Contacts of the helix formed by residues 75 - 83 (chain B) in PDB entry 4Q96
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 PRO 75 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71B LYS* 5.7 4.5 - - - -
74B GLY* 1.3 82.6 - - - +
76B GLU* 1.3 70.2 + - - +
77B PHE 3.4 2.2 - - - -
78B THR* 3.4 14.6 + - - +
79B ARG* 3.1 60.3 + - + +
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Residues in contact with GLU 76 (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 ARG* 3.6 48.3 - - - +
35B LYS* 5.2 1.9 - - - +
37B ALA* 3.9 10.8 - - + -
73B LYS 5.3 0.5 - - - +
74B GLY* 3.4 10.3 - - - -
75B PRO* 1.3 90.6 - - + +
77B PHE* 1.3 67.3 + - + +
79B ARG* 3.2 12.6 + - - +
80B GLU* 2.7 39.4 + - + +
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Residues in contact with PHE 77 (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 LEU* 3.5 31.4 - - + -
31B ILE* 4.4 2.7 - - - -
34B ARG* 3.5 24.7 - - + -
37B ALA* 3.8 26.7 - - + -
40B ILE* 3.7 32.5 - - + -
41B VAL* 4.2 5.4 - - + -
66B VAL* 3.6 30.7 - - + -
67B ILE* 4.8 1.8 - - - -
70B SER* 3.5 28.5 - - - +
74B GLY 4.6 2.0 + - - -
76B GLU* 1.3 83.7 - - + +
78B THR* 1.3 57.9 + - - +
80B GLU* 4.4 1.3 - - - +
81B PHE* 2.9 50.8 + + + -
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Residues in contact with THR 78 (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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116A VAL 3.8 15.7 - - - +
117A TYR* 2.8 50.0 + - + -
67B ILE* 3.7 19.1 + - + +
70B SER* 4.4 3.0 + - - -
71B LYS* 3.4 28.8 - - - +
75B PRO* 3.4 14.9 + - - +
76B GLU 3.3 0.4 - - - -
77B PHE* 1.3 78.3 - - - +
79B ARG* 1.3 59.4 + - + +
82B GLU* 3.1 12.0 + - - +
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Residues in contact with ARG 79 (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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75B PRO* 3.1 50.3 + - + +
76B GLU* 3.6 11.6 - - - +
78B THR* 1.3 76.9 - - + +
80B GLU* 1.3 71.4 + - - +
82B GLU* 3.1 25.2 + - - +
83B SER* 3.5 6.2 + - - -
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Residues in contact with GLU 80 (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 ALA* 3.9 7.9 - - + -
38B GLY* 3.5 37.3 - - - +
41B VAL* 3.6 30.2 - - + +
76B GLU* 2.7 27.5 + - + +
77B PHE* 4.0 2.2 - - - +
79B ARG* 1.3 74.8 - - - +
81B PHE* 1.3 57.7 + - - +
83B SER* 2.2 34.9 + - - -
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Residues in contact with PHE 81 (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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117A TYR* 3.5 12.3 - - - +
30B LEU* 6.1 1.8 - - + -
40B ILE* 5.6 2.2 - - + -
41B VAL* 3.8 21.8 - - + -
44B TRP* 3.7 41.3 - + + -
62B LEU* 6.1 0.4 - - + -
63B ALA* 3.5 32.1 - - + -
66B VAL* 3.7 17.7 - - + -
67B ILE* 3.5 22.7 - - + -
77B PHE* 2.9 49.1 + + - +
80B GLU* 1.3 75.3 - - - +
82B GLU* 1.3 63.6 + - - +
84B VAL* 2.9 14.7 + - + +
85B LEU* 3.1 24.7 + - + +
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Residues in contact with GLU 82 (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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117A TYR* 3.4 21.3 + - + -
121A PHE* 3.3 49.2 - - + +
78B THR* 3.1 16.5 + - - +
79B ARG* 3.1 17.6 + - - +
81B PHE* 1.3 75.4 - - - +
83B SER* 1.3 61.6 + - - +
84B VAL 3.4 0.7 + - - -
85B LEU 3.9 1.7 + - - -
86B VAL* 5.0 1.0 + - - +
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Residues in contact with SER 83 (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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41B VAL* 4.8 0.9 - - - +
79B ARG 3.5 4.8 + - - -
80B GLU* 2.2 34.2 + - - -
82B GLU* 1.3 79.3 - - - +
84B VAL* 1.3 66.3 + - - +
86B VAL 5.6 0.4 - - - -
87B ASP* 6.0 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