Contacts of the helix formed by residues 69 - 88 (chain B) in PDB entry 3D10
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 ASP 69 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PHE* 3.5 4.7 - - - -
25B HIS 4.3 1.1 - - - +
26B LYS* 4.0 33.7 - - + -
63B ASP* 3.5 21.5 - - - +
65B ASP* 5.5 1.3 - - - +
67B GLU 3.9 0.4 + - - -
68B CYS* 1.3 74.5 - - - +
70B PHE* 1.3 64.5 + - - +
71B GLN* 3.4 14.8 + - - +
72B GLU* 2.8 42.8 + - - +
73B PHE* 2.9 21.7 + - - +
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Residues in contact with PHE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A THR* 3.8 20.6 - - + -
82A THR* 4.3 12.1 - - + -
85A HIS* 3.3 54.1 - + + +
10B LEU 4.0 7.0 - - - -
11B ILE* 3.8 15.5 - - + -
14B PHE* 3.4 43.8 - + + -
15B HIS* 5.0 0.4 - + - -
25B HIS* 4.4 2.2 + - - +
69B ASP* 1.3 75.0 - - - +
71B GLN* 1.4 57.2 + - - +
73B PHE* 3.2 21.9 + + - +
74B MET* 2.9 57.2 + - + +
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Residues in contact with GLN 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A THR* 5.2 12.0 - - + +
69B ASP* 3.4 14.6 + - - +
70B PHE* 1.4 78.6 - - - +
72B GLU* 1.3 65.4 + - - +
74B MET* 3.2 9.4 + - + +
75B ALA* 3.1 21.0 + - - +
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Residues in contact with GLU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 3.5 25.6 - - - +
61B ASP* 3.2 5.5 - - - +
62B ASN* 3.2 8.1 + - + +
63B ASP* 2.8 26.2 + - - +
67B GLU 2.8 5.5 - - - +
68B CYS* 3.2 15.8 - - - -
69B ASP* 2.8 40.9 + - - +
71B GLN* 1.3 76.5 - - + +
73B PHE* 1.3 67.7 + - - +
75B ALA* 3.2 7.9 + - - +
76B PHE* 3.0 21.7 + - - +
93B CA 2.4 30.9 - - - -
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Residues in contact with PHE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 4.4 14.8 - - + -
10B LEU* 3.6 27.1 - - + -
13B VAL* 5.2 1.1 - - + -
14B PHE* 3.5 27.1 - + + -
27B LEU* 4.1 14.8 - - + -
32B LEU* 5.6 0.7 - - + -
35B LEU* 3.8 35.9 - - + -
68B CYS* 3.3 9.8 - - - -
69B ASP 2.9 18.8 + - - +
70B PHE* 3.4 18.2 - + - +
72B GLU* 1.3 77.7 - - - +
74B MET* 1.3 62.5 + - - +
76B PHE* 3.0 20.7 + + - +
77B VAL* 2.9 46.7 + - + +
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Residues in contact with MET 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 6.2 0.2 - - + -
74A MET 5.7 0.4 - - - +
77A VAL* 4.5 3.6 - - + +
78A ALA* 3.7 40.5 - - + +
81A THR* 4.1 10.5 - - + +
82A THR* 4.3 10.3 - - - +
10B LEU* 3.6 35.0 - - + -
70B PHE* 2.9 52.0 + - + +
71B GLN* 3.2 11.4 + - + +
73B PHE* 1.3 80.1 - - - +
75B ALA* 1.3 56.9 + - - +
77B VAL* 3.3 11.5 + - + +
78B ALA* 3.0 26.7 + - - +
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 6.5 0.2 - - + -
71B GLN 3.1 13.4 + - - +
72B GLU* 3.2 8.9 + - - +
74B MET* 1.3 75.7 - - - +
76B PHE* 1.3 57.6 + - - +
78B ALA* 3.3 9.1 + - - +
79B MET* 3.0 33.9 + - + +
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Residues in contact with PHE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 4.7 5.2 - - + -
35B LEU* 4.5 7.2 - - + -
36B ILE* 3.8 30.3 - - + -
40B LEU* 3.6 23.6 - - + -
44B LEU* 3.9 7.0 - - + -
56B VAL* 4.5 10.5 - - + -
60B LEU* 3.9 31.3 - - + +
72B GLU 3.0 12.7 + - - +
73B PHE* 3.0 27.6 + + - +
75B ALA* 1.3 73.4 - - - +
77B VAL* 1.3 70.8 + - + +
79B MET* 3.2 23.6 + - + +
80B VAL* 2.9 44.2 + - + +
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 4.3 0.7 - - + -
7A MET* 4.0 23.3 - - + -
10A LEU* 4.6 7.9 - - + -
74A MET* 6.1 0.4 - - - -
10B LEU* 3.9 34.3 - - + -
73B PHE* 2.9 50.6 + - + +
74B MET* 3.6 15.0 - - + +
76B PHE* 1.3 78.8 - - + +
78B ALA* 1.4 59.2 + - - +
80B VAL* 3.9 0.6 - - - +
81B THR* 2.8 44.8 + - - +
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLN* 4.3 8.5 - - - +
74A MET* 4.2 34.2 - - + +
78A ALA* 6.3 1.6 - - + -
74B MET 3.0 14.8 + - - +
