Contacts of the helix formed by residues 56 - 67 (chain B) in PDB entry 2VZ6
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 LYS 56 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B ARG* 3.0 60.7 + - + +
53B ASP* 4.0 10.5 - - - +
54B HIS 3.3 0.4 - - - -
55B GLN* 1.3 80.5 - - + +
57B LEU* 1.3 58.8 + - - +
58B GLU 3.2 1.1 - - - -
59B ARG* 3.2 50.7 + - + +
60B GLU* 3.1 24.3 + - - +
158B GLY 5.7 0.7 - - - +
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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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44B ILE* 3.9 24.5 - - + -
46B THR* 3.9 17.5 - - + -
49B LEU* 4.1 9.2 - - + -
53B ASP 3.5 9.3 + - - +
54B HIS* 3.1 25.3 + - + +
56B LYS* 1.3 75.4 - - - +
58B GLU* 1.3 59.7 - - - +
60B GLU* 3.4 26.6 - - - +
61B ALA* 2.9 31.9 + - - +
85B HIS* 3.7 43.4 + - + +
87B LEU* 4.9 4.7 - - + +
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Residues in contact with GLU 58 (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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54B HIS 4.4 0.4 + - - +
55B GLN* 3.3 37.7 + - - +
57B LEU* 1.3 78.7 - - - +
59B ARG* 1.3 59.7 + - - +
61B ALA* 3.7 6.2 + - - +
62B ARG* 3.2 37.0 + - - +
65B ARG* 4.9 1.4 + - - -
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Residues in contact with ARG 59 (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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52B ARG* 4.7 10.5 - - - +
55B GLN 4.4 0.2 + - - -
56B LYS* 3.2 60.1 + - + +
58B GLU* 1.3 76.3 - - - +
60B GLU* 1.3 60.0 + - - +
62B ARG* 3.2 19.1 + - - +
63B ILE* 2.9 40.9 + - + +
134B ARG* 4.3 9.5 - - - +
159B LEU 5.8 0.4 - - - -
160B ALA 3.5 19.9 + - - +
161B ILE* 3.8 30.7 - - - +
162B GLU* 3.7 24.0 + - - +
171B PHE* 5.1 9.3 + - - +
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Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LYS* 2.9 28.7 + - - +
56B LYS 3.1 12.1 + - - +
57B LEU* 3.4 29.5 - - - +
59B ARG* 1.3 77.9 - - - +
61B ALA* 1.3 62.0 + - - +
62B ARG 3.3 0.2 + - - -
63B ILE* 3.4 6.2 + - - +
64B CYS* 3.1 35.3 + - - -
87B LEU* 3.3 24.8 - - + +
89B PHE* 4.9 3.3 - - - -
157B PHE 3.8 22.2 + - - +
158B GLY* 3.5 24.8 + - - +
160B ALA 5.5 1.1 + - - -
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Residues in contact with ALA 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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57B LEU 2.9 21.0 + - - +
58B GLU* 3.9 6.3 - - - +
60B GLU* 1.3 72.7 - - - +
62B ARG* 1.3 61.6 + - - +
64B CYS* 3.5 1.1 + - - -
65B ARG* 3.2 40.5 + - - +
75B LEU* 3.5 14.1 - - + +
78B SER* 4.1 12.1 - - - +
85B HIS* 5.2 0.4 - - + +
87B LEU* 4.0 25.3 - - + +
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Residues in contact with ARG 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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58B GLU* 3.2 38.4 + - - +
59B ARG* 3.5 20.2 - - - +
60B GLU 3.2 0.2 - - - -
61B ALA* 1.3 76.9 - - - +
63B ILE* 1.3 66.4 + - - +
64B CYS 3.3 0.2 + - - -
65B ARG* 3.3 19.2 + - - +
66B LEU* 3.2 24.0 + - + +
162B GLU* 2.8 40.5 + - - +
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Residues in contact with ILE 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 ARG* 2.9 31.1 + - + +
60B GLU* 3.7 6.5 - - - +
62B ARG* 1.3 75.4 - - - +
64B CYS* 1.3 63.3 + - - +
66B LEU* 3.3 15.3 + - - +
67B LEU* 3.2 27.3 - - + +
131B VAL* 3.6 30.5 - - + -
157B PHE* 4.3 12.8 - - + -
160B ALA* 3.5 38.6 - - + +
161B ILE 3.9 11.9 - - - +
162B GLU* 3.8 19.5 - - + -
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Residues in contact with CYS 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 GLU* 3.1 25.7 + - - +
61B ALA 3.9 2.2 - - - +
63B ILE* 1.3 78.7 - - - +
65B ARG* 1.3 62.0 - - - +
67B LEU* 3.7 10.7 + - - +
73B VAL 5.2 2.5 - - - +
74B ARG* 3.3 23.0 - - - +
75B LEU* 3.8 23.5 + - + +
87B LEU* 6.0 0.2 - - - -
89B PHE* 3.9 25.6 - - + -
157B PHE* 3.9 35.2 - - - -
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Residues in contact with ARG 65 (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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58B GLU 4.9 2.0 + - - -
61B ALA* 3.2 33.2 + - - +
62B ARG* 3.3 17.6 + - - +
64B CYS* 1.3 75.7 - - - +
66B LEU* 1.3 64.1 + - - +
67B LEU 3.2 0.8 + - - -
68B LYS* 4.4 0.2 - - - +
74B ARG* 3.1 30.3 + - - +
75B LEU* 3.7 33.0 - - + +
76B HIS 6.4 0.4 - - - -
77B ASP* 6.0 0.6 - - - +
78B SER* 4.3 17.6 - - - +
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Residues in contact with LEU 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 ARG* 3.2 14.0 + - + +
63B ILE* 3.3 12.6 - - - +
65B ARG* 1.3 78.8 - - - +
67B LEU* 1.3 63.4 + - + +
68B LYS* 3.3 9.9 + - - +
125B HIS* 4.6 2.9 + - - -
129B MET* 3.7 47.9 - - + +
131B VAL* 4.1 13.7 - - + -
162B GLU* 5.6 6.1 - - + +
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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 ILE* 3.2 30.2 + - + +
64B CYS* 3.7 6.2 + - - +
65B ARG 3.2 2.0 - - - -
66B LEU* 1.3 76.4 - - + +
68B LYS* 1.3 60.9 - - - +
69B HIS* 4.0 2.0 + - - -
72B ILE* 4.4 18.8 - - + +
74B ARG* 3.1 27.5 - - - +
125B HIS* 3.8 20.9 - - + -
126B CYS* 3.9 23.8 - - - -
129B MET* 4.0 16.4 - - + -
131B VAL* 4.3 7.9 - - + -
157B PHE* 3.6 39.7 - - + -
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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