Contacts of the helix formed by residues 61 - 70 (chain B) in PDB entry 2W5U
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 GLN 61 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B GLY* 3.2 21.8 - - - -
10B THR 3.2 19.4 + - - -
11B ASP* 3.4 31.9 + - - +
53B PRO* 3.4 43.1 + - + +
54B THR 5.5 0.4 - - - -
55B ALA* 4.2 11.0 - - + +
59B ASP 3.7 1.4 + - - -
60B LEU* 1.3 74.3 - - - +
62B THR* 1.3 73.4 + - - +
63B ASP* 2.7 46.4 + - - +
64B TRP* 2.8 20.0 + - + +
65B GLU 3.1 2.4 + - - -
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Residues in contact with THR 62 (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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11B ASP* 4.6 7.7 + - - -
55B ALA* 5.3 1.4 - - - +
60B LEU 3.4 3.3 + - - -
61B GLN* 1.3 78.0 + - - +
63B ASP* 1.3 62.5 + - - +
65B GLU* 2.6 48.6 + - - +
66B ASP* 3.2 17.9 + - - +
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Residues in contact with ASP 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLY* 4.6 1.1 - - - -
10B THR* 3.5 12.6 + - - +
33B ASP* 4.8 0.7 - - - +
34B VAL* 3.8 15.1 - - + +
35B ALA* 3.8 33.0 - - + +
61B GLN* 2.7 26.9 + - - +
62B THR* 1.3 82.2 - - - +
64B TRP* 1.3 57.5 + - - +
66B ASP* 3.7 10.3 + - - +
67B PHE* 3.2 27.0 + - - +
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Residues in contact with TRP 64 (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 PHE* 3.6 15.9 - - + -
8B PHE 3.5 1.0 - - - -
9B GLY* 3.3 30.2 - - - +
34B VAL* 3.6 17.7 - - + -
42B PHE* 5.4 1.8 - + - -
50B LEU* 3.8 33.0 - - + -
51B VAL 2.7 19.5 + - - -
52B ALA* 3.3 22.8 - - + +
53B PRO* 4.4 1.3 - - + -
60B LEU* 3.4 20.5 - - + +
61B GLN* 2.8 15.3 + - - +
63B ASP* 1.3 72.7 - - - +
65B GLU* 1.3 60.0 + - - +
67B PHE* 3.4 31.6 - + - -
68B LEU* 3.0 46.6 + - + +
71B LEU* 5.3 2.2 - - + -
76B PHE* 6.0 1.3 - + - -
103B ILE* 4.0 22.7 - - + -
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Residues in contact with GLU 65 (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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55B ALA* 5.5 0.9 - - - +
59B ASP* 4.3 13.2 - - + +
60B LEU* 3.2 35.8 - - + +
61B GLN 3.1 4.2 + - - -
62B THR* 2.6 31.9 + - - +
64B TRP* 1.3 70.1 - - - +
66B ASP* 1.3 64.4 + - - +
68B LEU* 4.2 1.6 - - - +
69B GLY* 3.2 19.6 + - - -
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Residues in contact with ASP 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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62B THR* 3.2 26.6 + - - +
63B ASP* 4.2 8.6 - - - +
65B GLU* 1.3 77.9 - - - +
67B PHE* 1.3 67.7 + - - +
69B GLY* 3.2 9.1 + - - -
70B THR* 3.2 18.2 + - + +
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Residues in contact with PHE 67 (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 PHE* 3.7 35.7 - + - -
34B VAL* 3.6 26.7 - - + +
37B ALA* 3.7 7.0 - - + -
38B SER* 3.5 41.7 - - - -
39B LYS 4.5 0.7 - - - -
42B PHE* 4.0 19.5 - + + -
63B ASP 3.2 18.9 + - - +
64B TRP* 3.4 32.5 - + + +
66B ASP* 1.3 77.4 - - - +
68B LEU* 1.3 53.9 + - - +
70B THR* 2.6 43.4 + - + -
71B LEU* 3.6 13.2 - - + +
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Residues in contact with LEU 68 (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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60B LEU* 3.8 13.5 - - + -
64B TRP* 3.0 26.7 + - + +
65B GLU* 4.2 2.5 - - - +
67B PHE* 1.3 79.1 - - - +
69B GLY* 1.3 60.4 + - - +
71B LEU* 3.0 27.9 + - + +
76B PHE* 3.8 28.9 - - + -
102B HIS* 3.9 10.3 - - + +
103B ILE* 3.7 40.6 - - + +
106B LYS* 3.2 25.7 + - + +
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Residues in contact with GLY 69 (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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65B GLU 3.2 15.2 + - - -
66B ASP* 3.5 7.4 - - - -
67B PHE 3.0 1.4 - - - -
68B LEU* 1.3 79.4 - - - +
70B THR* 1.3 57.8 + - - +
71B LEU 3.2 4.0 + - - +
106B LYS* 4.5 6.7 + - - -
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Residues in contact with THR 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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38B SER* 5.3 0.9 - - - -
39B LYS* 4.1 23.1 + - - +
66B ASP* 3.2 17.5 - - + +
67B PHE* 2.6 34.2 + - + +
69B GLY* 1.3 72.6 - - - -
71B LEU* 1.3 71.1 + - - +
72B GLU* 5.6 1.1 - - - +
75B ASP* 4.2 0.3 - - - +
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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