Contacts of the helix formed by residues 58 - 70 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ASP* 2.7 36.9 + - - -
25A VAL 4.6 3.1 - - - -
26A LYS* 4.9 9.7 - - - -
56A LYS 3.9 1.2 + - - -
57A LEU* 1.3 67.0 - - - +
59A ARG* 1.3 57.2 + - - +
61A ILE* 2.9 12.4 + - - +
62A GLN* 2.6 43.7 + - - +
136A ARG* 4.4 2.4 + - - -
72B ASP* 4.9 5.5 + - - -
74B LEU* 3.8 27.9 + - - +
75B TRP* 5.0 0.9 + - - -
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Residues in contact with ARG 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A HIS* 3.1 38.8 + - + +
11A SER* 4.7 9.0 + - - -
20A THR* 3.1 22.7 - - - +
21A GLY 2.7 28.9 + - - +
23A VAL 2.9 25.3 + - - -
24A ASP* 4.7 0.2 - - - +
25A VAL* 3.0 26.4 + - - +
26A LYS 4.4 0.9 - - - -
27A LEU* 2.9 32.6 - - + +
57A LEU* 4.1 14.3 - - + +
58A SER* 1.3 73.9 - - - +
60A ALA* 1.3 52.2 + - - +
62A GLN* 4.3 6.3 + - - -
63A THR* 2.6 31.7 + - - -
86A GLU* 4.5 10.5 + - - +
181A HIS* 3.7 13.2 + - - -
302A BHC 5.4 3.6 + - - -
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Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A HIS* 4.1 13.7 - - + -
54A THR* 4.8 1.6 - - - -
55A SER* 3.3 21.3 - - - +
57A LEU 3.0 11.6 + - - +
58A SER 3.0 0.2 - - - -
59A ARG* 1.3 79.3 - - - +
61A ILE* 1.3 59.2 + - - +
62A GLN 3.3 0.2 - - - -
63A THR* 3.4 5.0 - - - -
64A ALA* 3.2 24.3 + - - +
179A ALA* 3.8 22.4 - - - +
180A ALA* 4.4 3.1 - - - -
181A HIS* 3.5 15.5 - - + +
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Residues in contact with ILE 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A THR* 3.7 19.7 - - - +
55A SER 4.1 1.8 - - - +
56A LYS 4.1 4.9 - - - -
57A LEU 3.2 21.5 - - - +
58A SER* 2.9 9.8 + - - +
60A ALA* 1.3 72.2 - - - +
62A GLN* 1.3 64.7 + - - +
64A ALA* 3.4 5.6 + - - +
65A ASN* 3.0 44.4 + - - +
80A ARG* 3.5 26.7 - - - +
74B LEU* 3.4 22.0 - - + +
75B TRP* 3.3 41.5 - - + +
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Residues in contact with GLN 62 (chain A).
