Contacts of the helix formed by residues 58 - 71 (chain B) in PDB entry 1BQ4
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 SER 58 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ASP* 4.8 4.2 + - - -
74A LEU* 4.0 26.8 + - - +
75A TRP* 5.4 0.9 + - - -
24B ASP* 2.5 42.9 + - - -
25B VAL 4.8 4.5 - - - -
26B LYS* 5.7 5.2 - - - -
27B LEU 5.9 0.2 - - - -
56B LYS 3.6 3.4 + - - -
57B LEU* 1.3 67.0 - - - +
59B ARG* 1.3 64.0 + - - +
61B ILE* 3.8 11.7 - - - +
62B GLN* 2.8 30.7 + - - +
136B ARG* 4.0 2.9 + - - -
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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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8B HIS* 2.9 40.2 + - + +
11B SER* 4.5 5.8 - - - -
20B THR* 2.8 28.5 - - - +
21B GLY 2.5 30.3 + - - -
23B VAL 3.0 14.5 + - - -
25B VAL* 3.4 22.5 + - - +
26B LYS 4.6 1.3 - - - +
27B LEU* 3.8 27.6 - - + +
57B LEU* 3.9 9.1 - - + +
58B SER* 1.3 73.5 - - - +
60B ALA* 1.3 59.9 + - - +
62B GLN* 4.7 0.2 - - - -
63B THR* 2.9 25.6 + - - -
86B GLU* 4.0 11.9 + - - +
181B HIS* 3.4 27.3 + - + -
303B SO4 2.8 25.9 + - - -
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Residues in contact with ALA 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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8B HIS* 4.1 10.2 - - - -
54B THR* 4.9 0.2 - - - -
55B SER* 3.1 29.4 - - - +
57B LEU 3.0 4.1 + - - +
59B ARG* 1.3 77.9 - - - +
61B ILE* 1.3 63.8 + - - +
63B THR* 3.1 18.4 + - - -
64B ALA 3.3 5.5 + - - -
179B ALA* 3.7 27.5 - - - +
180B ALA* 4.1 8.3 - - - +
181B HIS* 3.8 11.9 - - + +
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Residues in contact with ILE 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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74A LEU* 3.4 42.8 - - + +
75A TRP* 4.0 11.4 - - + -
54B THR* 3.8 25.8 - - - +
55B SER 3.9 6.5 - - - +
56B LYS 4.0 13.7 - - - +
57B LEU 3.7 18.2 - - - +
58B SER* 3.2 15.2 + - - +
60B ALA* 1.3 71.8 - - - +
62B GLN* 1.3 69.0 + - - +
63B THR 3.1 0.3 + - - -
64B ALA* 3.2 3.8 + - - +
65B ASN* 3.0 29.7 + - - +
80B ARG* 3.7 23.3 - - - +
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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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65A ASN 5.5 0.3 - - - +
69A GLU* 3.4 38.5 + - - +
74A LEU* 4.2 9.3 - - + +
26B LYS* 5.1 5.7 - - - +
27B LEU* 3.7 36.3 + - + +
32B GLN* 4.6 13.8 + - - +
58B SER* 2.8 18.5 + - - +
59B ARG 4.0 4.7 - - - +
61B ILE* 1.3 79.0 - - - +
63B THR* 1.3 59.5 + - - +
65B ASN* 3.4 9.6 - - + +
66B ILE* 3.2 40.5 + - + +
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Residues in contact with THR 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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6B VAL* 3.8 30.5 - - + +
7B ARG 4.9 0.4 - - - +
8B HIS* 3.1 26.3 - - - +
9B GLY 4.5 0.3 + - - -
27B LEU* 3.5 9.7 - - - +
31B GLY 4.9 0.2 + - - -
35B ALA* 4.0 23.3 - - + +
38B ALA* 5.7 0.4 - - + -
59B ARG 2.9 17.4 + - - -
60B ALA* 3.1 11.1 + - - -
61B ILE 3.1 0.6 - - - -
62B GLN* 1.3 76.5 - - - +
64B ALA* 1.3 60.8 + - - +
66B ILE 3.9 0.2 - - - -
67B ALA* 2.9 32.9 + - + +
177B MET* 5.7 0.2 - - + -
179B ALA* 5.0 2.7 - - + -
208B GLY* 6.2 1.3 - - - -
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Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 3.8 29.2 - - + -
54B THR* 4.1 4.9 - - + -
60B ALA 3.3 1.6 + - - +
61B ILE 3.2 8.4 + - - +
63B THR* 1.3 76.2 - - - +
65B ASN* 1.3 59.1 + - - +
67B ALA 3.1 0.3 + - - -
