3.5 16.9 - - - +
121B LEU* 1.3 76.4 - - - +
123B ILE* 1.3 63.2 + - - +
124B GLU* 3.4 14.8 - - - +
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Residues in contact with ILE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B SER 2.8 4.5 - - - +
32B GLY* 3.1 1.0 - - - -
33B GLN* 2.6 35.4 + - + +
51B ALA 4.7 1.6 - - - +
54B SER* 2.9 50.7 - - - +
55B LEU* 3.6 20.9 - - + +
58B VAL* 3.4 28.7 - - + -
75B THR* 4.8 7.9 - - + -
76B THR 3.6 6.7 - - - +
77B VAL* 4.1 15.7 - - + -
92B TYR* 6.2 0.4 - - + -
121B LEU* 4.1 7.0 - - + -
122B GLU* 1.3 82.6 - - - +
124B GLU* 1.3 67.9 + - - +
125B ALA* 4.9 0.7 - - + +
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LYS* 5.6 5.6 - - - -
108A SER* 3.1 20.2 + - - +
30B THR* 3.7 17.7 - - - +
32B GLY* 3.5 18.0 - - - +
76B THR* 2.8 54.9 + - + +
78B PHE* 2.7 49.2 - - + -
122B GLU* 3.4 11.5 - - - +
123B ILE* 1.3 78.0 - - - +
125B ALA* 1.3 60.3 + - - +
126B ILE* 5.7 1.7 - - - +
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Residues in contact with ALA 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B THR* 2.9 40.1 + - + +
58B VAL* 5.1 7.0 - - + -
62B ILE* 5.9 0.7 - - + -
72B ILE* 3.8 14.6 - - + -
74B LYS 3.0 19.3 - - - +
75B THR* 3.2 26.0 - - + +
123B ILE* 4.9 1.3 - - + +
124B GLU* 1.3 75.5 - - - +
126B ILE* 1.3 65.1 + - - +
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Residues in contact with ILE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LYS* 5.6 9.0 - - - +
27B LEU* 3.6 24.5 - - + -
28B VAL 2.9 22.4 - - - +
29B LEU* 3.6 32.8 - - + -
30B THR* 4.8 2.2 - - - +
72B ILE* 3.0 13.3 - - - +
73B VAL* 2.8 33.6 + - + -
74B LYS* 2.7 25.0 + - + +
124B GLU 5.7 1.6 - - - +
125B ALA* 1.3 84.3 - - - +
127B ALA* 1.3 60.7 + - - +
29C LEU* 6.5 1.6 - - + -
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Residues in contact with ALA 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LEU* 3.3 5.1 - - - +
28B VAL* 2.6 62.0 + - + +
30B THR* 6.0 0.6 - - + +
62B ILE* 4.3 17.9 - - + -
67B LEU* 4.5 3.6 - - + -
71B ASP* 4.3 2.9 - - + -
72B ILE* 3.8 22.7 - - + +
73B VAL 3.9 1.3 - - - +
126B ILE* 1.3 76.9 - - - +
128B VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ASN 3.2 8.1 - - - +
27B LEU* 3.1 26.5 - - + -
67B LEU* 2.8 24.0 - - - +
71B ASP* 3.1 25.6 + - - +
73B VAL* 3.0 34.3 - - + -
127B ALA* 1.3 72.1 - - - +
129B ARG* 1.3 63.8 + - - +
130B LYS* 4.7 5.2 - - + +
3C THR* 3.4 22.2 - - + -
24C LEU* 3.6 17.9 - - + -
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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