Contacts of the strand formed by residues 114 - 124 (chain B) 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 CYS 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B HIS* 4.0 24.9 - - + -
12B LYS* 4.0 33.2 - - - -
110B LEU* 4.0 4.2 - - - +
111B GLN* 2.6 53.6 + - - +
112B ASP 3.8 4.9 - - - +
113B GLY* 1.3 75.6 - - - +
115B LEU* 1.3 73.6 + - - +
116B ILE* 3.6 9.4 + - - +
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Residues in contact with LEU 115 (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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5B ILE* 4.7 1.6 - - + -
9B MET* 4.5 12.3 - - + -
10B HIS 3.1 16.5 + - - +
11B MET* 3.2 9.5 - - + +
12B LYS 2.9 26.2 + - - +
68B THR* 4.2 14.6 - - + +
69B PHE* 3.4 37.7 - - + -
84B PHE* 3.6 38.1 - - + -
108B THR* 4.2 8.3 - - + -
109B SER 3.4 5.8 - - - +
110B LEU* 3.9 15.7 - - + +
113B GLY 4.5 0.4 + - - -
114B CYS* 1.3 71.7 - - - +
116B ILE* 1.3 60.8 - - - +
117B TYR* 4.0 10.1 - - + +
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Residues in contact with ILE 116 (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* 3.4 17.7 - - + +
14B TYR* 4.1 26.2 - - + +
107B ASP 3.4 5.2 - - - +
108B THR* 3.5 1.9 - - - -
109B SER* 2.7 49.1 + - - +
111B GLN* 4.0 36.1 - - + +
114B CYS* 3.6 21.5 - - - +
115B LEU* 1.3 79.5 - - - +
117B TYR* 1.3 67.0 + - - +
118B ASN* 5.1 3.8 - - + +
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Residues in contact with TYR 117 (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* 3.7 19.6 - - + +
12B LYS 2.9 7.4 + - - -
13B LEU* 3.2 39.2 - - + -
14B TYR* 3.0 31.9 + - - -
41B MET* 3.8 14.6 - - + -
62B PHE 4.1 2.5 - - - -
63B NRQ 4.6 0.9 - - - -
66B SER* 2.5 41.4 + - - -
68B THR* 4.8 2.5 + - - -
69B PHE* 3.5 18.2 - - - -
88B PHE* 5.9 0.4 - + - -
106B GLN* 3.4 22.0 - - - +
107B ASP 3.5 2.5 - - - -
108B THR* 3.5 26.9 - - + -
115B LEU* 4.0 13.5 - - + +
116B ILE* 1.3 79.2 - - - +
118B ASN* 1.3 59.1 + - - +
119B VAL* 4.2 1.8 - - + -
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Residues in contact with ASN 118 (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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14B TYR* 3.6 29.8 + - - +
105B THR 3.8 0.5 - - - +
106B GLN* 3.3 5.2 - - - +
107B ASP* 3.0 44.6 + - + +
116B ILE* 4.2 4.4 - - + +
117B TYR* 1.3 71.9 - - - +
119B VAL* 1.3 63.8 + - - +
120B LYS* 4.5 21.1 - - - +
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Residues in contact with VAL 119 (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 20.2 - - + -
14B TYR 3.0 13.4 + - - +
15B MET* 3.3 12.6 - - + -
16B GLU* 3.2 22.5 + - - +
61B SER* 3.7 27.6 - - - +
90B TRP* 4.3 5.8 - - + -
104B ALA* 4.8 0.2 - - + -
105B THR 3.4 11.0 - - - +
106B GLN* 3.6 22.0 - - + +
117B TYR* 4.4 1.1 - - + -
118B ASN* 1.3 81.0 + - - +
120B LYS* 1.3 69.3 + - - +
121B ILE* 4.1 18.8 - - + -
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Residues in contact with LYS 120 (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* 3.3 23.6 - - + +
104B ALA* 3.2 4.5 - - - -
105B THR* 3.0 38.5 + - - +
118B ASN* 4.5 19.2 - - - +
119B VAL* 1.3 80.1 - - - +
121B ILE* 1.3 63.2 + - - +
18D THR* 5.4 3.9 + - - +
23D HIS* 5.0 13.7 - - - -
122D ARG* 3.6 38.6 - - - +
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Residues in contact with ILE 121 (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* 4.1 13.9 - - + -
16B GLU 3.0 8.7 + - - +
17B GLY* 3.2 5.0 - - - -
18B THR 3.1 24.9 + - - +
19B VAL* 4.7 0.2 - - + -
24B PHE* 4.0 23.8 - - + -
58B LEU* 4.3 10.8 - - + -
61B SER* 3.3 35.2 - - - +
102B LEU* 3.6 33.7 - - + -
103B THR 3.5 2.5 - - - +
104B ALA* 3.4 16.4 - - + -
119B VAL* 4.1 5.4 - - + -
120B LYS* 1.3 77.1 - - - +
122B ARG* 1.3 72.3 + - - +
122D ARG* 4.6 3.3 + - - -
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Residues in contact with ARG 122 (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* 4.9 7.5 - - - -
18B THR* 3.4 32.7 - - + +
101B VAL 3.9 1.2 - - - +
102B LEU* 3.7 0.2 - - - -
103B THR* 2.8 42.9 + - - +
121B ILE* 1.3 81.5 + - - +
123B GLY* 1.3 61.3 + - - +
124B VAL* 4.3 1.7 + - + -
103D THR* 3.6 31.0 + - - +
105D THR* 2.7 43.5 + - + +
120D LYS* 3.4 53.8 + - - +
121D ILE 4.7 1.2 + - - -
122D ARG* 4.2 28.1 - - + +
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Residues in contact with GLY 123 (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* 2.7 18.6 + - - +
19B VAL* 3.2 6.7 - - - +
20B ASN 2.9 25.8 + - - -
101B VAL 3.2 9.2 - - - -
102B LEU* 4.1 9.4 - - - -
121B ILE* 4.5 0.6 - - - +
122B ARG* 1.3 72.9 - - - +
124B VAL* 1.3 67.2 + - - +
126B PHE* 4.1 12.6 - - - -
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Residues in contact with VAL 124 (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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20B ASN* 3.7 4.7 - - - -
101B VAL* 2.9 35.5 + - + +
122B ARG* 4.2 2.0 - - + -
123B GLY* 1.3 78.4 - - - +
125B ASN* 1.3 65.5 - - + +
126B PHE* 3.2 6.4 + - - -
91D GLU* 3.7 29.2 - - + +
92D ARG 4.0 15.3 - - - +
93D VAL* 3.7 34.8 - - + -
103D THR* 4.0 17.9 - - + -
104D ALA 4.3 0.7 - - - +
105D THR* 4.0 17.3 - - + -
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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