68B LEU* 2.6 41.3 + - + +
80B ARG* 6.1 0.2 - - - +
177B MET* 3.6 28.3 - - + -
179B ALA* 4.0 9.2 - - + -
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Residues in contact with ASN 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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65A ASN* 3.5 46.4 + - + +
74A LEU* 4.0 11.1 - - - +
80A ARG* 5.8 2.8 - - - +
52B LEU* 5.5 2.0 - - - +
61B ILE* 3.0 27.0 + - - +
62B GLN* 3.4 13.9 - - + +
64B ALA* 1.3 79.5 - - - +
66B ILE* 1.3 59.6 + - + +
68B LEU* 5.0 4.1 - - - +
69B GLU* 3.2 26.7 + - - +
74B LEU* 3.3 12.1 - - - +
80B ARG* 4.3 15.2 + - - +
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Residues in contact with ILE 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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27B LEU* 4.8 0.2 - - + -
32B GLN* 3.6 36.8 - - + +
35B ALA* 3.4 23.1 - - + -
36B ALA* 3.5 17.7 - - + +
62B GLN* 3.2 38.2 + - + +
65B ASN* 1.3 77.7 - - + +
67B ALA* 1.3 65.7 + - - +
69B GLU* 3.2 20.6 - - - +
70B LYS* 3.3 12.4 + - + +
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Residues in contact with ALA 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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6B VAL* 5.9 1.1 - - + -
35B ALA 3.7 15.5 - - - +
38B ALA* 4.5 7.0 - - + -
39B GLY* 3.2 27.8 - - - +
42B LEU* 4.7 5.8 - - + -
63B THR* 2.9 22.4 + - + +
64B ALA* 3.6 5.8 - - - +
66B ILE* 1.3 78.6 - - - +
68B LEU* 1.3 62.2 + - - +
70B LYS 3.1 10.7 + - - -
71B ALA* 3.1 11.4 + - - +
177B MET* 4.5 10.5 - - + -
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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
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80A ARG* 6.3 0.2 - - - +
42B LEU* 5.0 4.0 - - + -
49B PRO* 4.5 7.0 - - + -
52B LEU* 4.0 28.3 - - + -
64B ALA* 2.6 26.8 + - + +
65B ASN* 4.8 3.6 - - - +
67B ALA* 1.3 70.5 - - - +
69B GLU* 1.3 58.6 + - - +
70B LYS 3.3 0.2 - - - -
71B ALA* 4.4 5.2 - - + +
72B ASP* 3.0 23.9 + - - -
73B ARG* 3.1 32.3 + - + +
74B LEU* 3.6 18.8 + - + +
76B ILE* 3.7 31.9 - - + -
177B MET* 3.8 23.6 - - - -
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Residues in contact with GLU 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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26A LYS* 3.9 19.6 - - + +
32A GLN* 5.1 2.2 + - - -
62A GLN* 2.7 47.6 + - + +
65B ASN 3.2 15.4 + - - +
66B ILE* 3.2 15.2 - - - +
68B LEU* 1.3 77.7 - - - +
70B LYS* 1.3 87.6 + - - +
72B ASP* 3.5 16.3 + - - +
74B LEU* 3.7 12.0 - - + +
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Residues in contact with LYS 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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36B ALA* 4.0 20.2 - - + +
39B GLY* 4.0 3.7 - - - -
40B GLU* 3.1 44.0 + - + +
43B LYS* 3.0 31.5 + - - +
66B ILE* 3.8 9.6 - - + +
67B ALA 3.1 8.8 + - - +
69B GLU* 1.3 98.1 + - - +
71B ALA* 1.3 55.2 + - - +
72B ASP* 3.4 2.2 - - - -
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Residues in contact with ALA 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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39B GLY 3.8 12.6 - - - +
42B LEU* 4.1 17.9 - - + -
43B LYS* 3.9 17.0 - - - +
47B VAL 5.8 0.4 - - - +
48B TYR* 4.9 9.5 - - + -
49B PRO* 5.9 0.9 - - + -
67B ALA 3.1 15.0 + - - +
68B LEU* 3.4 8.9 + - + +
70B LYS* 1.3 75.0 - - - +
72B ASP* 1.3 71.9 + - - +
73B ARG* 3.3 20.3 + - + +
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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