Contacts of the helix formed by residues 66 - 87 (chain B) in PDB entry 2HQT
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 THR 66 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLU* 3.7 23.1 - - + +
12B SER* 5.7 3.1 - - - -
22B PHE* 4.3 14.8 - - + -
60B VAL* 3.8 7.8 - - - +
62B THR* 3.7 24.2 - - + +
64B TYR* 3.7 10.5 - - + +
65B PRO* 1.3 80.5 - - - +
67B SER* 1.3 60.6 + - - +
68B THR* 3.4 19.0 + - - -
69B ASP* 2.9 30.3 + - - +
70B VAL* 3.1 15.0 + - - +
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Residues in contact with SER 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLU* 2.6 41.5 + - - +
66B THR* 1.3 71.3 - - - +
68B THR* 1.3 62.8 + - - +
70B VAL* 3.7 11.2 - - - +
71B HIS* 2.8 57.1 + - - -
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Residues in contact with THR 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLU* 4.3 0.5 + - - -
22B PHE* 5.4 1.4 - - - -
30B ALA* 3.8 19.2 + - - +
33B TRP* 3.9 29.4 - - + -
37B LEU* 6.1 0.9 - - + -
59B ILE* 3.9 14.6 - - + -
60B VAL* 3.5 33.8 - - + +
66B THR* 3.1 4.9 + - - -
67B SER* 1.3 81.0 + - - +
69B ASP* 1.3 61.8 + - - +
71B HIS* 3.9 5.2 - - - +
72B VAL* 3.0 27.1 + - + +
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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
----------------------------------------------------------
58B PHE* 3.5 19.7 - - - +
59B ILE* 3.0 26.7 + - - +
60B VAL 4.7 0.7 + - - -
62B THR* 4.5 1.0 + - - -
65B PRO* 4.2 3.4 - - + -
66B THR* 2.9 38.9 + - - +
68B THR* 1.3 76.6 - - - +
70B VAL* 1.3 59.3 + - - +
73B PHE* 2.9 32.7 + - - +
103B TRP* 2.8 33.2 + - - +
107B MET* 3.9 17.7 - - + -
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Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PRO* 5.7 2.7 - - + -
66B THR 3.1 14.2 + - - +
67B SER* 3.2 12.5 + - - +
69B ASP* 1.3 78.4 - - - +
71B HIS* 1.3 67.5 + - + +
73B PHE* 3.6 4.0 - - + +
74B GLU* 3.0 32.2 + - + +
107B MET* 4.0 19.1 - - + -
110B LEU* 5.9 1.3 - - + -
111B LEU* 4.2 24.5 - - + -
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Residues in contact with HIS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLU* 5.8 2.5 + - - -
37B LEU* 3.9 21.6 - - + +
67B SER* 2.8 46.3 + - - +
68B THR* 4.0 4.3 + - - +
70B VAL* 1.3 82.3 - - + +
72B VAL* 1.3 61.4 + - - +
74B GLU* 3.3 28.4 + - - +
75B VAL* 3.5 14.0 + - - +
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Residues in contact with VAL 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TRP* 4.0 32.1 - - + -
37B LEU* 4.1 18.6 - - + -
42B ILE* 4.2 15.0 - - + +
49B LEU* 3.9 26.5 - - + -
59B ILE* 3.5 27.4 - - + -
68B THR 3.0 17.1 + - - +
71B HIS* 1.3 72.1 - - - +
73B PHE* 1.3 54.8 + - - +
75B VAL* 3.2 4.7 + - - +
76B ALA* 2.7 34.4 + - + +
103B TRP* 3.9 2.2 - - + -
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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
----------------------------------------------------------
69B ASP 2.9 22.4 + - - +
70B VAL* 3.6 5.6 - - + +
72B VAL* 1.3 76.9 - - - +
74B GLU* 1.3 61.0 + - + +
76B ALA* 4.4 0.9 - - - +
77B LEU* 2.8 65.1 + - + +
103B TRP* 3.4 18.1 - + + -
104B ILE* 4.0 29.6 - - + -
107B MET* 3.7 30.3 - - + -
108B GLN* 3.9 22.4 - - + -
111B LEU* 4.4 14.8 - - + -
113B VAL* 4.0 17.5 - - + -
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Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B VAL* 3.0 20.8 + - + +
71B HIS* 3.4 24.0 - - - +
73B PHE* 1.3 82.7 - - + +
75B VAL* 1.3 59.1 + - + +
77B LEU* 4.8 0.8 - - - +
78B PRO* 3.2 22.0 - - - +
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 3.6 25.4 - - + -
42B ILE* 3.8 29.6 - - + -
71B HIS 3.7 5.8 - - - +
72B VAL 3.2 5.8 + - - +
74B GLU* 1.3 78.1 - - + +
76B ALA* 1.3 64.8 + - - +
78B PRO* 3.2 12.0 - - - +
79B LEU* 3.6 20.8 + - + +
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 4.6 6.3 - - + +
46B LEU* 4.5 9.6 - - + -
49B LEU* 4.3 15.3 - - + -
72B VAL* 2.7 25.9 + - + +
73B PHE 4.2 1.1 - - - +
75B VAL* 1.3 71.3 - - - +