75B ALA* 3.5 11.2 - - - +
76B PHE 3.2 0.2 - - - -
77B VAL* 1.4 78.4 - - - +
79B MET* 1.3 53.5 + - - +
81B THR* 3.5 1.2 + - - -
82B THR* 2.7 38.0 + - - -
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Residues in contact with MET 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B THR* 4.9 19.3 - - + +
60B LEU* 5.6 6.7 - - + -
75B ALA* 3.0 21.2 + - + +
76B PHE* 3.2 28.0 + - + +
78B ALA* 1.3 73.1 - - - +
80B VAL* 1.3 66.5 + - + +
82B THR* 3.4 6.1 + - - -
83B ALA* 3.0 23.7 + - + +
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A MET* 3.7 25.8 - - + -
40B LEU* 4.3 7.2 - - + -
43B PHE* 4.0 15.9 - - + -
44B LEU* 4.1 26.9 - - + -
76B PHE* 2.9 51.4 + - + +
77B VAL 3.9 2.5 - - - +
79B MET* 1.3 79.0 - - + +
81B THR* 1.3 64.4 + - - +
83B ALA* 3.1 7.7 + - + +
84B CYS* 3.0 21.7 + - - +
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Residues in contact with THR 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A MET* 3.3 36.0 - - + +
10A LEU* 4.3 3.9 - - + +
11A ILE* 3.7 26.0 - - + +
70A PHE* 3.7 2.9 - - + -
74A MET* 3.6 31.0 - - + -
77B VAL* 2.8 34.2 + - - +
78B ALA 3.9 0.2 - - - -
80B VAL* 1.3 73.3 - - - +
82B THR* 1.3 62.2 + - - +
84B CYS* 3.3 5.3 + - - +
85B HIS* 3.0 22.3 + - - +
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Residues in contact with THR 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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70A PHE* 3.4 18.3 - - + -
71A GLN* 3.0 32.7 + - - +
74A MET* 4.3 0.3 - - - +
78B ALA 2.7 23.1 + - - -
79B MET* 3.7 6.9 - - - -
81B THR* 1.3 77.4 - - - +
83B ALA* 1.3 63.1 + - - +
85B HIS* 3.3 4.0 + - - +
86B GLU* 3.1 43.5 + - + +
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 6.3 2.5 - - + -
79B MET* 3.0 14.2 + - + +
80B VAL* 3.1 9.6 + - + +
82B THR* 1.3 77.4 - - - +
84B CYS* 1.3 57.9 + - - +
86B GLU* 3.4 10.5 + - - +
87B PHE* 2.9 30.0 + - - +
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Residues in contact with CYS 84 (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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7A MET* 5.7 0.7 - - + -
8A VAL* 4.4 10.3 - - - -
11A ILE* 4.0 14.6 - - + -
43B PHE* 3.8 42.8 - - + -
80B VAL 3.0 15.7 + - - +
81B THR* 3.8 5.8 - - - +
82B THR 3.2 0.2 - - - -
83B ALA* 1.3 75.9 - - - +
85B HIS* 1.3 63.9 + - - +
87B PHE* 3.2 14.4 + - - +
88B PHE* 3.3 37.9 - - - +
94B PGE 6.1 2.0 - - - -
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Residues in contact with HIS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 3.6 22.1 - - + +
15A HIS* 3.5 13.8 + + - -
25A HIS* 3.6 12.6 - + - -
70A PHE* 3.9 37.5 - + + -
94A ZN 2.2 36.4 - - - -
81B THR 3.0 16.9 + - - +
82B THR* 3.4 8.9 + - - +
84B CYS* 1.3 79.1 - - - +
86B GLU* 1.3 68.9 + - + +
88B PHE* 3.4 9.1 + - - +
89B GLU* 2.9 24.0 + - - +
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Residues in contact with GLU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B THR* 3.1 36.7 + - - +
83B ALA* 3.8 8.6 - - - +
85B HIS* 1.3 82.3 - - + +
87B PHE* 1.3 67.5 + - - +
89B GLU* 3.0 26.8 + - - +
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Residues in contact with PHE 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ALA 2.9 18.4 + - - +
84B CYS* 3.2 10.5 + - - +
86B GLU* 1.3 78.0 - - - +
88B PHE* 1.3 86.8 + + + +
89B GLU 3.2 6.3 + - - +
90B HIS 5.0 1.2 - - - +
94B PGE 4.1 38.6 - - - -
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Residues in contact with PHE 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 5.9 1.6 - + - -
84B CYS* 3.3 35.6 + - - +
85B HIS* 3.4 4.7 + - - +
86B GLU 3.1 1.0 - - - -
87B PHE* 1.3 103.4 - + + +
89B GLU* 1.3 60.1 + - - +
90B HIS 4.3 4.8 - - - +
94B PGE 4.0 30.7 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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