Contacts of the helix formed by residues 67 - 81 (chain B) in PDB entry 1OUQ
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 GLU 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B LYS* 4.8 19.0 + - + +
65B PRO* 3.6 9.8 + - + +
66B ALA* 1.3 76.3 - - - +
68B PRO* 1.3 80.6 - - + +
69B GLU* 3.4 3.4 - - + +
70B ASP* 2.7 41.1 + - - +
71B VAL* 3.0 9.1 + - - -
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Residues in contact with PRO 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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25A LYS* 6.3 1.1 - - - +
66B ALA 3.9 4.8 - - - +
67B GLU* 1.3 86.6 - - + +
69B GLU* 1.3 71.6 + - + +
71B VAL* 2.8 15.1 + - + +
72B ARG* 2.9 12.5 + - - +
107B PRO* 5.3 4.5 - - + +
110B SER* 3.4 34.3 - - - +
112B ALA* 4.9 8.3 - - + -
113B VAL* 4.0 17.3 - - + +
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Residues in contact with GLU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 4.3 18.2 + - - +
29A ASP* 4.4 0.2 - - - +
32A ARG* 3.2 37.0 + - - -
67B GLU* 3.1 2.6 + - + -
68B PRO* 1.3 84.4 - - + +
70B ASP* 1.3 58.1 + - - +
72B ARG* 3.0 13.9 + - - +
73B ASP* 2.7 46.9 + - - +
112B ALA* 4.5 4.9 - - - +
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Residues in contact with ASP 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B TRP* 4.0 16.4 - - + -
55B TRP* 4.1 2.9 - - - -
61B ARG* 3.0 50.2 + - + +
62B LYS 4.8 6.0 + - - +
67B GLU* 2.7 47.8 + - - +
69B GLU* 1.3 74.8 - - - +
71B VAL* 1.3 66.1 + - - +
73B ASP* 3.1 9.5 + - - +
74B TYR* 3.0 20.6 + - - +
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B TRP* 3.8 11.4 - - + -
66B ALA* 3.7 25.4 - - + -
67B GLU 3.0 12.0 + - - +
68B PRO 2.8 10.6 + - - +
70B ASP* 1.3 72.5 - - - +
72B ARG* 1.3 52.9 + - - +
74B TYR* 3.0 6.3 + - + +
75B LEU* 2.7 54.4 + - + +
92B LEU* 4.5 6.1 - - + -
95B LEU* 4.3 19.1 - - + -
107B PRO* 3.7 26.7 - - + -
113B VAL* 4.1 15.7 - - + -
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Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ARG* 3.1 56.8 - - - +
33A ASP* 2.9 24.4 + - - -
68B PRO 2.9 10.4 + - - +
69B GLU* 3.1 18.5 + - - +
71B VAL* 1.3 74.5 - - - +
73B ASP* 1.3 60.7 + - - +
75B LEU* 3.0 7.8 + - - +
76B LEU* 2.7 55.7 + - + +
112B ALA* 4.0 17.7 - - - +
113B VAL* 4.7 4.9 - - + +
116B VAL* 3.1 32.5 - - + +
119B ARG* 4.8 4.4 - - - +
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Residues in contact with ASP 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TRP* 4.0 19.2 - - + -
61B ARG* 3.9 21.2 + - - +
69B GLU* 2.7 28.7 + - - +
70B ASP* 3.6 8.1 - - - +
72B ARG* 1.3 76.1 + - - +
74B TYR* 1.3 56.8 + - - +
76B LEU* 3.1 14.3 - - - +
77B TYR* 2.9 24.9 + - - +
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Residues in contact with TYR 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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48B VAL* 5.6 0.9 - - + -
51B SER* 3.3 22.0 + - - -
52B TRP* 3.3 49.1 + + + +
55B TRP* 4.0 25.3 - + + -
70B ASP 3.0 4.5 + - - +
71B VAL 3.0 10.5 + - - +
72B ARG 3.0 0.4 - - - -
73B ASP* 1.3 73.1 - - - +
75B LEU* 1.3 63.3 + - + +
