Contacts of the strand formed by residues 9 - 19 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C LEU 3.9 6.5 - - - +
5C ILE* 3.7 27.1 - - + -
6C THR* 3.4 35.7 - - - +
8C ASN* 1.3 71.7 - - - +
10C HIS* 1.3 66.1 + - - +
31C GLU* 3.3 5.0 - - - +
32C GLY 2.9 32.9 + - - -
34C PRO* 3.6 19.9 - - + +
69C PHE* 3.9 23.9 - - + -
110C LEU* 3.7 23.1 - - + -
113C GLY* 4.2 15.9 - - - +
115C LEU* 3.8 14.8 - - + +
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Residues in contact with HIS 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ASN* 5.4 3.8 - - + +
9C MET* 1.3 84.1 - - - +
11C MET* 1.3 62.0 + - - +
30C GLY 3.4 16.6 + - - +
31C GLU* 3.8 24.0 + - + +
69C PHE* 5.1 0.2 - - - -
113C GLY 4.4 7.2 + - - +
114C CYS* 3.6 13.9 - - - -
115C LEU* 2.9 27.3 + - - +
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Residues in contact with MET 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C HIS* 1.3 74.9 - - - +
12C LYS* 1.3 63.4 + - - +
28C SER 4.5 0.2 - - - -
29C GLU* 3.5 5.2 - - - +
30C GLY 3.1 40.0 + - - +
31C GLU* 3.7 6.7 - - - +
39C GLN* 4.1 14.1 - - + +
40C THR 3.0 30.1 - - - +
41C MET* 3.4 34.8 - - + +
66C SER* 4.5 0.4 - - - -
69C PHE* 3.7 29.2 - - - -
114C CYS* 3.9 5.2 - - - -
115C LEU* 3.0 22.7 - - + +
117C TYR* 3.9 16.6 - - + -
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Residues in contact with LYS 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C MET* 1.3 77.4 - - - +
13C LEU* 1.3 61.0 + - - +
14C TYR* 4.0 25.6 + - + +
28C SER 3.4 4.3 - - - +
29C GLU* 3.0 26.5 - - - +
114C CYS* 3.9 15.3 - - - +
115C LEU 2.8 6.1 + - - +
116C ILE* 3.4 30.1 - - + +
117C TYR* 2.9 26.3 + - - +
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Residues in contact with LEU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LYS* 1.3 74.9 - - - +
14C TYR* 1.3 81.6 + - - +
15C MET* 3.7 8.7 - - + +
26C CYS 4.2 4.0 - - - +
27C THR* 3.1 9.2 - - - -
28C SER* 2.8 47.2 + - - +
41C MET* 4.7 2.0 - - + -
62C PHE* 3.5 61.9 - - + +
106C GLN* 5.8 0.2 - - - +
117C TYR* 3.3 18.8 - - + +
119C VAL* 3.5 26.7 - - + -
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Residues in contact with TYR 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LYS* 4.0 30.3 + - + +
13C LEU* 1.3 81.5 - - - +
15C MET* 1.3 54.9 + - - +
26C CYS 3.6 3.4 - - - +
27C THR* 4.0 18.4 - - + -
116C ILE* 4.0 20.2 - - + +
117C TYR 2.8 17.7 + - - +
118C ASN* 3.4 25.5 + - - +
119C VAL* 2.7 33.4 + - - +
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Residues in contact with MET 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 3.7 9.2 - - + -
14C TYR* 1.3 75.0 - - - +
16C GLU* 1.3 62.5 + - - +
24C PHE* 4.0 21.2 - - + -
25C LYS* 3.4 5.7 - - - +
26C CYS* 2.8 42.9 + - + +
58C LEU* 4.5 4.9 - - - +
61C SER* 3.8 28.7 - - - +
62C PHE* 3.7 41.5 - - + -
119C VAL* 3.2 22.2 - - + +
121C ILE* 3.8 25.1 - - + -
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Residues in contact with GLU 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LYS* 6.1 1.4 - - - -
14C TYR 4.3 0.2 - - - -
15C MET* 1.3 78.4 - - - +
17C GLY* 1.3 61.8 + - - +
23C HIS* 3.0 23.4 + - - +
24C PHE* 3.9 3.1 - - - -
25C LYS* 3.5 33.8 - - + -
119C VAL 3.0 7.7 + - - +
120C LYS* 3.4 15.2 - - + +
121C ILE* 3.0 22.6 + - - +
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Residues in contact with GLY 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C GLU* 1.3 82.2 - - - +
18C THR* 1.3 67.6 + - - -
23C HIS* 3.1 17.5 - - - -
24C PHE* 3.3 30.7 + - - -
121C ILE* 3.2 15.0 - - - -
122C ARG* 4.9 5.8 - - - -
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Residues in contact with THR 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A THR* 4.6 12.6 - - + +
17C GLY* 1.3 78.1 + - - -
19C VAL* 1.3 64.7 + - - +
20C ASN 4.3 0.7 - - - +
21C ASN* 3.8 25.8 - - - +
22C HIS 3.3 12.8 - - - +
23C HIS* 3.8 17.3 - - - +
24C PHE* 3.9 2.2 - - - -
121C ILE 3.4 6.3 + - - -
122C ARG* 3.4 30.6 + - - +
123C GLY 2.7 31.6 + - - +
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Residues in contact with VAL 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C THR* 1.3 80.3 - - - +
20C ASN* 1.3 75.7 + - + +
22C HIS* 2.9 26.0 + - - +
24C PHE* 4.1 8.1 - - + -
53C PHE* 3.5 55.1 - - + -
57C ILE* 4.3 9.0 - - + -
58C LEU* 4.7 0.9 - - + -
102C LEU* 4.3 16.6 - - + -
121C ILE* 4.6 4.0 - - + -
123C GLY 3.4 9.2 - - - +
126C PHE* 4.4 15.9 - - + -
133C MET* 4.6 4.1 - - - +
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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