Contacts of the strand formed by residues 31 - 38 (chain B) in PDB entry 4JE4
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 TYR 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LYS* 3.7 23.0 - - - +
29B VAL* 3.1 12.3 - - - +
30B ASP* 1.3 81.0 - - + +
32B TYR* 1.3 60.8 + - - +
33B VAL* 3.8 22.0 - - + -
50B GLU* 3.5 27.8 - - - +
51B VAL 3.4 13.5 - - - +
52B PRO* 4.4 2.2 - - + -
53B GLY 3.7 4.3 - - - +
76B GLY* 2.9 40.3 + - - -
77B TYR 3.4 20.0 - - - -
78B TYR* 3.5 35.2 - + - +
82B THR* 3.5 10.2 - - - +
83B TYR* 2.8 26.2 + - - -
84B TYR* 3.7 5.5 - + + -
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Residues in contact with TYR 32 (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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5B PRO* 4.2 13.0 - - + -
22B TRP* 3.5 29.3 + + + -
24B ALA* 3.4 30.0 - - - +
25B PRO* 3.5 8.4 - - + +
29B VAL* 3.6 30.1 - - + +
31B TYR* 1.3 73.9 - - - +
33B VAL* 1.3 63.6 + - - +
34B ILE* 4.1 8.7 - - + +
50B GLU* 3.4 7.6 - - - +
51B VAL* 2.9 43.0 + - + +
52B PRO 3.9 8.3 - - - -
53B GLY 3.7 17.1 + - - -
55B LYS 3.5 25.6 - - - -
56B SER* 5.3 1.4 - - - -
73B VAL* 3.8 9.2 - - + -
74B TYR 3.4 16.2 - - - +
75B ALA* 4.5 0.2 - - - -
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Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A SER* 4.4 4.5 - - - +
31B TYR* 3.8 16.8 + - + -
32B TYR* 1.3 78.7 - - - +
34B ILE* 1.3 66.3 + - - +
35B THR* 5.6 0.2 - - - -
48B GLU* 3.9 27.1 - - - +
49B PHE 3.8 8.3 - - - +
50B GLU* 4.7 9.4 - - + +
73B VAL* 3.4 2.4 - - - -
74B TYR* 2.8 47.6 + - + -
84B TYR* 3.8 49.1 - - + -
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Residues in contact with ILE 34 (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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20B ILE* 4.2 16.8 - - + -
22B TRP* 3.9 18.4 - - + -
32B TYR* 4.1 8.1 - - + +
33B VAL* 1.3 79.5 - - - +
35B THR* 1.3 69.2 + - - +
36B TYR* 4.8 0.4 - - + -
48B GLU* 3.1 6.6 - - - +
49B PHE* 3.0 71.6 + - + +
51B VAL* 3.8 28.9 - - + -
60B ILE* 4.5 7.0 - - + -
71B ILE* 4.6 2.5 - - + -
72B THR 3.3 7.9 - - - +
73B VAL* 3.9 18.8 - - + -
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Residues in contact with THR 35 (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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12A THR* 5.9 1.7 - - - -
13A GLY 6.0 0.2 + - - -
14A VAL* 3.9 24.3 + - + +
33B VAL* 4.2 0.6 + - - -
34B ILE* 1.3 74.6 - - - +
36B TYR* 1.3 65.2 + - - +
46B TRP* 3.6 17.8 - - + +
47B GLN 2.9 17.7 + - - -
48B GLU* 3.9 15.3 + - - +
71B ILE* 3.6 2.3 - - - +
72B THR* 2.8 54.6 + - - +
74B TYR* 3.9 16.2 - - + -
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Residues in contact with TYR 36 (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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34B ILE* 4.8 0.7 - - + -
35B THR* 1.3 82.3 + - - +
37B GLY* 1.3 64.2 + - - +
46B TRP* 3.3 9.5 - - - +
47B GLN* 3.1 64.8 + - + +
49B PHE* 3.9 25.7 - + - -
60B ILE* 3.5 42.6 - - + +
61B SER 3.8 14.9 + - - -
63B LEU* 3.9 19.3 - - + -
69B TYR* 5.0 2.9 - + + -
70B THR 3.2 13.2 - - - +
71B ILE* 4.0 15.0 - - + -
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Residues in contact with GLY 37 (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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36B TYR* 1.3 80.8 - - - +
38B GLU* 1.3 64.8 + - - -
46B TRP* 3.5 25.2 - - - -
69B TYR* 3.6 13.0 - - - -
70B THR 2.9 27.9 + - - +
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Residues in contact with GLU 38 (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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37B GLY* 1.3 71.4 - - - -
39B THR* 1.3 67.9 + - - +
40B GLY 3.4 0.5 + - - -
41B SER* 2.8 35.5 + - - +
46B TRP* 3.5 8.8 + - - +
64B LYS* 2.7 37.2 + - - +
67B VAL* 3.8 21.2 - - + +
68B ASP 3.5 9.0 - - - +
69B TYR* 3.8 18.7 + - + -
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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