Contacts of the helix formed by residues 53 - 68 (chain B) in PDB entry 2HV1
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 ASP 53 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B CYS* 3.5 9.8 - - - -
50B HIS* 2.7 44.6 + - + +
52B GLU* 1.3 82.5 - - - +
54B GLN* 1.3 64.8 + - - +
55B GLN 3.5 1.6 - - - -
56B LEU* 3.2 25.6 - - + +
57B LEU* 3.1 18.5 + - - +
75B MET 4.7 0.5 - - - +
76B PHE* 3.6 26.3 - - + +
77B ARG* 3.9 11.0 + - - +
87B TRP* 4.9 8.1 - - - -
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Residues in contact with GLN 54 (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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46B VAL* 2.9 48.2 + - + +
47B GLU* 4.8 4.0 + - - +
49B CYS* 3.9 12.6 + - - +
50B HIS 2.9 17.4 + - - +
51B PRO* 3.1 23.5 + - - +
53B ASP* 1.3 78.3 - - - +
55B GLN* 1.3 59.4 + - - +
57B LEU* 3.2 5.0 + - - +
58B ARG* 2.8 28.6 + - - +
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Residues in contact with GLN 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B PRO 4.6 1.2 + - - -
52B GLU 5.3 0.8 - - - +
53B ASP 3.5 0.4 - - - -
54B GLN* 1.3 75.1 - - - +
56B LEU* 1.3 60.8 + - - +
58B ARG* 2.9 44.7 + - - +
59B ASP* 2.8 50.2 + - + +
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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
----------------------------------------------------------
52B GLU 5.0 2.6 + - - +
53B ASP* 3.2 31.7 - - - +
55B GLN* 1.3 79.8 - - - +
57B LEU* 1.3 55.1 + - - +
59B ASP* 4.0 4.0 - - - +
60B SER* 2.7 33.7 + - - +
74B VAL* 3.9 18.2 - - + -
75B MET 3.5 24.7 - - - +
76B PHE* 4.1 6.1 - - + -
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Residues in contact with LEU 57 (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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45B ILE* 3.9 30.1 - - + -
46B VAL* 5.0 4.0 - - + +
49B CYS* 4.1 12.8 - - + -
53B ASP 3.1 7.8 + - - +
54B GLN 3.6 6.5 - - - +
56B LEU* 1.3 76.9 - - - +
58B ARG* 1.3 61.2 - - - +
60B SER* 3.1 7.9 + - - -
61B PHE* 2.9 54.2 + - + -
74B VAL* 3.8 23.3 - - + -
76B PHE* 3.5 42.6 - - + -
90B THR* 5.0 5.8 - - + -
92B SER* 5.1 1.8 - - - +
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Residues in contact with ARG 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 5.8 3.4 - - + -
54B GLN 2.8 17.1 + - - +
55B GLN* 2.9 36.1 + - - +
57B LEU* 1.3 77.1 - - - +
59B ASP* 1.3 62.9 + - - +
61B PHE* 3.1 26.6 + - - +
62B GLN* 3.3 21.6 + - + +
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Residues in contact with ASP 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLN* 2.8 34.6 + - + +
56B LEU* 4.0 4.6 - - - +
58B ARG* 1.3 73.2 - - - +
60B SER* 1.3 57.8 + - - +
62B GLN* 3.1 13.1 + - - +
63B GLN* 2.7 60.1 + - - +
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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
----------------------------------------------------------
56B LEU* 2.7 20.8 + - - +
57B LEU* 3.1 14.7 + - - -
59B ASP* 1.3 77.6 + - - +
61B PHE* 1.3 56.7 + - - +
63B GLN* 3.2 10.0 + - - +
64B VAL* 2.9 28.4 + - - +
72B LEU* 3.4 25.1 - - - +
74B VAL* 3.5 29.6 - - - +
92B SER* 5.5 3.5 - - - -
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Residues in contact with PHE 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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16B HIS* 3.5 27.6 - + - -
