Contacts of the helix formed by residues 66 - 87 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11R GLU* 4.0 21.8 - - + +
12R SER* 5.8 3.1 - - - +
22R PHE* 4.2 16.4 - - + -
60R VAL* 3.9 8.1 - - + +
62R THR* 3.7 34.8 - - + +
64R TYR 4.0 1.1 - - - +
65R PRO* 1.3 75.5 - - - +
67R SER* 1.3 59.6 + - - +
68R THR* 3.5 19.6 + - - -
69R ASP* 2.9 28.8 + - - +
70R VAL* 3.2 17.3 + - - +
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Residues in contact with SER 67 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11R GLU* 2.6 44.4 + - - +
66R THR* 1.3 71.6 - - - +
68R THR* 1.3 56.7 + - - +
70R VAL* 3.2 9.9 + - - +
71R HIS* 2.7 62.8 + - - -
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Residues in contact with THR 68 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11R GLU* 5.4 0.5 + - - -
22R PHE* 5.3 1.6 - - - -
30R ALA* 3.7 25.1 + - - +
33R TRP* 3.9 29.6 - - + -
34R GLU 5.7 0.4 - - - +
37R LEU* 6.1 0.9 - - + -
59R ILE* 4.0 12.6 - - + -
60R VAL* 3.7 19.1 - - + +
66R THR* 3.1 12.6 + - - -
67R SER* 1.3 80.0 + - - +
69R ASP* 1.3 65.0 + - - +
71R HIS* 4.5 4.5 - - - -
72R VAL* 3.0 31.3 + - + +
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Residues in contact with ASP 69 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58R PHE* 3.5 16.2 - - - +
59R ILE* 2.9 32.4 + - - +
60R VAL 4.9 0.3 + - - -
62R THR* 4.5 0.9 + - - -
64R TYR 4.5 0.2 - - - +
65R PRO* 3.5 7.6 - - + +
66R THR* 2.9 37.8 + - - +
68R THR* 1.3 77.9 - - - +
70R VAL* 1.3 58.0 + - - +
73R PHE* 2.9 32.2 + - - +
103R TRP* 2.9 31.3 + - - +
107R MET* 4.0 15.3 - - + -
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Residues in contact with VAL 70 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65R PRO* 5.6 2.7 - - + -
66R THR 3.2 15.9 + - - +
67R SER* 3.6 12.1 - - - +
68R THR 3.2 0.6 - - - -
69R ASP* 1.3 77.9 - - - +
71R HIS* 1.3 64.0 + - + +
73R PHE* 3.3 4.4 + - + +
74R GLU* 2.9 34.3 + - + +
107R MET* 3.9 19.3 - - + -
110R LEU* 6.1 0.7 - - + -
111R LEU* 4.2 24.5 - - + -
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Residues in contact with HIS 71 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37R LEU* 3.5 22.9 - - + +
67R SER* 2.7 48.1 + - - +
68R THR* 4.1 4.3 + - - +
70R VAL* 1.3 81.1 - - + +
72R VAL* 1.3 63.2 + - - +
74R GLU* 3.3 29.1 + - - +
75R VAL* 3.4 13.0 + - - +
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Residues in contact with VAL 72 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R TRP* 4.1 31.6 - - + -
37R LEU* 4.1 17.9 - - + -
42R ILE* 4.0 15.4 - - + +
49R LEU* 3.8 26.5 - - + -
59R ILE* 3.5 27.1 - - + -
68R THR* 3.0 18.0 + - + +
71R HIS* 1.3 75.7 - - - +
73R PHE* 1.3 50.5 + - - +
75R VAL* 3.2 4.0 + - - +
76R ALA* 2.8 33.7 + - + +
103R TRP* 4.0 2.5 - - + -
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Residues in contact with PHE 73 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69R ASP 2.9 21.7 + - - +
70R VAL* 3.5 6.3 - - + +
71R HIS 3.3 0.2 - - - -
72R VAL* 1.3 76.3 - - - +
74R GLU* 1.3 61.3 + - + +
76R ALA* 4.3 1.1 - - - -
77R LEU* 2.9 64.0 + - + +
103R TRP* 3.5 15.3 - + + -
104R ILE* 3.8 33.2 - - + -
107R MET* 3.5 31.4 - - + -
108R GLN* 3.6 21.5 - - + -
111R LEU* 4.2 17.7 - - + -
113R VAL* 4.0 17.0 - - + -
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Residues in contact with GLU 74 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70R VAL* 2.9 16.5 + - + +
71R HIS* 3.4 27.3 - - - +
73R PHE* 1.3 82.4 - - + +
75R VAL* 1.3 61.2 + - + +
77R LEU* 5.4 0.7 - - - -
78R PRO* 3.2 22.3 - - - +
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Residues in contact with VAL 75 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37R LEU* 3.5 26.9 - - + +
42R ILE* 3.6 29.6 - - + -
71R HIS 3.4 4.2 + - - +
72R VAL 3.2 7.0 + - - +
73R PHE 3.2 0.2 - - - -
74R GLU* 1.3 82.4 - - + +
76R ALA* 1.3 61.4 + - - +
77R LEU 3.4 0.2 - - - -
78R PRO* 3.4 15.2 - - - +
79R LEU* 3.5 14.0 + - + +
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Residues in contact with ALA 76 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42R ILE* 4.7 7.0 - - + -
46R LEU* 4.7 9.0 - - + -
49R LEU* 4.5 13.7 - - + -
72R VAL* 2.8 21.7 + - + +
73R PHE 4.1 1.6 - - - +
75R VAL* 1.3 70.0 - - - +
77R LEU* 1.3 61.7 + - - +
