Contacts of the helix formed by residues 45 - 56 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32G GLN* 6.0 1.6 - - + -
33G TRP* 3.9 18.1 - - + -
36G VAL* 3.7 30.9 - - + +
41G GLN* 3.0 30.1 - - + +
42G ILE* 2.8 11.7 + - - +
44G PRO* 1.3 76.8 - - - +
46G LEU* 1.3 58.7 + - - +
47G ASP 3.4 2.2 - - - -
48G GLN* 2.9 30.1 + - - +
49G LEU* 2.9 27.8 + - - +
88H LYS* 3.6 41.3 + - + +
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Residues in contact with LEU 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G ILE* 3.7 14.6 - - + +
43G GLN* 3.3 37.4 + - + +
44G PRO 3.4 0.6 - - - -
45G HIS* 1.3 75.2 - - - +
47G ASP* 1.3 61.4 + - - +
49G LEU* 3.2 17.2 + - + +
50G ASN* 2.9 26.3 + - - +
76G ALA* 4.4 15.5 - - + -
79G LEU* 4.4 11.4 - - + -
80G ILE* 4.2 10.8 - - + -
83G LEU* 4.2 24.5 - - + -
97G TYR* 4.4 14.1 - - + +
100G ILE* 3.5 24.3 - - + +
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Residues in contact with ASP 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G PRO 4.9 4.3 + - - +
45G HIS 3.4 0.6 - - - -
46G LEU* 1.3 76.1 - - - +
48G GLN* 1.3 62.1 + - - +
50G ASN* 3.4 8.5 + - - +
51G LEU* 3.0 22.0 + - - +
96G THR* 4.9 0.7 - - - +
97G TYR* 3.8 22.4 + - - -
92H SER* 3.7 15.2 - - - +
93H THR* 4.7 9.3 + - - +
96H THR* 3.5 39.6 + - - +
97H TYR* 4.6 9.9 + - - -
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Residues in contact with GLN 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G GLN* 3.7 33.5 + - - +
33G TRP* 4.3 2.6 - - + -
44G PRO 5.5 0.2 + - - -
45G HIS* 2.9 41.0 + - - +
46G LEU 3.3 0.4 - - - -
47G ASP* 1.3 75.8 - - - +
49G LEU* 1.3 61.0 + - - +
51G LEU* 3.1 3.3 + - + +
52G VAL* 2.8 43.1 + - + +
88H LYS* 4.9 2.8 + - + -
89H ASP* 3.7 32.3 + - + +
92H SER* 3.2 20.5 + - - +
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Residues in contact with LEU 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G TRP* 3.8 24.1 - - + -
42G ILE* 5.7 2.0 - - + -
45G HIS 2.9 14.0 + - - +
46G LEU* 3.4 20.6 - - + +
48G GLN* 1.3 74.5 - - - +
50G ASN* 1.3 58.3 + - - +
52G VAL* 3.2 4.4 + - + +
53G LEU* 2.9 49.1 + - + +
59G ILE* 3.7 28.7 - - + -
72G VAL* 3.9 20.2 - - + -
76G ALA* 4.3 4.7 - - + -
100G ILE* 3.9 18.4 - - + -
103G TRP* 4.3 13.0 - - + -
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Residues in contact with ASN 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G LEU 2.9 16.1 + - - +
47G ASP* 3.6 8.5 - - - +
48G GLN 3.2 0.2 - - - -
49G LEU* 1.3 78.6 - - - +
51G LEU* 1.3 56.3 + - - +
53G LEU 3.4 0.3 + - - -
54G ARG 2.9 22.5 + - - -
95G THR 5.4 0.2 - - - +
96G THR 3.2 22.4 - - - +
97G TYR* 3.3 13.7 - - + +
98G ARG 4.3 0.7 + - - -
99G HIS* 3.0 51.3 - - - +
100G ILE* 3.1 23.7 - - + +
96H THR* 5.6 2.0 + - - +
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Residues in contact with LEU 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G ASP 3.0 14.0 + - - +
48G GLN* 3.1 7.8 + - + +
50G ASN* 1.3 73.8 + - - +
52G VAL* 1.3 69.3 + - + +
54G ARG* 3.2 59.0 + - - +
55G ASP* 3.7 7.9 + - - +
99G HIS* 5.3 0.7 - - - -
89H ASP* 4.3 3.6 - - - +
91H LYS* 4.0 25.8 - - + +
92H SER* 3.3 37.0 - - - +
95H THR* 4.6 10.5 - - + +
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Residues in contact with VAL 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G GLN* 5.2 2.5 - - - +
33G TRP* 4.1 21.3 - - + +
48G GLN* 2.8 23.7 + - + +
49G LEU* 3.5 10.1 - - + +
51G LEU* 1.3 76.9 - - + +
53G LEU* 1.3 67.5 + - + +
55G ASP 3.2 2.3 + - - -
56G ASN* 2.9 43.6 + - + +
59G ILE* 3.6 38.8 - - + +
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Residues in contact with LEU 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E ARG* 4.1 2.3 + - - -
49G LEU* 2.9 44.4 + - + +
51G LEU 3.2 0.2 - - - -
52G VAL* 1.3 75.7 - - + +
54G ARG* 1.3 66.1 + - - +
55G ASP 3.2 0.2 - - - -
56G ASN 3.2 18.6 + - - +
57G THR 3.9 2.7 - - - +
58G PHE 4.2 0.4 - - - -
59G ILE* 4.2 17.9 - - + +
99G HIS* 3.6 23.2 + - + +
100G ILE* 4.1 9.0 - - - -
102G ARG* 3.1 25.9 + - - +
103G TRP* 3.6 53.6 - - + +
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Residues in contact with ARG 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E ARG* 3.5 48.3 - - + +
99E HIS* 4.6 10.3 + - + -
102E ARG* 3.8 17.2 + - - +
2004E SO4 3.3 29.9 + - - -
50G ASN 2.9 7.9 + - - +
51G LEU* 3.3 35.3 - - - +
52G VAL 3.1 0.4 - - - -
53G LEU* 1.3 80.1 - - - +
55G ASP* 1.3 92.1 + - - +
99G HIS* 3.5 40.4 - - + +
91H LYS* 4.4 8.3 - - - +
95H THR* 4.2 8.2 - - - +
98H ARG* 3.8 8.5 - - - +
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Residues in contact with ASP 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E ARG* 4.5 12.4 + - - +
102E ARG* 3.7 23.4 - - - +
105E ASP* 4.4 9.0 - - - +
121E ILE* 6.0 1.4 - - - +
51G LEU* 3.7 7.0 + - - +
52G VAL 3.2 2.9 + - - +
54G ARG* 1.3 124.6 + - - +
56G ASN* 1.3 75.6 + - - +
91H LYS* 5.7 0.2 + - - -
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Residues in contact with ASN 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E ARG* 3.8 4.7 - - - +
105E ASP* 4.7 6.9 - - - +
52G VAL* 2.9 36.6 + - + +
53G LEU* 3.2 11.1 - - - +
54G ARG 3.5 0.8 - - - -
55G ASP* 1.3 94.4 - - - +
57G THR* 1.3 64.7 + - - +
58G PHE 3.5 16.3 + - - +
59G ILE 5.3 0.4 - - - -
61G SER* 2.6 30.3 + - - +
102G ARG* 3.0 14.4 + - - -
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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