76B LEU 2.7 4.0 - - - -
77B TYR* 2.5 60.4 + + - +
78B LEU* 2.9 31.6 + - + +
91B HIS* 3.3 31.9 + - + -
95B LEU* 4.6 11.4 - - + -
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Residues in contact with LEU 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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71B VAL* 2.7 36.8 + - + +
72B ARG* 3.7 7.4 - - - +
74B TYR* 1.3 78.7 - - + +
76B LEU* 1.3 61.6 + - - +
78B LEU* 3.7 12.7 + - + +
79B GLN 3.4 12.1 + - - -
88B ILE* 3.4 36.6 - - + +
91B HIS* 4.8 1.3 - - + -
92B LEU* 3.8 40.2 - - + +
95B LEU* 6.2 0.7 - - + -
113B VAL* 4.1 8.5 - - + -
116B VAL* 4.4 12.1 - - + -
117B MET* 4.4 6.1 - - - -
120B ILE* 3.3 23.2 - - + +
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Residues in contact with LEU 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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72B ARG* 2.7 45.0 + - + +
73B ASP* 3.1 20.0 - - - +
74B TYR 2.7 0.4 + - - -
75B LEU* 1.3 77.0 - - - +
77B TYR* 1.3 67.5 + - - +
79B GLN* 3.0 32.6 + - - +
80B ALA* 3.2 9.8 + - - +
116B VAL* 4.3 10.8 - - + -
119B ARG* 5.1 15.7 - - - +
120B ILE* 4.3 7.4 - - + -
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Residues in contact with TYR 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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51B SER* 5.6 0.7 - - - -
55B TRP* 3.2 44.5 - + + +
73B ASP 2.9 14.0 + - - +
74B TYR* 2.5 36.8 + + - +
76B LEU* 1.3 69.5 - - - +
78B LEU* 1.3 61.4 + - + -
80B ALA* 2.5 41.8 + - + +
81B ARG* 3.0 51.7 + - + -
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B SER* 5.0 0.2 - - - +
74B TYR* 2.9 58.9 + - + +
75B LEU* 3.9 9.6 - - + +
77B TYR* 1.3 82.6 - - + +
79B GLN* 1.3 61.7 + - - +
80B ALA 3.2 0.3 + - - -
81B ARG* 3.3 19.4 + - - +
83B LEU* 3.3 49.4 + - + +
88B ILE* 4.0 22.2 - - + -
91B HIS* 3.8 31.2 - - + +
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Residues in contact with GLN 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 LEU 3.4 6.8 + - - +
76B LEU* 3.0 27.8 + - - +
77B TYR 2.9 0.2 + - - -
78B LEU* 1.3 78.9 - - - +
80B ALA* 1.3 62.1 + - - +
82B GLY* 3.4 11.8 + - - -
83B LEU 4.4 2.8 + - - +
88B ILE* 4.3 8.5 - - + +
119B ARG* 5.7 2.9 + - - -
120B ILE* 3.3 41.5 + - + +
123B GLU* 4.2 19.7 + - - +
124B ASN* 3.1 30.6 + - - +
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Residues in contact with ALA 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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76B LEU 3.2 5.6 + - - +
77B TYR* 2.5 27.5 + - + +
79B GLN* 1.3 70.9 - - - +
81B ARG* 1.3 51.3 + - - +
82B GLY* 2.6 18.2 + - - -
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Residues in contact with ARG 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B SER* 3.9 19.6 + - - -
77B TYR* 3.0 50.9 + - + +
78B LEU* 3.3 20.9 + - - +
80B ALA* 1.3 73.3 - - - +
82B GLY* 1.3 58.3 + - - +
83B LEU* 3.5 21.6 + - + +
91B HIS* 5.6 1.4 + - - -
111C T 5.7 0.2 - - - -
112C A 3.6 33.4 + - - -
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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