17B ASN 5.0 0.4 - - - -
18B ILE* 4.1 16.4 - - + +
19B GLU 5.5 1.3 - - - -
20B GLY* 4.6 6.5 - - - -
45B ILE* 3.5 34.3 - - + -
46B VAL* 5.9 3.1 - - + -
57B LEU* 2.9 46.8 + - + -
58B ARG* 3.1 13.2 + - - +
60B SER* 1.3 77.9 - - - +
62B GLN* 1.3 68.0 + - - +
64B VAL* 3.0 22.8 - - + +
65B VAL* 3.1 12.8 - - - +
92B SER* 4.6 3.1 - - - -
106B ILE* 3.8 23.8 - - + -
108B CYS* 3.8 12.8 - - - -
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Residues in contact with GLN 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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18B ILE 5.4 2.1 - - - +
58B ARG* 3.4 25.6 + - + +
59B ASP* 3.1 13.6 + - - +
61B PHE* 1.3 78.9 - - - +
63B GLN* 1.3 67.2 + - - +
65B VAL* 3.2 14.9 + - - +
66B LYS* 3.0 33.2 + - + +
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Residues in contact with GLN 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 ASP* 2.7 49.4 + - - +
60B SER* 3.2 13.5 + - - +
62B GLN* 1.3 76.5 - - - +
64B VAL* 1.3 56.7 + - - +
66B LYS* 3.1 14.8 + - + +
67B LEU* 3.0 32.1 + - + +
72B LEU* 3.6 30.1 - - + +
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Residues in contact with VAL 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 2.9 13.0 + - - +
61B PHE* 3.0 24.7 - - - +
63B GLN* 1.3 76.6 - - - +
65B VAL* 1.3 56.1 + - - +
67B LEU* 3.4 8.4 - - + +
68B LYS 2.9 15.4 + - - -
70B GLN 3.6 8.7 - - - +
72B LEU* 4.4 7.6 - - + +
92B SER* 3.2 37.2 - - - +
94B THR* 2.8 50.4 + - + +
106B ILE* 4.1 18.8 - - + -
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Residues in contact with VAL 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 4.2 26.0 - - + -
61B PHE 3.1 17.9 - - - +
62B GLN* 3.2 19.2 + - - +
63B GLN 3.2 0.8 - - - -
64B VAL* 1.3 80.1 - - + +
66B LYS* 1.3 65.0 + - + +
68B LYS* 3.6 22.3 - - - +
94B THR* 4.0 6.7 - - + -
103B ILE* 3.8 19.0 - - + +
106B ILE* 4.6 3.4 - - + -
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Residues in contact with LYS 66 (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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62B GLN* 3.0 26.7 + - + +
63B GLN* 3.1 13.2 + - + +
65B VAL* 1.3 78.3 - - + +
67B LEU* 1.3 65.1 + - + +
68B LYS* 4.7 1.2 - - - +
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Residues in contact with LEU 67 (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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63B GLN* 3.0 18.3 + - + +
64B VAL* 3.4 15.7 - - - +
65B VAL 3.2 0.4 - - - -
66B LYS* 1.3 79.1 - - + +
68B LYS* 1.3 76.4 + - - +
70B GLN* 3.6 37.5 + - + +
71B VAL 4.6 4.0 - - - +
72B LEU* 4.1 30.5 - - + -
94B THR* 4.6 0.2 - - - +
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Residues in contact with LYS 68 (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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64B VAL 2.9 11.1 + - - -
65B VAL* 3.6 16.4 - - - +
66B LYS 4.7 1.1 - - - +
67B LEU* 1.3 88.5 - - - +
69B GLY* 1.3 63.7 + - - +
70B GLN* 4.2 5.5 + - - -
94B THR* 3.3 8.4 + - - -
96B GLN* 3.2 27.7 + - + +
101B ASP* 2.7 46.2 + - - +
103B ILE* 3.8 28.7 - - + -
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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