Contacts of the helix formed by residues 66 - 86 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J GLU* 3.5 11.0 - - - +
22J PHE* 4.2 7.9 - - + -
60J VAL* 3.7 18.0 - - + +
62J THR* 3.6 23.8 - - + +
64J TYR* 3.6 24.9 - - + +
65J PRO* 1.3 71.1 - - - +
67J SER* 1.3 64.4 + - - +
68J THR* 3.1 22.0 + - - -
69J ASP* 2.8 27.6 + - - +
70J VAL* 3.1 23.3 + - - +
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Residues in contact with SER 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J MET* 6.0 2.4 - - - +
7J VAL* 5.4 1.9 - - - +
11J GLU* 2.9 32.4 + - - -
66J THR* 1.3 72.1 - - - +
68J THR* 1.3 59.9 + - - +
70J VAL* 3.1 10.6 + - - +
71J HIS* 2.9 51.5 + - - -
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Residues in contact with THR 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J PHE* 5.0 2.6 - - - -
30J ALA* 3.8 24.4 + - - +
33J TRP* 3.7 30.3 - - + -
34J GLU 5.4 0.2 - - - +
37J LEU* 5.4 3.4 - - + -
59J ILE* 3.9 7.0 - - + -
60J VAL* 3.8 21.2 - - + +
66J THR* 3.1 13.1 + - - -
67J SER* 1.3 80.2 + - - +
69J ASP* 1.3 61.1 + - - +
71J HIS* 4.1 3.9 - - - +
72J VAL* 3.1 32.9 + - + +
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Residues in contact with ASP 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58J PHE* 3.6 14.6 - - - +
59J ILE* 2.9 32.3 + - - +
60J VAL 4.9 0.2 + - - -
62J THR* 4.7 0.2 + - - -
65J PRO* 3.7 5.5 - - - +
66J THR* 2.8 41.2 + - - +
68J THR* 1.3 76.9 - - - +
70J VAL* 1.3 56.1 + - - +
73J PHE* 2.9 31.5 + - - +
103J TRP* 2.9 31.1 + - - +
107J MET* 3.7 18.4 - - + -
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Residues in contact with VAL 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65J PRO* 5.8 1.1 - - + -
66J THR 3.1 16.1 + - - +
67J SER* 3.1 11.4 + - - +
69J ASP* 1.3 76.4 - - - +
71J HIS* 1.3 69.1 + - + +
73J PHE* 3.2 3.4 + - + +
74J GLU* 2.9 32.3 + - + +
107J MET* 3.7 20.0 - - + -
110J LEU* 5.2 2.7 - - + -
111J LEU* 4.0 29.2 - - + -
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Residues in contact with HIS 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J LEU* 3.8 23.9 - - + +
67J SER* 2.9 46.7 + - - +
68J THR* 4.2 2.5 - - - +
70J VAL* 1.3 80.2 - - + +
72J VAL* 1.3 63.4 + - - +
74J GLU* 3.4 17.1 + - - +
75J VAL* 3.4 17.3 + - - +
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Residues in contact with VAL 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J TRP* 4.3 12.8 - - + -
37J LEU* 4.0 28.0 - - + -
42J ILE* 4.0 18.2 - - + -
49J LEU* 4.0 16.6 - - + -
59J ILE* 3.7 30.7 - - + -
68J THR 3.1 18.9 + - - +
69J ASP 4.0 1.8 - - - +
71J HIS* 1.3 74.5 - - - +
73J PHE* 1.3 58.5 + - - +
75J VAL* 3.1 4.5 + - - +
76J ALA* 2.8 31.3 + - + +
103J TRP* 4.0 11.4 - - + -
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Residues in contact with PHE 73 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69J ASP 2.9 20.4 + - - +
70J VAL* 3.5 4.9 - - + +
72J VAL* 1.3 78.2 - - - +
74J GLU* 1.3 68.1 + - + +
76J ALA* 4.3 0.7 - - - +
77J LEU* 2.9 55.4 + - + +
103J TRP* 3.5 17.2 - + + -
104J ILE* 3.9 32.1 - - + -
107J MET* 3.5 31.2 - - + -
108J GLN* 3.7 25.1 - - + -
111J LEU* 4.1 17.3 - - + -
113J VAL* 3.9 17.7 - - + -
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Residues in contact with GLU 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D LYS* 5.7 3.0 + - - -
70J VAL* 2.9 25.2 + - + +
71J HIS* 3.6 11.5 + - - +
72J VAL 3.3 0.2 - - - -
73J PHE* 1.3 82.2 - - + +
75J VAL* 1.3 59.7 + - + +
77J LEU* 5.4 0.7 - - - -
78J PRO* 3.3 23.1 - - - +
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Residues in contact with VAL 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D LYS 4.5 1.4 - - - +
37J LEU* 4.1 12.8 - - + -
42J ILE* 3.9 29.4 - - + -
71J HIS 3.4 13.0 + - - +
72J VAL 3.1 5.7 + - - +
73J PHE 3.1 0.4 - - - -
74J GLU* 1.3 80.4 - - + +
76J ALA* 1.3 62.7 + - - +
77J LEU 3.5 0.2 - - - -
78J PRO* 3.5 14.2 - - - +
79J LEU* 3.5 19.4 - - + +
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Residues in contact with ALA 76 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J ILE* 4.5 4.3 - - + -
46J LEU* 4.4 9.9 - - + -
49J LEU* 4.4 15.7 - - + -
72J VAL 2.8 22.5 + - - +
73J PHE 4.1 1.1 - - - +
75J VAL* 1.3 72.0 - - - +
77J LEU* 1.3 60.1 + - - +
79J LEU* 3.1 11.7 + - - +
