Contacts of the strand formed by residues 30 - 37 (chain B) in PDB entry 4JOQ
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 GLY 30 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LYS* 3.5 6.4 - - - +
29B VAL* 1.3 84.1 - - - +
31B THR* 1.3 63.9 + - - -
64B GLN 3.7 0.4 + - - +
65B LEU* 3.5 8.5 - - - +
66B ASP* 3.0 22.9 + - - +
92B SER* 3.8 12.1 - - - -
287B LEU* 4.3 11.0 - - - -
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Residues in contact with THR 31 (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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28B LYS* 6.1 0.2 - - - +
30B GLY* 1.3 71.7 - - - -
32B ILE* 1.3 65.8 + - - +
66B ASP* 3.3 30.9 + - + +
68B VAL* 3.9 22.9 - - + -
89B ARG* 4.4 8.4 + - + +
90B ASN 4.2 14.0 + - - -
91B ILE* 3.4 22.0 - - + -
92B SER* 2.8 34.2 + - - -
93B ALA 3.4 3.6 + - - -
287B LEU* 4.6 0.7 - - - -
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Residues in contact with ILE 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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31B THR* 1.3 74.1 - - - +
33B GLY* 1.3 67.3 + - - +
34B ILE* 3.4 20.1 - - + +
65B LEU* 4.3 6.5 - - + -
66B ASP 3.0 6.9 + - - +
67B PHE* 3.3 36.0 - - + -
68B VAL 2.9 24.5 + - - -
93B ALA* 3.5 8.7 - - + +
95B VAL* 4.1 16.6 - - + -
280B ILE* 4.9 2.9 - - + +
283B THR* 4.1 12.3 - - + -
284B ALA* 3.9 31.6 - - + +
287B LEU* 3.6 27.1 - - + -
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Residues in contact with GLY 33 (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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32B ILE* 1.3 75.0 - - - +
34B ILE* 1.3 56.2 - - - +
68B VAL 3.3 9.0 - - - -
85B MSE 3.9 15.7 - - - -
91B ILE* 3.9 12.0 - - - +
93B ALA 2.9 12.0 + - - +
94B LEU* 3.4 7.9 - - - -
95B VAL* 2.7 32.9 + - - +
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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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32B ILE* 3.4 25.6 - - + +
33B GLY* 1.3 80.7 - - - +
35B ALA* 1.3 58.1 + - - +
36B ILE* 3.8 19.1 - - + -
51B ALA* 4.8 1.8 - - + -
55B ILE* 4.1 13.5 - - + -
67B PHE* 3.9 16.6 - - + -
68B VAL 2.9 12.2 + - - +
69B LEU* 3.4 23.6 - - + +
70B ALA 2.8 31.5 + - - +
85B MSE 3.8 4.7 - - - +
95B VAL* 3.2 13.9 - - + +
276B ILE* 4.7 3.6 - - + -
280B ILE* 4.1 31.6 - - + -
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Residues in contact with ALA 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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33B GLY 4.3 0.6 - - - -
34B ILE* 1.3 70.8 - - - +
36B ILE* 1.3 62.0 + - - +
70B ALA* 3.3 9.6 - - + +
78B MSE 3.9 15.0 - - + +
81B ASP* 5.7 2.0 - - + -
82B ILE* 3.9 34.3 - - + -
85B MSE 5.0 4.9 - - + -
94B LEU* 4.4 5.2 - - + -
95B VAL 2.9 9.0 + - - +
96B VAL* 3.4 7.2 - - + +
97B LEU 2.9 25.8 + - - -
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Residues in contact with ILE 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* 3.8 17.0 - - + -
35B ALA* 1.3 80.2 - - - +
37B PRO* 1.3 80.6 - - + +
47B LEU* 3.9 17.5 - - + -
48B ASN* 3.6 35.7 - - - +
51B ALA* 4.1 15.3 - - + -
69B LEU* 4.3 10.3 - - + -
70B ALA 3.1 4.2 + - - +
71B THR* 3.0 19.0 - - + -
72B ALA 3.0 18.9 + - - -
78B MSE 3.3 7.9 - - - +
95B VAL 5.1 0.2 - - - +
97B LEU* 4.0 9.6 - - + +
276B ILE* 3.9 20.0 - - + -
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Residues in contact with PRO 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 ILE* 1.3 92.0 - - + +
38B SER* 1.3 61.7 + - - +
44B MSE 3.8 29.8 - - + +
48B ASN* 3.0 23.0 + - - -
71B THR* 4.3 0.2 - - - -
72B ALA 3.3 8.1 - - - +
78B MSE 3.4 6.9 - - + -
97B LEU* 3.6 34.5 - - + +
99B PHE* 4.1 24.7 - - + -
123B ARG* 5.2 2.7 - - - +
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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