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* 3.0 27.9 - - - +
27A LEU* 3.4 23.1 + - + +
32A GLN* 4.0 23.0 - - - +
58A SER 2.6 22.2 + - - +
59A ARG 4.0 4.7 - - - +
61A ILE* 1.3 73.9 - - - +
63A THR* 1.3 56.5 + - - +
65A ASN* 3.4 6.4 + - + +
66A ILE* 2.9 39.9 + - + +
69B GLU* 2.7 37.8 + - + +
74B LEU* 3.4 22.7 - - + +
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Residues in contact with THR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 3.5 32.5 - - + +
7A ARG 4.7 0.4 - - - +
8A HIS* 3.0 24.9 - - - +
9A GLY 4.4 1.0 + - - +
27A LEU* 3.4 10.6 - - - +
35A ALA* 3.7 25.9 - - + +
59A ARG 2.6 20.5 + - - -
60A ALA* 3.4 9.9 - - - -
62A GLN* 1.3 74.8 - - - +
64A ALA* 1.3 60.8 + - - +
67A ALA* 2.9 35.0 + - + +
179A ALA* 5.2 2.2 - - + -
208A GLY* 6.4 0.7 - - - -
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Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU* 3.5 34.8 - - + -
54A THR* 4.0 10.3 - - + -
60A ALA 3.2 10.1 + - - +
61A ILE* 3.6 8.5 - - - +
63A THR* 1.3 78.9 - - - +
65A ASN* 1.3 61.9 + - - +
66A ILE 3.1 0.7 + - - -
68A LEU* 2.9 36.9 + - - +
80A ARG* 5.3 0.2 - - - +
177A MET* 4.4 13.0 - - - -
179A ALA* 4.4 2.5 - - + -
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Residues in contact with ASN 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU* 5.4 2.8 - - - +
61A ILE* 3.0 34.9 + - - +
62A GLN* 3.6 6.9 - - - +
64A ALA* 1.3 79.2 - - - +
66A ILE* 1.3 61.7 + - + +
68A LEU* 5.4 0.2 - - - -
69A GLU* 3.3 17.3 - - - +
74A LEU* 3.5 13.3 - - - +
80A ARG* 4.8 8.6 + - - +
62B GLN* 5.5 0.5 - - - +
65B ASN* 3.5 42.9 + - + +
74B LEU* 4.0 13.0 - - - +
80B ARG* 5.7 2.0 - - - +
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Residues in contact with ILE 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 4.0 6.5 - - + -
32A GLN* 3.8 31.9 - - + +
35A ALA* 3.5 20.4 - - + -
36A ALA* 3.5 33.0 - - + +
62A GLN* 2.9 31.1 + - + +
65A ASN* 1.3 75.2 - - + +
67A ALA* 1.3 62.1 + - - +
69A GLU* 2.9 27.0 + - - +
70A LYS* 3.3 15.9 + - - +
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 5.5 0.2 - - + -
35A ALA* 3.5 18.4 - - - +
38A ALA* 4.5 6.1 - - + -
39A GLY* 3.0 34.6 - - - +
42A LEU* 4.7 2.7 - - + -
63A THR* 2.9 21.0 + - + +
64A ALA 3.8 1.3 - - - +
66A ILE* 1.3 77.6 - - - +
68A LEU* 1.3 59.9 + - - +
69A GLU 3.1 4.0 + - - -
70A LYS* 3.2 8.3 + - - -
71A ALA* 3.3 5.2 + - - +
177A MET* 4.3 17.5 - - + -
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LEU* 4.5 6.5 - - + -
49A PRO* 4.2 12.3 - - + -
52A LEU* 4.2 20.9 - - + -
64A ALA 2.9 19.3 + - - +
65A ASN* 5.4 0.2 - - - -
67A ALA* 1.3 73.7 - - - +
69A GLU* 1.3 60.0 + - - +
71A ALA* 3.8 6.3 - - + -
72A ASP 3.3 0.5 + - - -
73A ARG* 3.1 44.7 + - + +
74A LEU* 3.3 17.7 + - + +
76A ILE* 3.2 40.4 - - + -
177A MET* 3.7 25.8 - - - -
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Residues in contact with GLU 69 (chain A).
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 3.3 16.0 + - - +
66A ILE* 2.9 15.2 + - - +
68A LEU* 1.3 80.2 - - - +
70A LYS* 1.3 88.4 + - - +
71A ALA 3.2 1.6 - - - -
72A ASP* 3.3 17.9 + - - +
74A LEU* 3.8 22.6 - - + +
26B LYS* 4.0 23.3 - - + +
32B GLN* 6.2 0.9 - - - -
62B GLN* 3.4 32.4 + - - +
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Residues in contact with LYS 70 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ALA* 3.7 37.6 - - + +
39A GLY 4.1 2.2 - - - -
40A GLU* 4.0 25.9 - - + +
43A LYS* 2.8 38.7 + - - +
66A ILE* 3.5 17.3 - - - +
67A ALA 3.2 6.3 + - - +
69A GLU* 1.3 95.8 + - - +
71A ALA* 1.3 51.8 + - - +
72A ASP* 3.4 2.0 - - - -
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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