Contacts of the helix formed by residues 13 - 24 (chain B) in PDB entry 1B0N
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 GLN 13 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A GLN* 6.0 0.2 - - - +
9A TYR* 3.5 30.7 + - + +
12A GLU* 3.7 39.1 + - + +
13A LYS* 3.8 24.3 - - - +
54A LEU 5.4 0.2 - - - +
55A ASP 4.6 1.7 + - - +
56A VAL* 3.7 24.6 - - + +
11B LEU* 3.3 29.1 + - - +
12B ASP* 1.4 71.1 + - - +
14B GLU* 1.3 64.4 + - - +
16B VAL* 3.5 15.5 - - - +
17B GLU* 3.2 20.4 + - - +
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Residues in contact with GLU 14 (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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55A ASP 3.8 15.2 + - - +
56A VAL* 3.3 3.8 - - - +
57A SER* 2.8 38.1 + - - -
59A HIS* 5.4 1.4 - - - -
60A THR* 2.7 24.7 + - - -
92A LYS* 3.8 21.5 - - + +
96A ARG* 2.8 32.3 + - - +
12B ASP* 3.0 9.6 + - - +
13B GLN* 1.3 75.7 - - - +
15B TRP* 1.3 60.5 + - - +
17B GLU* 3.2 5.4 + - - +
18B LEU* 2.9 38.2 + - + +
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Residues in contact with TRP 15 (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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82A VAL* 3.9 17.3 - - + +
85A ALA* 3.5 36.8 - - + -
86A MET* 3.7 22.0 - - + +
90A VAL* 3.4 27.4 - - + -
91A SER* 3.7 7.2 - - - -
92A LYS* 3.6 32.2 - - + +
95A PHE* 3.6 43.7 - + + -
12B ASP* 3.1 38.6 + - + +
14B GLU* 1.3 73.6 - - - +
16B VAL* 1.4 66.1 + - - +
18B LEU* 3.3 11.8 + - + +
19B MET* 3.0 34.3 + - + +
36B LEU* 5.2 0.2 - - + -
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Residues in contact with VAL 16 (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* 4.1 13.6 - - + +
82A VAL* 4.0 13.0 - - + -
11B LEU* 3.8 34.1 - - + -
12B ASP 2.9 19.3 + - - +
13B GLN* 3.5 23.1 - - - +
15B TRP* 1.4 76.6 - - - +
17B GLU* 1.3 58.0 + - - +
19B MET* 3.2 2.8 + - - +
20B VAL* 2.8 36.0 + - + +
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Residues in contact with GLU 17 (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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5A ARG* 4.2 6.4 + - - -
9A TYR* 5.0 3.0 + - - +
59A HIS* 3.6 9.8 + - + -
60A THR* 3.4 34.5 - - + +
63A ASP* 2.7 7.9 - - - +
66A HIS* 3.2 11.1 + - - -
1001A ZN 2.0 37.3 - - - -
13B GLN 3.2 11.0 + - - +
14B GLU* 3.2 9.4 + - - +
16B VAL* 1.3 81.6 - - - +
18B LEU* 1.3 64.7 + - + +
20B VAL* 3.3 6.4 + - - +
21B GLU* 2.9 40.6 + - + +
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Residues in contact with LEU 18 (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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59A HIS* 6.6 0.4 - - + -
92A LYS* 4.1 36.3 - - + +
95A PHE* 3.9 16.2 - - + -
96A ARG* 3.6 31.0 - - + +
99A LEU* 3.9 20.2 - - + +
14B GLU* 2.9 30.4 + - + +
15B TRP* 3.7 23.6 - - + +
17B GLU* 1.3 82.4 - - + +
19B MET* 1.3 57.0 + - - +
21B GLU* 3.4 6.4 + - + +
22B ALA* 2.9 27.2 + - - +
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Residues in contact with MET 19 (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* 4.1 9.0 - - + -
78A TRP* 3.5 26.3 - - + -
81A LEU* 3.7 15.3 - - + +
82A VAL* 3.6 25.8 - - + +
85A ALA* 3.6 30.1 - - + -
95A PHE* 3.7 33.2 - - + -
15B TRP* 3.0 23.9 + - + +
16B VAL 3.7 3.6 - - - +
18B LEU* 1.3 73.5 - - - +
20B VAL* 1.4 66.7 + - - +
22B ALA* 4.2 1.1 - - - -
23B LYS* 2.9 25.6 + - - +
32B ILE* 4.0 19.7 - - + -
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Residues in contact with VAL 20 (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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66A HIS* 3.6 33.7 - - + +
74A LEU* 3.5 31.0 - - + +
1005A ZN 4.0 1.1 - - - -
16B VAL* 2.8 30.5 + - + +
17B GLU* 3.3 8.9 + - - +
19B MET* 1.4 78.3 - - - +
21B GLU* 1.3 57.7 + - - +
23B LYS* 3.3 2.4 + - - +
24B GLU* 2.9 41.3 + - + +
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Residues in contact with GLU 21 (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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59A HIS* 5.1 4.5 - - - +
65A LYS* 2.8 26.6 + - - +
66A HIS* 2.9 7.7 + - - -
99A LEU* 4.3 15.3 - - + -
103A LYS* 4.2 17.9 + - - +
1001A ZN 2.1 29.2 - - - -
17B GLU* 2.9 33.7 + - + +
18B LEU* 3.7 7.2 - - + +
19B MET 3.3 0.2 - - - -
20B VAL* 1.3 78.0 - - - +
22B ALA* 1.3 61.8 + - - +
24B GLU* 3.4 7.1 + - - +
25B ALA* 2.9 25.3 + - - +
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Residues in contact with ALA 22 (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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78A TRP* 4.2 0.9 - - - -
95A PHE* 4.4 5.4 - - + -
99A LEU* 3.4 26.2 - - + +
18B LEU 2.9 14.9 + - - +
19B MET* 3.3 8.0 + - - +
21B GLU* 1.3 74.8 - - - +
23B LYS* 1.3 64.1 + - - +
25B ALA 3.2 6.2 + - - -
27B ILE* 3.0 34.4 + - + +
32B ILE* 3.9 25.8 - - + -
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Residues in contact with LYS 23 (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* 4.2 13.9 - - + +
75A ASP* 5.1 9.5 + - - +
78A TRP* 3.4 58.0 - - + +
19B MET 2.9 17.2 + - - +
20B VAL* 3.6 4.9 - - - +
22B ALA* 1.3 78.1 - - - +
24B GLU* 1.3 63.9 + - + +
26B ASN* 3.1 19.8 + - - -
27B ILE 4.6 0.7 - - - -
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Residues in contact with GLU 24 (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 LYS* 3.9 9.9 - - - +
66A HIS* 3.1 16.7 - - - -
1005A ZN 2.0 37.4 - - - -
20B VAL* 2.9 21.9 + - + +
21B GLU* 3.9 8.8 - - - +
23B LYS* 1.3 78.9 - - + +
25B ALA* 1.3 56.3 + - - +
26B ASN* 3.2 12.4 + - - +
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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