Contacts of the strand formed by residues 114 - 124 (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 CYS 114 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C HIS* 3.6 20.9 - - - -
11C MET* 3.9 2.5 - - - -
12C LYS* 3.9 28.0 - - - +
110C LEU* 3.4 8.4 - - - +
111C GLN 3.0 36.2 + - - +
112C ASP 3.1 4.6 - - - +
113C GLY* 1.3 82.4 - - - +
115C LEU* 1.3 74.2 + - - +
116C ILE* 3.5 14.2 + - + +
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Residues in contact with LEU 115 (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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5C ILE* 4.3 1.1 - - + -
9C MET* 3.8 19.3 - - + -
10C HIS 2.9 13.6 + - - +
11C MET* 3.0 13.8 - - + +
12C LYS 2.8 27.2 + - - +
68C THR* 4.0 16.2 - - + -
69C PHE* 3.5 37.5 - - + -
84C PHE* 3.3 39.9 - - + -
108C THR* 4.4 4.9 - - + -
109C SER 3.4 5.8 - - - +
110C LEU* 3.9 9.9 - - + -
113C GLY 4.3 0.4 + - - -
114C CYS* 1.3 71.3 - - - +
116C ILE* 1.3 60.1 + - - +
117C TYR* 3.9 13.5 - - + +
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Residues in contact with ILE 116 (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* 3.4 46.2 - - + +
14C TYR* 4.0 20.9 - - + -
107C ASP 3.3 4.5 - - - +
108C THR* 3.6 0.3 - - - -
109C SER* 2.7 47.8 + - - +
111C GLN* 4.0 28.7 - - + +
114C CYS* 4.0 17.0 - - + +
115C LEU* 1.3 74.9 - - - +
117C TYR* 1.3 63.6 + - - +
118C ASN* 4.0 18.4 + - - +
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Residues in contact with TYR 117 (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* 3.9 23.1 - - + -
12C LYS 2.9 12.5 + - - +
13C LEU* 3.3 22.6 - - + -
14C TYR* 2.8 35.6 + - - -
41C MET* 4.6 1.6 - - - -
62C PHE 3.7 15.5 - - - -
63C NRQ 4.9 0.2 - - - -
66C SER* 2.7 45.9 + - - -
68C THR* 4.8 2.4 + - - -
69C PHE* 3.2 19.6 - - - -
88C PHE* 6.1 0.2 - + - -
106C GLN* 3.5 22.9 - - - +
107C ASP 3.3 3.8 - - - -
108C THR* 3.6 26.9 - - + -
115C LEU* 3.9 17.0 - - + +
116C ILE* 1.3 78.6 - - - +
118C ASN* 1.3 57.2 + - - +
119C VAL* 4.1 1.3 - - + -
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Residues in contact with ASN 118 (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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14C TYR* 3.4 24.6 + - - +
105C THR 3.8 1.0 - - - +
106C GLN* 3.2 3.3 - - - -
107C ASP* 3.0 48.1 + - + +
109C SER* 5.5 0.9 + - - -
116C ILE* 4.0 15.8 - - - +
117C TYR* 1.3 75.4 - - - +
119C VAL* 1.3 62.3 + - - +
120C LYS* 4.9 8.8 + - + +
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Residues in contact with VAL 119 (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* 3.5 33.7 - - + -
14C TYR 2.7 14.3 + - - +
15C MET* 3.2 13.9 - - + -
16C GLU* 3.0 25.8 + - - +
61C SER* 3.8 20.4 - - - +
90C TRP* 4.4 4.7 - - + -
104C ALA* 4.9 0.2 - - + -
105C THR 3.5 8.7 - - - +
106C GLN* 4.0 16.8 - - + -
117C TYR* 4.7 0.2 - - + -
118C ASN* 1.3 77.9 - - - +
120C LYS* 1.3 66.8 + - - +
121C ILE* 3.9 23.6 - - + -
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Residues in contact with LYS 120 (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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18A THR* 4.0 12.1 + - - +
23A HIS* 6.2 3.1 - - - -
122A ARG* 3.3 42.2 - - - +
16C GLU* 3.4 13.9 - - + +
104C ALA* 3.2 4.5 - - - +
105C THR* 2.7 61.3 + - - +
106C GLN* 5.1 1.8 - - - +
107C ASP* 6.3 0.6 - - - +
118C ASN* 4.9 10.0 + - + +
119C VAL* 1.3 77.3 - - - +
121C ILE* 1.3 61.7 + - - +
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Residues in contact with ILE 121 (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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122A ARG* 4.7 3.2 + - - -
15C MET* 3.8 29.4 - - + -
16C GLU 3.0 7.9 + - - +
17C GLY* 3.2 23.1 - - - -
18C THR 3.4 2.3 + - - +
19C VAL* 4.6 7.4 - - + -
24C PHE* 4.4 5.6 - - + -
58C LEU* 4.1 15.9 - - + -
61C SER* 3.4 35.2 - - - +
102C LEU* 3.6 28.0 - - + -
103C THR 3.6 3.4 - - - -
104C ALA* 3.8 13.0 - - + -
119C VAL* 3.9 8.7 - - + -
120C LYS* 1.3 74.7 - - - +
122C ARG* 1.3 75.2 + - - +
123C GLY 4.5 1.3 - - - +
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Residues in contact with ARG 122 (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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103A THR* 3.7 34.0 + - - +
105A THR* 2.5 45.1 + - + -
120A LYS* 3.4 45.5 + - - +
121A ILE 4.7 0.8 - - - +
122A ARG* 4.4 27.4 - - + +
17C GLY* 4.9 4.6 - - - -
18C THR* 3.4 33.1 + - - +
23C HIS* 6.3 0.4 - - - -
101C VAL 3.8 1.6 - - - +
102C LEU* 3.6 0.4 - - - -
103C THR* 2.8 43.4 + - - +
121C ILE* 1.3 84.9 + - - +
123C GLY* 1.3 59.0 + - - +
124C VAL* 4.2 1.5 + - + -
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Residues in contact with GLY 123 (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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91A GLU* 4.7 0.3 - - - +
105A THR* 5.2 1.0 - - - +
18C THR* 2.7 17.7 + - - +
19C VAL* 3.4 7.5 - - - +
20C ASN* 2.8 26.6 + - - -
21C ASN 4.9 0.2 + - - -
101C VAL 3.3 8.5 - - - -
102C LEU* 4.0 8.3 - - - +
122C ARG* 1.3 72.1 - - - +
124C VAL* 1.3 67.2 + - - +
126C PHE* 4.0 14.8 - - - -
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Residues in contact with VAL 124 (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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91A GLU* 3.6 35.4 - - + -
92A ARG* 3.9 15.9 - - - +
93A VAL* 3.7 35.9 - - + +
103A THR* 4.2 15.9 - - + -
105A THR* 4.0 13.9 - - + -
175A LYS 5.5 0.2 - - - +
20C ASN* 3.5 1.8 - - - -
101C VAL* 2.9 37.4 + - + +
122C ARG* 4.2 1.8 + - + -
123C GLY* 1.3 78.9 - - - +
125C ASN* 1.3 67.8 + - + +
126C PHE* 3.2 6.5 + - - -
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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