Contacts of the helix formed by residues 45 - 56 (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 HIS 45 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88Q LYS* 3.5 37.7 + - + +
32R GLN* 4.3 1.7 + - - -
33R TRP* 4.0 10.3 - - + -
36R VAL* 3.5 30.6 - - + +
41R GLN* 2.8 48.2 + - - +
42R ILE* 2.8 14.4 + - - +
44R PRO* 1.3 72.4 - - - +
46R LEU* 1.3 60.4 + - - +
47R ASP 3.3 2.2 - - - -
48R GLN* 3.0 30.6 + - - +
49R LEU* 2.8 29.5 + - - +
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Residues in contact with LEU 46 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42R ILE* 3.1 19.5 + - + +
43R GLN* 3.1 21.2 + - + +
45R HIS* 1.3 78.9 - - - +
47R ASP* 1.3 64.2 + - - +
49R LEU* 3.2 10.9 + - + -
50R ASN* 3.0 22.9 + - - +
76R ALA* 4.7 7.4 - - + -
79R LEU* 3.3 34.1 - - + -
80R ILE* 4.1 13.7 - - + -
83R LEU* 3.7 24.9 - - + -
97R TYR* 4.1 19.0 - - + +
100R ILE* 3.6 21.9 - - + +
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Residues in contact with ASP 47 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92Q SER* 3.7 15.4 - - - +
93Q THR* 4.9 8.1 + - - +
96Q THR* 3.4 40.8 + - - +
97Q TYR* 4.9 9.7 + - - -
43R GLN 4.9 0.6 + - - -
44R PRO 4.7 5.8 + - - +
45R HIS* 3.3 1.0 - - - +
46R LEU* 1.3 78.4 - - - +
48R GLN* 1.3 62.5 + - - +
50R ASN* 3.3 8.4 + - - +
51R LEU* 3.1 22.2 + - - +
96R THR* 4.7 1.0 - - - +
97R TYR* 3.8 21.7 + - - -
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Residues in contact with GLN 48 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88Q LYS* 4.7 5.2 + - + -
89Q ASP* 3.9 29.5 + - + +
92Q SER* 3.3 19.5 - - - +
32R GLN* 3.0 31.4 + - - +
33R TRP* 4.1 8.3 - - + -
44R PRO 5.3 0.4 + - - -
45R HIS* 3.0 41.2 + - + +
47R ASP* 1.3 76.2 - - - +
49R LEU* 1.3 64.8 + - - +
51R LEU* 3.0 3.5 + - + +
52R VAL* 2.9 32.9 + - + +
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Residues in contact with LEU 49 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R TRP* 3.7 27.3 - - + -
42R ILE* 5.6 1.6 - - + -
45R HIS 2.8 19.2 + - - +
46R LEU* 3.6 17.0 - - + +
48R GLN* 1.3 72.4 - - - +
50R ASN* 1.3 57.7 + - - +
52R VAL* 3.3 3.8 + - + +
53R LEU* 3.0 45.3 + - + +
59R ILE* 3.7 30.5 - - + -
72R VAL* 3.8 22.0 - - + -
76R ALA* 4.5 4.0 - - + -
100R ILE* 3.9 19.1 - - + -
103R TRP* 4.5 12.1 - - + -
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Residues in contact with ASN 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96Q THR* 5.6 1.6 + - - +
46R LEU 3.0 13.8 + - - +
47R ASP* 3.5 12.3 - - - +
49R LEU* 1.3 76.6 - - - +
51R LEU* 1.3 56.1 + - - +
54R ARG 3.0 22.5 + - - -
96R THR 3.2 23.3 - - - +
97R TYR* 3.3 12.4 - - + +
98R ARG 4.3 0.5 + - - -
99R HIS* 3.0 52.6 - - - +
100R ILE* 3.1 22.7 - - + +
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Residues in contact with LEU 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89Q ASP* 4.2 3.8 - - - +
91Q LYS* 3.9 25.8 - - + +
92Q SER* 3.3 37.0 - - - +
95Q THR* 4.5 10.3 - - + +
47R ASP 3.1 11.8 + - - +
48R GLN* 3.0 8.6 + - + +
50R ASN* 1.3 75.8 + - - +
52R VAL* 1.3 67.9 + - + +
54R ARG* 3.4 54.0 + - - +
55R ASP* 3.8 9.2 + - - +
99R HIS* 5.3 0.2 - - - -
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Residues in contact with VAL 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29R GLN* 5.0 6.5 - - - +
32R GLN* 6.0 1.1 - - - +
33R TRP* 4.3 17.9 - - + +
48R GLN* 2.9 25.4 + - + +
49R LEU* 3.5 10.3 - - + +
51R LEU* 1.3 77.6 - - + +
53R LEU* 1.3 60.3 + - + +
55R ASP 3.2 2.3 + - - -
56R ASN* 2.9 46.8 + - + +
59R ILE* 3.5 40.2 - - + +
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Residues in contact with LEU 53 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49R LEU* 3.0 38.8 + - + +
52R VAL* 1.3 74.3 - - + +
54R ARG* 1.3 67.0 + - - +
55R ASP 3.2 0.9 - - - -
56R ASN 3.2 18.0 + - - +
57R THR 3.8 6.1 - - - +
58R PHE 4.1 0.7 - - - -
59R ILE* 4.1 20.6 - - + +
99R HIS* 3.6 17.6 + - + +
100R ILE* 4.0 10.5 - - - -
102R ARG* 3.0 27.8 + - - +
103R TRP* 3.6 55.9 - - + -
102T ARG* 4.1 1.2 - - - -
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Residues in contact with ARG 54 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91Q LYS* 3.9 12.1 - - - +
95Q THR* 4.1 8.2 - - - +
98Q ARG* 3.9 7.1 - - - +
2009Q SO4 3.2 23.0 + - - -
50R ASN 3.0 8.0 + - - +
51R LEU* 3.4 34.9 - - - +
52R VAL 3.3 0.2 - - - -
53R LEU* 1.3 78.7 - - - +
55R ASP* 1.3 89.7 + - - +
99R HIS* 3.5 41.5 - - + +
98T ARG* 3.5 45.0 - - - +
99T HIS* 4.5 11.8 + - + +
102T ARG* 3.9 15.8 - - - +
123T HIS 4.3 6.5 + - - -
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Residues in contact with ASP 55 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51R LEU* 4.1 8.4 - - - +
52R VAL 3.2 3.2 + - - +
53R LEU 3.2 0.2 - - - -
54R ARG* 1.3 123.0 + - - +
56R ASN* 1.3 75.2 + - - +
98T ARG* 4.4 9.6 - - - +
102T ARG* 3.8 21.2 - - - +
105T ASP* 4.5 9.7 - - - +
121T ILE* 5.8 3.7 - - + +
123T HIS 3.5 26.6 - - - +
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Residues in contact with ASN 56 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29R GLN* 5.8 1.2 - - - +
52R VAL* 2.9 34.5 + - + +
53R LEU* 3.2 10.9 - - - +
54R ARG 3.6 0.6 - - - -
55R ASP* 1.3 94.3 - - - +
57R THR* 1.3 66.2 + - - +
58R PHE 3.4 17.0 + - - +
61R SER* 3.0 28.8 + - - +
102R ARG* 3.1 13.5 + - - -
102T ARG* 3.9 4.9 - - - -
105T ASP* 4.8 6.4 - - - +
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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