Contacts of the helix formed by residues 54 - 66 (chain B) in PDB entry 2HQR
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 ASN 54 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 2.9 30.7 - - + +
52B ASP* 3.2 4.9 - - + +
53B LYS* 1.3 76.3 - - - +
55B ALA* 1.3 63.5 + - - +
56B LEU* 3.1 2.9 - - - -
57B SER* 3.0 36.3 + - - +
58B PHE 3.3 4.2 + - - -
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Residues in contact with ALA 55 (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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33B LEU* 5.1 0.2 - - - -
50B VAL* 4.1 20.4 - - + -
52B ASP* 3.0 19.2 + - - +
53B LYS 2.7 5.7 + - - +
54B ASN* 1.3 78.4 - - - +
56B LEU* 1.3 66.2 + - + +
58B PHE* 2.8 10.4 + - - -
59B VAL* 2.7 30.6 + - + +
73B VAL* 3.4 30.1 - - + -
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Residues in contact with LEU 56 (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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53B LYS 3.8 15.0 - - - +
54B ASN* 3.1 1.1 - - - +
55B ALA* 1.3 81.6 - - + +
57B SER* 1.3 63.0 + - - +
59B VAL* 3.2 10.7 - - - +
60B SER* 3.2 22.3 + - - -
73B VAL* 5.3 6.1 - - + -
82B GLU* 6.0 8.5 - - + +
85B HIS* 3.8 33.7 - - + +
86B ALA* 5.5 5.8 - - + -
89B GLN* 3.8 29.4 - - + +
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Residues in contact with SER 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ASN* 3.0 35.5 + - - -
55B ALA 3.0 0.6 - - - -
56B LEU* 1.3 77.2 - - - +
58B PHE* 1.3 64.1 + - - +
60B SER* 3.3 7.4 - - - -
61B ARG* 2.5 40.4 + - - -
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Residues in contact with PHE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 4.6 5.4 - - + -
6B ILE* 3.9 19.7 - - + -
33B LEU* 3.5 43.7 - - + +
36B GLY 4.6 4.9 - - - -
37B GLU* 4.3 33.4 - - + -
40B MET* 5.0 2.5 - - + -
48B VAL* 3.8 19.1 - - + -
50B VAL* 4.4 11.2 - - + -
54B ASN* 3.3 3.1 + - - +
55B ALA* 2.8 9.6 + - - +
57B SER* 1.3 76.8 - - - +
59B VAL* 1.3 68.7 + - - +
61B ARG* 2.8 38.8 - - - +
62B ILE* 2.9 40.6 + - + +
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Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B VAL* 4.5 10.1 - - + -
55B ALA* 2.7 37.5 + - + +
56B LEU* 3.2 15.3 - - + +
58B PHE* 1.3 74.1 - - + +
60B SER* 1.3 62.3 + - - +
62B ILE* 4.2 9.2 - - - -
63B LYS* 2.7 35.4 + - - +
71B VAL* 3.4 25.8 - - + -
73B VAL* 4.7 8.3 - - + -
86B ALA* 6.5 0.2 - - - -
89B GLN* 4.5 8.3 - - + -
90B GLY 3.5 24.2 - - - +
91B ALA* 5.4 4.3 - - + -
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Residues in contact with SER 60 (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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56B LEU 3.2 16.3 + - - -
57B SER* 3.3 9.9 - - - -
58B PHE 3.0 0.6 - - - -
59B VAL* 1.3 86.7 - - - +
61B ARG* 1.3 62.1 + - - +
63B LYS* 3.4 3.6 + - - +
64B GLU* 3.3 31.6 + - - +
89B GLN* 4.4 23.4 + - - -
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Residues in contact with ARG 61 (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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33B LEU* 5.8 1.4 - - - +
37B GLU* 4.8 18.3 + - - -
54B ASN* 5.4 0.6 + - - -
57B SER* 2.5 46.7 + - - -
58B PHE* 2.8 45.6 - - + +
60B SER* 1.3 79.0 - - - +
62B ILE* 1.3 62.4 + - + +
64B GLU* 3.9 5.4 - - - -
65B LYS* 2.8 69.4 + - + +
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Residues in contact with ILE 62 (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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40B MET* 3.5 32.3 - - + -
48B VAL* 4.2 18.2 - - + -
58B PHE* 2.9 58.5 + - + +
59B VAL* 3.7 7.0 - - - +
61B ARG* 1.3 82.5 - - + +
63B LYS* 1.3 58.7 + - - +
65B LYS* 4.6 4.5 - - + -
66B HIS* 2.8 37.8 + - + +
69B ILE* 3.6 26.2 - - + -
71B VAL* 4.3 7.2 - - + -
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Residues in contact with LYS 63 (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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59B VAL 2.7 21.6 + - - +
60B SER* 3.8 4.9 - - - +
62B ILE* 1.3 74.5 - - - +
64B GLU* 1.3 58.0 + - - +
67B SER* 2.7 55.9 + - - +
69B ILE* 3.5 19.4 + - - +
71B VAL* 3.3 26.4 - - + +
89B GLN 5.1 1.8 - - - +
90B GLY* 3.0 46.9 - - - +
91B ALA* 4.2 2.2 - - - +
92B ASP* 5.6 2.7 - - - +
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Residues in contact with GLU 64 (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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60B SER* 3.3 23.3 + - - +
61B ARG* 3.4 9.0 - - - +
63B LYS* 1.3 79.3 - - - +
65B LYS* 1.3 102.5 + - + +
66B HIS 3.1 1.9 + - - -
67B SER* 4.1 3.8 + - - -
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Residues in contact with LYS 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLU* 6.0 1.8 - - - -
61B ARG* 2.8 51.1 + - + +
62B ILE* 4.6 4.3 - - + +
64B GLU* 1.3 100.6 + - + +
66B HIS* 1.3 92.5 + - + +
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Residues in contact with HIS 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B MET* 4.4 24.1 - - + +
44B ASN* 5.6 5.5 + - - -
62B ILE* 2.8 17.2 + - + +
65B LYS* 1.3 106.0 + - + +
67B SER* 1.3 60.9 + - - +
68B SER* 3.0 5.3 + - - +
69B ILE* 2.8 42.1 - - + +
145B LYS* 4.0 36.3 + - + +
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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