77B LEU* 1.3 66.7 + - - +
79B LEU* 3.2 7.3 + - - +
80B ILE* 3.0 31.2 + - + +
100B ILE* 5.1 2.2 - - + -
103B TRP* 4.3 17.9 - - + -
104B ILE* 4.8 0.9 - - + -
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B PHE* 2.8 52.5 + - + +
74B GLU* 4.8 1.1 - - - +
76B ALA* 1.3 73.8 - - - +
78B PRO* 1.4 66.3 - - + +
80B ILE* 3.7 1.6 - - - +
81B LYS* 2.8 47.6 + - + +
104B ILE* 4.3 15.2 - - + +
108B GLN* 4.2 4.3 - - - +
113B VAL* 4.2 13.7 - - + -
117B ASP* 3.5 22.7 - - + +
119B LEU* 4.0 17.3 - - + +
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Residues in contact with PRO 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B GLU 3.2 17.3 - - - +
75B VAL* 3.2 15.0 - - - +
77B LEU* 1.4 95.0 - - + +
79B LEU* 1.3 64.4 + - - +
81B LYS* 3.7 9.4 - - + +
82B ASP* 2.9 25.9 + - - +
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 3.9 18.2 - - + -
43B GLN* 3.7 44.6 - - + +
46B LEU* 3.8 21.3 - - + -
75B VAL* 3.6 15.7 - - + +
76B ALA* 3.2 7.2 + - - +
78B PRO* 1.3 80.8 - - + +
80B ILE* 1.3 54.4 + - - +
82B ASP* 3.4 4.6 + - + +
83B LEU* 2.7 43.2 + - + +
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 4.2 15.7 - - + -
76B ALA* 3.0 20.5 + - + +
77B LEU 3.8 2.2 - - - +
79B LEU* 1.3 72.4 - - - +
81B LYS* 1.3 67.2 + - - +
83B LEU* 3.5 23.9 - - + +
84B VAL* 2.9 30.4 + - + +
93B THR* 6.0 0.7 - - + -
97B TYR* 4.2 25.8 - - + -
100B ILE* 4.1 17.0 - - + -
101B LEU* 3.9 14.8 - - + -
104B ILE* 3.9 16.8 - - + -
119B LEU* 3.8 23.8 - - + -
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Residues in contact with LYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 2.8 30.0 + - + +
78B PRO* 3.7 9.4 - - + +
80B ILE* 1.3 78.8 - - - +
82B ASP* 1.3 55.4 + - - +
84B VAL* 3.4 2.9 + - - +
85B ALA* 2.9 29.9 + - - +
116B THR 3.0 21.8 + - - -
117B ASP* 3.3 19.9 + - - +
118B LYS 3.0 22.8 + - - +
119B LEU* 3.7 25.8 - - + +
120B GLU 5.5 0.2 - - - +
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Residues in contact with ASP 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PRO 2.9 17.6 + - - +
79B LEU* 3.7 6.1 - - + +
81B LYS* 1.3 72.6 - - - +
83B LEU* 1.3 63.3 + - + +
85B ALA* 3.2 7.1 + - - +
86B SER* 2.7 46.4 + - - -
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Residues in contact with LEU 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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43B GLN* 5.8 4.9 - - + -
46B LEU* 3.7 28.0 - - + -
79B LEU* 2.7 39.3 + - + +
80B ILE* 3.5 20.2 - - + +
82B ASP* 1.3 82.0 - - + +
84B VAL* 1.3 53.0 + - - +
86B SER* 3.3 4.1 + - - -
87B SER* 2.8 36.0 + - - -
93B THR* 4.4 14.0 + - + +
97B TYR* 4.0 20.6 - - + +
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE* 2.9 27.9 + - + +
81B LYS 3.5 5.2 - - - +
83B LEU* 1.3 72.4 - - - +
85B ALA* 1.3 65.1 + - - +
86B SER 3.2 0.9 + - - -
87B SER* 3.3 19.3 + - - -
90B VAL* 4.1 17.3 - - + +
93B THR* 4.1 17.3 - - + -
94B TYR* 4.3 28.9 - - + +
101B LEU* 5.6 0.7 - - + -
119B LEU* 4.3 22.4 - - + -
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LYS 2.9 21.0 + - - +
82B ASP* 3.6 9.9 - - - +
84B VAL* 1.3 74.7 - - - +
86B SER* 1.3 61.2 + - - +
87B SER 3.8 1.7 + - - +
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Residues in contact with SER 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ASP* 2.7 37.0 + - - -
83B LEU* 3.5 4.0 - - - -
84B VAL 3.2 0.2 - - - -
85B ALA* 1.3 74.6 - - - +
87B SER* 1.3 65.0 + - - +
88B LYS* 3.5 10.4 + - - +
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Residues in contact with SER 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU 2.8 13.7 + - - -
84B VAL 3.3 13.6 + - - +
85B ALA 3.5 1.1 - - - +
86B SER* 1.3 79.3 - - - +
88B LYS* 1.3 62.3 + - - +
89B ASP 2.9 26.0 + - - -
90B VAL* 4.2 10.9 - - - +
93B THR* 2.6 30.2 + - - -
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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
------------------------------------------------------------
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