Contacts of the helix formed by residues 62 - 73 (chain B) in PDB entry 6BZE
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 ARG 62 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ARG* 6.1 3.6 - - - +
50A GLU* 3.3 49.1 + - + +
53A GLU* 4.6 2.5 - - - +
28B LEU* 3.3 33.0 + - - +
29B CYS* 5.2 13.1 - - - +
60B SER* 3.2 0.8 - - - +
61B SER* 1.3 81.9 - - - +
63B LYS* 1.3 66.0 + - + +
65B ALA* 3.2 5.6 - - - +
66B GLY* 3.1 18.7 + - - -
37E HIS* 2.6 32.3 + - - -
38E PHE* 4.6 8.2 - - - +
41E LEU* 4.6 19.2 - - - +
88E ARG* 5.4 6.7 - - - +
90E LYS* 5.1 4.6 - - - +
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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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50A GLU* 2.8 25.2 + - - -
54A GLU* 4.1 5.2 - - - +
58B ARG 4.9 2.7 - - - +
59B THR* 3.6 18.4 - - + -
60B SER* 3.4 10.5 - - - +
61B SER 4.5 0.2 - - - +
62B ARG* 1.3 77.1 - - + +
64B ARG* 1.3 55.2 + - - +
65B ALA 3.1 1.1 - - - -
66B GLY* 2.9 5.8 + - - -
67B LYS* 2.5 44.2 + - + +
35E GLU 5.1 0.2 + - - -
36E ARG* 2.1 58.1 + - - +
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Residues in contact with ARG 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 5.9 2.6 - - - +
35B GLU* 2.7 63.3 + - - +
36B ARG* 4.2 15.4 - - - +
40B HIS* 5.0 9.7 + - + +
55B ILE* 3.3 18.8 - - + -
56B SER* 3.3 38.9 + - - +
59B THR* 2.9 21.6 + - + +
61B SER* 4.1 25.2 - - - +
63B LYS* 1.3 76.0 - - - +
65B ALA* 1.3 59.3 + - - +
67B LYS* 3.0 16.6 - - - +
68B LEU* 2.6 38.4 + - + +
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 3.4 18.6 - - + +
32B ILE* 3.5 19.5 - - + -
35B GLU* 3.1 15.1 + - - +
61B SER 3.3 19.6 + - - +
62B ARG* 3.2 13.6 + - - +
64B ARG* 1.3 80.6 - - - +
66B GLY* 1.3 62.0 + - - +
68B LEU* 3.9 0.5 - - - +
69B LEU* 3.1 28.6 + - - +
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Residues in contact with GLY 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG* 3.3 24.5 + - - -
28B LEU* 3.4 14.1 - - - +
62B ARG 3.1 4.8 + - - -
63B LYS* 2.9 7.4 + - - -
65B ALA* 1.3 77.6 - - - +
67B LYS* 1.3 53.4 + - - +
69B LEU* 3.4 1.4 + - - +
70B ASP* 2.7 37.6 + - - +
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Residues in contact with LYS 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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54B GLU* 4.9 1.3 - - - -
55B ILE* 2.1 71.3 + - + +
58B ARG 5.0 2.2 - - - -
59B THR* 2.9 24.8 - - - +
63B LYS* 2.5 23.0 + - + +
64B ARG* 3.0 12.3 - - - +
66B GLY* 1.3 70.3 - - - +
68B LEU* 1.3 57.3 + - - +
70B ASP* 2.7 28.5 + - - +
71B TYR* 2.9 30.3 + - + +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ILE* 5.2 1.8 - - + -
35B GLU* 3.5 34.8 - - + +
39B ASP* 4.2 24.2 - - + +
40B HIS* 5.1 11.4 - - + +
47B LEU* 5.0 17.8 - - + +
55B ILE* 4.6 7.5 - - + +
64B ARG* 2.6 21.5 + - + +
65B ALA 3.9 2.2 - - - +
67B LYS* 1.3 72.5 - - - +
69B LEU* 1.3 82.2 + - + +
71B TYR* 3.5 13.3 + - - +
72B LEU* 3.4 30.2 - - + +
81B THR* 5.4 7.4 - - + +
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Residues in contact with LEU 69 (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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21B LEU* 3.6 47.1 - - + +
24B LEU* 4.8 3.4 - - + +
25B ARG* 4.8 16.4 - - - +
27B TYR 4.8 4.9 - - - +
28B LEU* 3.6 17.9 - - + -
32B ILE* 3.7 33.2 - - + -
65B ALA 3.1 25.5 + - - +
66B GLY 3.7 3.1 - - - +
67B LYS 3.1 0.8 - - - -
68B LEU* 1.3 93.7 - - + +
70B ASP* 1.3 66.6 + - - +
72B LEU* 3.1 19.6 + - + +
73B GLN* 4.0 0.4 + - - -
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Residues in contact with ASP 70 (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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25B ARG* 4.4 10.4 + - - +
66B GLY 2.7 20.0 + - - +
67B LYS* 2.7 16.8 + - - +
69B LEU* 1.3 72.8 - - - +
71B TYR* 1.3 68.2 + - + -
72B LEU 3.2 1.0 + - - -
73B GLN* 3.6 26.4 + - - +
74B GLU* 4.5 4.5 + - - +
44E LYS* 3.8 11.1 + - - +
49E ARG* 3.2 37.5 + - - -
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Residues in contact with TYR 71 (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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47B LEU* 6.3 2.2 - - + -
48B SER* 4.9 11.2 - - - -
51B ASP* 3.0 20.3 + - + -
55B ILE* 3.4 30.3 - - + +
67B LYS* 2.9 42.7 + - + +
68B LEU* 3.7 9.6 - - - +
69B LEU 3.1 0.4 - - - -
70B ASP* 1.3 86.0 - - + +
72B LEU* 1.3 63.4 + - + +
74B GLU* 3.2 41.0 - - - +
75B ASN* 4.2 1.4 + - - -
31F LYS* 5.1 1.9 + - - -
33F ILE* 3.5 22.8 - - + +
36F ARG* 2.9 27.7 + - - -
37F HIS* 5.3 0.9 - + - -
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Residues in contact with LEU 72 (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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21B LEU* 4.7 9.0 - - + -
43B ALA* 6.5 0.4 - - + -
47B LEU* 4.9 17.0 - - + -
68B LEU* 3.4 28.0 - - + +
69B LEU* 3.1 14.8 + - + +
71B TYR* 1.3 80.7 - - + +
73B GLN* 1.3 65.9 + - - +
74B GLU 3.0 2.0 - - - -
75B ASN* 3.0 48.1 + - - +
78B GLY* 5.0 5.4 - - - -
81B THR* 3.5 24.9 - - - +
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Residues in contact with GLN 73 (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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14B THR* 4.7 3.6 + - - +
15B GLU* 5.2 1.2 - - - +
18B LYS* 3.4 47.9 + - + +
21B LEU* 3.5 34.4 - - + +
22B GLU* 2.0 42.4 + - - +
25B ARG* 4.9 4.8 - - - +
69B LEU 4.1 1.1 - - - +
70B ASP* 3.8 26.2 - - - +
71B TYR 3.4 0.2 - - - -
72B LEU* 1.3 73.2 - - - +
74B GLU* 1.3 68.9 + - - +
75B ASN 3.8 2.6 - - - +
44E LYS* 4.9 3.0 + - - +
49E ARG* 5.7 2.1 + - - -
30F GLU* 4.9 2.3 - - - +
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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