Contacts of the strand formed by residues 83 - 89 (chain E) in PDB entry 3LAW
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 83 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10E LYS 3.5 3.0 + - - +
11E VAL* 3.5 11.5 - - + +
12E ILE* 3.3 23.0 + - - +
81E ALA* 4.8 2.8 - - - +
82E ASP* 1.3 80.8 + - - +
84E CYS* 1.3 71.6 + - - +
85E VAL* 4.5 0.2 - - - -
106E PHE* 5.1 0.2 - - - -
118E PHE* 3.6 6.4 - - - -
119E PRO* 3.5 23.8 - - + +
121E VAL* 4.4 9.2 - - - -
169E ILE* 3.6 35.4 - - - +
172E ASN* 4.7 0.7 - - - -
173E ALA* 3.5 19.5 - - + +
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Residues in contact with CYS 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E ILE* 3.8 14.8 - - - -
14E LEU* 4.0 28.0 - - - -
83E CYS* 1.3 74.6 - - - +
85E VAL* 1.3 64.1 + - - +
86E LEU* 4.1 6.5 - - - -
106E PHE* 3.6 22.0 - - + -
118E PHE* 3.4 1.1 - - + -
119E PRO 3.2 7.7 + - - -
120E PHE* 3.3 40.3 - - + -
121E VAL 2.9 25.8 + - - +
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Residues in contact with VAL 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E VAL* 3.8 12.6 - - + -
12E ILE 2.9 13.1 + - - +
13E ILE* 3.3 16.2 - - + +
14E LEU 2.7 33.3 + - - +
83E CYS* 4.5 0.9 - - - -
84E CYS* 1.3 75.3 - - - +
86E LEU* 1.3 58.6 + - - +
87E VAL* 4.4 8.5 - - + -
121E VAL* 3.4 4.5 - - + +
123E LEU* 3.7 34.8 - - + -
166E PHE* 5.1 3.6 - - + -
169E ILE* 3.0 45.1 - - + -
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Residues in contact with LEU 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E LEU* 3.4 20.2 - - + +
84E CYS* 4.1 11.7 - - - -
85E VAL* 1.3 72.5 - - - +
87E VAL* 1.3 55.7 + - - +
99E LEU* 3.6 25.1 - - + +
102E TRP* 3.8 30.5 - - + -
103E ARG* 4.4 5.4 - - + +
120E PHE* 3.8 28.7 - - + -
121E VAL 2.8 11.3 + - - +
122E VAL* 3.2 14.7 - - + +
123E LEU* 2.7 32.1 + - - +
142E TRP* 4.2 24.5 - - + -
149E ILE* 5.2 0.2 - - + -
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Residues in contact with VAL 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E ILE* 3.6 29.8 - - + -
14E LEU 2.8 12.8 + - - +
15E GLY* 3.8 17.5 - - - -
16E ASP 4.3 0.3 + - - -
19E VAL* 3.8 27.1 - - + +
21E LYS* 4.0 4.5 - - + +
24E LEU* 3.7 31.0 - - + -
85E VAL* 4.3 7.4 - - + +
86E LEU* 1.3 78.4 - - - +
88E PHE* 1.3 71.5 + - - +
95E THR 4.3 2.8 - - - +
99E LEU* 4.2 6.9 - - - +
123E LEU* 3.6 13.0 - - + +
125E ASN* 3.8 15.9 - - + -
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Residues in contact with PHE 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E VAL* 3.8 11.9 - - - -
87E VAL* 1.3 76.2 - - - +
89E ASP* 1.3 75.9 + - - +
90E VAL* 3.7 20.0 - - + -
95E THR 3.3 25.6 - - - +
96E PHE* 3.8 33.0 - + + -
99E LEU* 4.0 11.2 - - + -
122E VAL* 3.7 14.1 - - + -
123E LEU 3.2 16.4 + - - -
124E GLY* 3.5 16.6 - - - -
125E ASN* 2.8 32.6 + - - +
132E ARG* 6.0 0.2 - - - -
134E VAL* 4.1 13.0 - - + -
139E ALA* 4.1 6.1 - - + -
151E TYR* 3.5 35.2 - + - -
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Residues in contact with ASP 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 5.0 0.7 - - - +
18E GLY 3.6 4.3 - - - +
19E VAL* 3.6 16.8 - - + +
88E PHE* 1.3 79.4 - - - +
90E VAL* 1.3 57.6 + - - +
91E THR* 2.6 38.8 + - - +
92E ALA* 2.9 37.7 + - + +
95E THR* 3.0 14.9 + - + +
125E ASN 3.7 4.0 - - - -
126E LYS* 2.5 46.2 + - - +
134E VAL* 4.8 0.3 - - - +
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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