79R LEU* 3.4 5.9 + - - +
80R ILE* 2.8 38.1 + - + +
100R ILE* 5.0 1.3 - - + -
103R TRP* 4.2 21.1 - - + -
104R ILE* 4.5 6.1 - - + -
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Residues in contact with LEU 77 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73R PHE* 2.9 46.5 + - + +
74R GLU* 5.0 0.9 - - - +
76R ALA* 1.3 77.4 - - - +
78R PRO* 1.3 72.9 - - + +
80R ILE* 3.3 1.2 + - - +
81R LYS* 3.0 27.9 + - + +
104R ILE* 3.9 16.5 - - + +
108R GLN* 3.7 19.3 - - - +
113R VAL* 4.3 15.0 - - + -
117R ASP* 3.7 20.4 - - + +
119R LEU* 3.8 24.7 - - + +
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Residues in contact with PRO 78 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74R GLU 3.2 24.0 - - - +
75R VAL* 3.4 10.8 - - - +
77R LEU* 1.3 97.1 - - + +
79R LEU* 1.3 53.0 + - - +
81R LYS* 3.4 11.0 + - + +
82R ASP* 3.0 38.3 + - - +
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Residues in contact with LEU 79 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42R ILE* 4.0 16.4 - - + -
43R GLN* 3.2 39.9 - - + +
46R LEU* 3.3 42.6 - - + -
75R VAL* 3.5 14.7 + - + +
76R ALA 3.4 6.9 + - - +
77R LEU 3.2 0.4 - - - -
78R PRO* 1.3 76.0 - - - +
80R ILE* 1.3 59.4 + - - +
82R ASP* 3.1 9.7 + - + +
83R LEU* 2.8 35.0 + - + +
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Residues in contact with ILE 80 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46R LEU* 4.1 31.6 - - + -
76R ALA* 2.8 25.2 + - + +
77R LEU 4.0 2.2 - - - +
79R LEU* 1.3 67.7 - - - +
81R LYS* 1.3 60.2 + - - +
83R LEU* 3.2 7.9 + - + +
84R VAL* 2.8 34.9 + - + +
93R THR* 5.7 1.6 - - + -
97R TYR* 4.2 29.8 - - + -
100R ILE* 4.4 11.0 - - + -
101R LEU* 4.0 12.3 - - + -
104R ILE* 4.0 15.0 - - + -
119R LEU* 3.8 26.0 - - + -
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Residues in contact with LYS 81 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77R LEU* 3.0 21.3 + - + +
78R PRO* 3.6 11.4 - - + +
80R ILE* 1.3 75.2 - - - +
82R ASP* 1.3 61.1 + - - +
84R VAL* 3.4 3.6 + - - +
85R ALA* 2.9 28.9 + - - +
116R THR 3.2 20.2 + - - -
117R ASP* 3.3 21.0 + - - +
118R LYS 2.5 26.3 + - - +
119R LEU* 3.9 27.8 - - + +
120R GLU 5.5 0.4 - - - +
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Residues in contact with ASP 82 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78R PRO* 3.0 24.1 + - - +
79R LEU* 3.5 8.7 - - + +
81R LYS* 1.3 78.2 - - - +
83R LEU* 1.3 62.8 + - + +
85R ALA* 3.2 8.2 + - - +
86R SER* 3.0 27.1 + - - -
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Residues in contact with LEU 83 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43R GLN* 4.5 18.6 - - + +
46R LEU* 3.7 29.2 - - + -
79R LEU* 2.8 22.6 + - + +
80R ILE* 3.6 13.0 - - + +
82R ASP* 1.3 74.9 - - + +
84R VAL* 1.3 57.0 + - - +
86R SER* 3.3 8.3 + - - +
87R SER* 2.9 31.6 + - - -
93R THR* 4.5 11.8 - - + +
97R TYR* 4.2 23.1 - - + +
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Residues in contact with VAL 84 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80R ILE* 2.8 23.9 + - + +
81R LYS* 3.6 9.9 - - - +
83R LEU* 1.3 72.5 - - - +
85R ALA* 1.3 64.1 + - - +
86R SER 3.3 0.7 + - - -
87R SER* 3.3 19.1 + - - -
90R VAL* 3.9 26.5 - - + +
93R THR* 4.2 16.4 - - + -
94R TYR* 4.0 27.6 - - + +
101R LEU* 6.0 0.2 - - + -
119R LEU* 4.2 16.6 - - + -
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Residues in contact with ALA 85 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81R LYS 2.9 20.6 + - - +
82R ASP* 3.2 10.7 + - - +
84R VAL* 1.3 75.9 - - - +
86R SER* 1.3 58.9 + - - +
87R SER 3.4 2.0 + - - +
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Residues in contact with SER 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82R ASP 3.0 16.9 + - - -
83R LEU* 3.6 11.3 + - - +
85R ALA* 1.3 75.9 - - - +
87R SER* 1.3 67.3 + - - +
88R LYS* 3.5 10.4 + - - +
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Residues in contact with SER 87 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83R LEU 2.9 13.3 + - - -
84R VAL* 3.3 14.7 + - - +
85R ALA 3.4 1.8 - - - +
86R SER* 1.3 79.6 - - - +
88R LYS* 1.3 61.0 + - - +
89R ASP 2.9 21.4 + - - -
90R VAL* 4.0 15.3 - - - +
93R THR* 2.7 29.1 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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