Contacts of the strand formed by residues 9 - 19 (chain F) in PDB entry 3BXB
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4F LEU 3.5 19.1 - - - +
5F ILE* 3.8 20.2 - - - -
6F THR* 3.3 35.4 - - + +
8F ASN* 1.3 80.1 - - - +
10F HIS* 1.3 68.5 + - - +
31F GLU* 3.0 7.5 - - - +
32F GLY 2.9 32.6 + - - -
34F PRO* 3.9 12.9 - - + +
68F THR* 5.6 0.2 - - - -
69F PHE* 4.2 11.6 - - + -
110F LEU* 4.3 5.4 - - + -
113F GLY* 2.9 40.2 - - - +
114F CYS* 5.1 0.7 - - - -
115F LEU* 4.8 10.1 - - + -
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Residues in contact with HIS 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F ASN* 5.7 3.1 - - - +
9F MET* 1.3 76.7 - - - +
11F MET* 1.3 67.7 + - - +
30F GLY 3.3 9.5 + - - +
31F GLU* 3.7 24.8 + - + +
113F GLY 4.5 7.8 + - - +
114F CYS* 3.7 19.1 - - + -
115F LEU* 3.1 25.8 + - - +
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Residues in contact with MET 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F HIS* 1.3 80.5 - - - +
12F LYS* 1.3 63.6 + - - +
29F GLU* 3.4 8.0 - - - +
30F GLY* 2.9 32.4 + - - +
31F GLU 3.6 33.4 - - - +
39F GLN* 3.5 26.7 - - + +
40F THR 3.6 13.5 - - - +
41F MET* 3.5 31.4 - - + -
66F SER* 3.9 4.0 - - - -
69F PHE* 3.7 29.6 - - + -
114F CYS* 4.0 1.3 - - - -
115F LEU* 3.3 11.0 - - + +
117F TYR* 4.0 10.5 - - + -
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Residues in contact with LYS 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F MET* 1.3 75.9 - - - +
13F LEU* 1.3 62.3 + - - +
14F TYR* 4.7 23.3 - - + +
28F SER 3.4 6.1 - - - +
29F GLU* 3.5 21.0 + - - +
41F MET* 4.9 0.2 - - - -
114F CYS* 3.3 32.3 - - - +
115F LEU 2.8 9.7 + - - +
116F ILE* 3.4 23.2 - - + -
117F TYR* 2.9 26.9 + - - +
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Residues in contact with LEU 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F LYS* 1.3 75.7 - - - +
14F TYR* 1.3 76.4 + - - +
15F MET* 4.0 15.0 - - + +
26F CYS 4.4 0.4 - - - +
27F THR* 3.4 8.3 - - - -
28F SER* 2.8 50.6 + - - +
41F MET* 3.8 15.3 - - + -
61F SER 4.1 0.2 - - - +
62F PHE* 3.5 58.8 - - + +
117F TYR* 3.4 16.8 - - + -
119F VAL* 3.9 18.6 - - + -
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Residues in contact with TYR 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F LYS* 4.7 20.9 - - + +
13F LEU* 1.3 83.6 - - - +
15F MET* 1.3 59.9 + - - +
26F CYS 3.8 4.5 - - - +
27F THR* 4.4 16.2 - - + -
116F ILE* 3.9 22.4 - - + -
117F TYR 2.9 15.7 + - - -
118F ASN* 3.6 20.4 - - - +
119F VAL* 2.9 27.2 + - - +
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Residues in contact with MET 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F LEU* 4.0 4.7 - - + +
14F TYR* 1.3 74.8 - - - +
16F GLU* 1.3 63.7 + - - +
24F PHE* 4.1 25.8 - - + -
25F LYS* 3.2 9.9 - - - +
26F CYS* 2.8 43.4 + - + +
58F LEU* 4.4 5.2 - - - -
61F SER* 3.5 40.8 - - - +
62F PHE* 3.4 41.1 - - + -
119F VAL* 3.3 17.5 - - + +
121F ILE* 4.1 13.0 - - + -
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Residues in contact with GLU 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F MET* 1.3 77.4 - - - +
17F GLY* 1.3 62.9 + - - +
23F HIS* 2.7 27.6 + - - +
24F PHE* 3.4 11.0 - - - +
25F LYS* 3.2 32.1 + - + +
119F VAL 3.0 8.4 + - - +
120F LYS* 3.4 25.8 - - + +
121F ILE* 2.9 25.1 + - - +
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Residues in contact with GLY 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F GLU* 1.3 80.2 - - - +
18F THR* 1.3 63.6 - - - -
23F HIS* 3.3 11.3 - - - -
24F PHE* 3.0 43.6 + - - -
120F LYS* 6.0 0.2 - - - -
121F ILE* 3.1 14.1 - - - -
122F ARG* 4.8 4.5 - - - -
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Residues in contact with THR 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F GLY* 1.3 76.6 + - - -
19F VAL* 1.3 70.4 + - - +
20F ASN 4.2 0.2 - - - -
21F ASN* 3.4 20.6 - - - +
22F HIS 3.2 31.0 - - - +
23F HIS* 4.1 9.7 - - + +
24F PHE* 3.5 2.0 - - - -
121F ILE* 3.2 6.0 + - - +
122F ARG* 2.6 35.8 + - - +
123F GLY 2.8 25.7 + - - +
105G THR* 4.5 7.0 + - + +
120G LYS* 5.5 1.2 - - - +
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Residues in contact with VAL 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F THR* 1.3 81.0 - - - +
20F ASN* 1.3 70.6 + - - +
22F HIS* 3.0 33.6 + - - +
24F PHE* 3.9 8.3 - - + -
53F PHE* 3.7 43.7 - - + -
57F ILE* 3.9 19.7 - - + -
58F LEU* 4.8 0.4 - - + -
102F LEU* 4.2 13.5 - - + -
121F ILE* 4.7 0.9 - - + -
123F GLY 3.4 3.6 - - - +
126F PHE* 3.8 27.1 - - + -
133F MET* 4.4 5.8 - - - -
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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