Contacts of the strand formed by residues 9 - 19 (chain B) in PDB entry 3BX9
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 MET 9 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B LEU 3.6 17.0 - - - +
5B ILE* 3.7 28.9 - - + -
6B THR* 3.4 32.1 - - + +
8B ASN* 1.3 77.1 - - - +
10B HIS* 1.3 66.6 + - - +
31B GLU* 3.2 6.6 - - - +
32B GLY 3.0 30.4 + - - -
34B PRO* 3.2 20.9 - - + -
69B PHE* 3.9 18.3 - - + -
110B LEU* 4.8 7.4 - - + -
113B GLY* 4.2 18.8 - - - +
115B LEU* 4.3 12.8 - - + -
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Residues in contact with HIS 10 (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 ASN* 5.1 4.7 - - - +
9B MET* 1.3 83.4 - - - +
11B MET* 1.3 63.6 + - - +
30B GLY 3.4 10.7 + - - +
31B GLU* 4.5 15.2 + - + +
113B GLY 5.0 6.2 + - - +
114B CYS* 3.9 20.0 - - + -
115B LEU* 3.0 29.8 + - - +
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Residues in contact with MET 11 (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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10B HIS* 1.3 78.7 - - - +
12B LYS* 1.3 66.5 + - - +
29B GLU* 3.3 4.7 - - - +
30B GLY* 2.8 38.8 + - - +
31B GLU 3.3 39.3 - - - +
39B GLN* 3.5 15.7 - - + +
40B THR 3.6 12.3 - - - +
41B MET* 3.7 21.8 - - + -
66B SER* 3.5 23.8 - - - -
69B PHE* 3.5 22.2 - - + -
114B CYS* 4.0 1.6 - - - -
115B LEU* 3.2 11.2 - - + +
117B TYR* 3.7 17.5 - - + +
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Residues in contact with LYS 12 (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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11B MET* 1.3 76.8 - - - +
13B LEU* 1.3 62.7 + - - +
14B TYR* 4.3 24.6 + - + +
28B SER 3.3 4.7 - - - +
29B GLU* 3.6 32.8 - - + +
114B CYS* 3.9 16.8 - - - +
115B LEU 2.9 6.3 + - - +
116B ILE* 3.4 29.0 - - + +
117B TYR* 2.8 25.6 + - - +
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Residues in contact with LEU 13 (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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12B LYS* 1.3 77.7 - - - +
14B TYR* 1.3 80.3 + - - +
15B MET* 4.0 7.0 - - + +
26B CYS 4.3 0.7 - - - +
27B THR* 3.2 10.4 - - - -
28B SER* 2.7 54.5 + - - +
41B MET* 4.3 2.2 - - + -
62B PHE* 3.7 58.6 - - + +
117B TYR* 3.3 23.8 - - + +
119B VAL* 3.7 23.3 - - + -
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Residues in contact with TYR 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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12B LYS* 4.3 31.9 + - + +
13B LEU* 1.3 84.1 - - - +
15B MET* 1.3 54.5 + - - +
26B CYS 3.7 4.0 - - - -
27B THR* 4.2 18.2 - - + -
116B ILE* 4.4 18.2 - - + -
117B TYR 2.8 14.4 + - - +
118B ASN* 3.2 23.8 - - - +
119B VAL* 2.8 31.9 + - - +
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Residues in contact with MET 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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13B LEU* 4.0 6.5 - - + +
14B TYR* 1.3 75.1 - - - +
16B GLU* 1.3 66.3 + - - +
24B PHE* 4.0 21.8 - - + -
25B LYS* 3.1 5.0 - - - +
26B CYS* 2.7 47.4 + - + +
58B LEU* 4.4 6.3 - - - +
61B SER* 3.7 34.3 - - - +
62B PHE* 3.5 43.5 - - + -
119B VAL* 3.2 21.1 - - + +
121B ILE* 4.1 15.5 - - + -
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Residues in contact with GLU 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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15B MET* 1.3 79.6 - - - +
17B GLY* 1.3 62.9 + - - +
23B HIS* 2.5 34.9 + - + +
24B PHE 3.5 7.2 - - - +
25B LYS* 3.4 30.4 + - + -
119B VAL 3.0 7.2 + - - +
120B LYS* 3.2 17.4 - - + +
121B ILE* 3.0 21.7 + - - +
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Residues in contact with GLY 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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16B GLU* 1.3 78.8 - - - +
18B THR* 1.3 67.6 + - - -
23B HIS* 3.3 4.6 - - - -
24B PHE* 2.9 51.4 + - - +
121B ILE* 3.0 14.4 - - - -
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Residues in contact with THR 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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17B GLY* 1.3 78.9 + - - -
19B VAL* 1.3 65.7 + - - +
21B ASN* 3.5 32.5 - - - +
22B HIS 3.2 8.3 - - - +
23B HIS* 3.8 16.9 - - + +
24B PHE* 3.7 0.6 - - - -
121B ILE 3.1 5.1 + - - +
122B ARG* 3.4 47.7 + - - +
123B GLY 2.9 22.6 + - - -
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Residues in contact with VAL 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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18B THR* 1.3 78.1 - - - +
20B ASN* 1.3 77.1 + - + +
21B ASN 3.1 0.2 - - - -
22B HIS* 2.9 24.6 + - - +
24B PHE* 3.9 8.0 - - + -
53B PHE* 3.7 39.8 - - + -
57B ILE* 3.9 27.8 - - + -
58B LEU* 4.7 0.2 - - + -
102B LEU* 4.3 0.9 - - + -
121B ILE* 4.2 10.8 - - + -
123B GLY* 3.5 13.2 - - - +
126B PHE* 4.2 17.9 - - + -
133B MET* 4.4 8.1 - - - +
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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