80J ILE* 2.8 38.7 + - + +
100J ILE* 5.2 1.3 - - + -
103J TRP* 4.3 17.9 - - + -
104J ILE* 4.7 0.7 - - + -
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Residues in contact with LEU 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73J PHE* 2.9 47.6 + - + +
74J GLU* 5.2 0.7 - - - -
76J ALA* 1.3 72.3 - - - +
78J PRO* 1.3 69.6 - - + +
80J ILE* 3.8 0.9 - - - +
81J LYS* 2.9 30.4 + - + +
104J ILE* 4.0 19.0 - - + +
108J GLN* 4.0 7.4 - - - +
113J VAL* 4.3 15.5 - - + -
117J ASP* 3.8 21.3 - - + +
119J LEU* 3.9 33.7 - - + +
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Residues in contact with PRO 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D LYS* 3.3 50.6 - - + +
39D SER* 4.1 2.1 - - - -
74J GLU 3.3 22.4 - - - +
75J VAL* 3.5 9.9 - - - +
77J LEU* 1.3 103.5 - - + +
79J LEU* 1.3 60.0 + - - +
81J LYS* 3.5 11.2 + - + +
82J ASP* 3.2 22.7 + - - +
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Residues in contact with LEU 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D LYS 4.0 3.8 - - - +
39D SER 3.5 8.9 - - - +
40D GLY* 3.5 34.5 - - - +
42J ILE* 3.9 22.2 - - + -
43J GLN* 3.9 42.2 - - + +
46J LEU* 4.0 19.3 - - + -
75J VAL* 3.5 19.4 + - + +
76J ALA* 3.1 6.8 + - - +
78J PRO* 1.3 77.8 - - - +
80J ILE* 1.3 63.9 + - - +
82J ASP* 3.3 4.9 + - - +
83J LEU* 3.0 27.8 + - + +
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Residues in contact with ILE 80 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46J LEU* 4.4 10.1 - - + -
76J ALA 2.8 20.1 + - - +
77J LEU 3.9 1.1 - - - +
79J LEU* 1.3 74.3 - - - +
81J LYS* 1.3 67.3 + - - +
83J LEU* 3.1 22.9 + - + +
84J VAL* 2.9 28.2 + - + +
93J THR* 5.8 0.4 - - + -
97J TYR* 4.0 28.5 - - + -
100J ILE* 3.8 19.5 - - + -
101J LEU* 3.8 27.8 - - + -
104J ILE* 3.8 18.8 - - + -
119J LEU* 3.9 11.0 - - + -
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Residues in contact with LYS 81 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77J LEU* 2.9 21.4 + - + +
78J PRO* 3.7 9.6 - - + +
80J ILE* 1.3 77.1 - - - +
82J ASP* 1.3 57.0 + - - +
84J VAL* 3.5 3.8 + - - +
85J ALA* 2.9 27.9 + - - +
116J THR 4.0 14.5 + - - -
117J ASP* 3.3 22.2 - - - +
118J LYS 2.7 24.1 + - - +
119J LEU* 3.7 32.6 - - + +
120J GLU 4.9 1.2 - - - +
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Residues in contact with ASP 82 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C LYS* 5.8 1.0 + - - -
39D SER* 3.6 28.7 - - - +
41D GLN* 3.5 26.2 - - - +
78J PRO 3.2 14.5 + - - +
79J LEU 3.6 4.3 - - - +
80J ILE 3.2 0.4 - - - -
81J LYS* 1.3 78.8 - - - +
83J LEU* 1.3 61.4 + - - +
85J ALA* 3.7 8.6 - - - +
86J SER* 2.9 42.7 + - - -
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Residues in contact with LEU 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D GLN* 6.1 0.4 - - - +
47I ASP* 6.1 0.4 - - - +
43J GLN* 6.2 3.6 - - - +
46J LEU* 4.0 15.3 - - + -
79J LEU* 3.0 19.1 + - + +
80J ILE* 3.1 23.1 + - + +
82J ASP* 1.3 74.7 - - - +
84J VAL* 1.3 66.1 + - - +
86J SER* 3.8 7.4 + - - +
87J SER* 3.1 24.8 + - - -
93J THR* 4.1 15.5 + - + -
97J TYR* 3.9 33.4 - - + +
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Residues in contact with VAL 84 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80J ILE* 2.9 30.0 + - + +
81J LYS 3.6 4.9 - - - +
83J LEU* 1.3 75.5 - - - +
85J ALA* 1.3 62.6 + - - +
87J SER* 3.2 18.7 + - - -
90J VAL* 3.9 25.7 - - + +
93J THR* 4.1 19.5 - - + -
94J TYR* 4.1 24.0 - - + +
101J LEU* 5.4 1.1 - - + -
119J LEU* 4.3 21.3 - - + -
120J GLU 6.1 0.7 - - - +
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Residues in contact with ALA 85 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81J LYS 2.9 18.4 + - - +
82J ASP* 3.3 13.0 + - - +
84J VAL* 1.3 78.5 - - - +
86J SER* 1.3 59.9 + - - +
87J SER 3.3 1.9 + - - +
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Residues in contact with SER 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C LYS* 6.3 0.9 - - - -
82J ASP* 2.9 32.4 + - - -
83J LEU* 3.8 9.7 + - - +
85J ALA* 1.3 76.7 - - - +
87J SER* 1.3 66.4 + - - +
88J LYS* 3.5 8.5 + - - +
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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
------------------------------------------------------------
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