Contacts of the helix formed by residues 64 - 75 (chain B) in PDB entry 6W4E
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 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ILE* 4.7 12.5 - - + +
59B ALA* 3.4 42.9 - - + +
61B GLN* 3.5 26.0 + - + +
62B GLU* 3.1 31.2 + - - +
63B GLU* 1.3 83.9 - - + +
65B SER* 1.3 57.1 + - - +
66B ALA 3.3 3.1 - - - -
67B MET* 3.0 33.5 + - + +
68B ARG* 2.7 56.1 + - + +
71B TYR* 5.8 1.3 - - + +
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Residues in contact with SER 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLU* 5.1 4.1 + - - -
63B GLU* 3.5 13.9 + - - -
64B TYR* 1.3 77.3 + - - +
66B ALA* 1.3 59.7 + - - +
68B ARG* 5.5 3.3 - - - +
69B ASP* 3.4 27.5 + - - +
99B GLN* 4.3 6.7 + - - +
102B ARG* 5.5 0.2 + - - -
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Residues in contact with ALA 66 (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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64B TYR 3.3 0.4 - - - -
65B SER* 1.3 77.3 - - - +
67B MET* 1.3 59.7 + - - +
69B ASP* 4.5 5.5 - - - +
70B GLN* 4.3 13.3 + - - +
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Residues in contact with MET 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ILE* 3.5 36.8 - - + +
37B GLU* 4.1 27.6 - - + +
58B THR* 4.6 7.9 - - + -
59B ALA* 5.7 1.1 - - - +
64B TYR* 3.0 37.2 + - + +
66B ALA* 1.3 80.4 - - - +
68B ARG* 1.3 65.8 + - - +
69B ASP 3.3 0.2 - - - -
70B GLN* 3.1 23.0 + - - +
71B TYR* 3.2 21.2 - - + -
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Residues in contact with ARG 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 5.3 0.2 - - + -
59B ALA 5.0 2.6 + - - -
60B GLY* 5.2 0.4 - - - -
62B GLU* 2.8 41.6 + - - +
64B TYR* 2.7 42.4 + - + +
65B SER* 5.7 2.6 - - - +
67B MET* 1.3 75.1 - - - +
69B ASP* 1.3 62.9 + - - +
70B GLN 3.1 1.2 + - - -
71B TYR* 3.3 29.6 + - + +
72B MET* 3.1 41.1 + - + +
92B ASP* 5.9 0.4 + - - -
96B TYR* 3.3 44.0 + - - +
99B GLN* 2.8 38.7 + - - +
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Residues in contact with ASP 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B SER 3.4 15.2 + - - +
66B ALA* 4.8 4.9 - - - +
67B MET 3.3 0.6 - - - -
68B ARG* 1.3 74.5 - - - +
70B GLN* 1.3 64.4 + - - +
72B MET 4.0 0.7 - - - -
73B ARG* 3.6 12.2 + - - +
99B GLN* 2.6 32.6 + - - -
102B ARG* 3.1 25.0 + - - -
103B VAL* 3.2 44.8 - - + +
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Residues in contact with GLN 70 (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 GLU* 5.5 6.1 + - - -
66B ALA 4.3 9.6 + - - +
67B MET* 3.1 20.9 + - - +
68B ARG 3.1 1.0 - - - -
69B ASP* 1.3 80.8 - - - +
71B TYR* 1.3 67.0 + - + +
73B ARG* 3.2 24.1 + - - +
74B THR* 3.8 6.8 + - - -
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Residues in contact with TYR 71 (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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7B VAL* 3.6 30.2 - - + +
9B VAL* 4.3 9.3 - - + +
37B GLU* 4.1 12.6 - - - +
56B LEU* 4.0 21.8 - - + -
58B THR* 3.0 44.1 + - + -
59B ALA 4.6 4.2 + - - -
64B TYR* 5.8 1.4 - - + +
67B MET* 3.2 37.7 - - + -
68B ARG* 3.3 38.2 - - + +
70B GLN* 1.3 79.0 - - + +
72B MET* 1.3 64.3 + - + +
73B ARG 3.1 0.4 - - - -
74B THR* 3.4 10.4 + - - -
75B GLY* 2.8 27.4 + - - -
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Residues in contact with MET 72 (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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9B VAL* 4.5 4.7 - - + -
68B ARG* 3.1 33.9 + - + +
70B GLN 3.1 0.4 - - - -
71B TYR* 1.3 82.6 - - + +
73B ARG* 1.3 61.0 + - - +
75B GLY 3.8 1.4 + - - -
78B PHE* 3.2 37.5 - - + -
96B TYR* 3.9 21.5 - - + +
99B GLN* 3.5 41.3 - - - +
100B ILE* 3.7 30.3 - - + -
103B VAL* 3.8 22.7 - - + -
104B LYS* 3.4 15.2 - - - +
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Residues in contact with ARG 73 (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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69B ASP* 3.6 18.2 + - - +
70B GLN* 3.2 19.1 + - - +
71B TYR 3.1 0.6 - - - -
72B MET* 1.3 79.4 - - - +
74B THR* 1.3 59.0 + - - +
103B VAL* 3.7 24.7 + - + +
104B LYS* 3.0 27.3 + - + +
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Residues in contact with THR 74 (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 LYS* 3.6 26.7 - - + +
70B GLN 3.8 11.6 + - - -
71B TYR* 3.4 8.9 + - - -
73B ARG* 1.3 75.1 - - - +
75B GLY* 1.3 66.1 + - - +
76B GLU* 3.2 14.9 + - - +
104B LYS* 4.6 0.5 + - - -
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Residues in contact with GLY 75 (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 LYS* 4.6 4.0 - - - -
7B VAL* 3.6 23.3 - - - -
71B TYR 2.8 17.5 + - - -
72B MET 3.8 0.2 + - - -
73B ARG 3.3 1.0 - - - -
74B THR* 1.3 74.7 - - - +
76B GLU* 1.3 58.9 + - - -
77B GLY 3.7 0.4 - - - -
78B PHE* 3.6 14.5 - - - -
104B LYS* 2.7 31.5 + - - -
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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