Contacts of the strand formed by residues 112 - 117 (chain E) in PDB entry 1J8H
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 THR 112 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E GLN* 2.9 23.0 + - - +
7E SER* 5.1 1.9 + - - +
8E SER* 2.8 35.5 + - - +
9E ARG 3.7 3.6 - - - +
11E LEU* 4.6 9.4 - - + -
21E LEU* 4.2 27.7 - - + +
22E GLU 5.3 0.3 + - - -
34E TRP* 5.0 1.6 - - - -
88E SER 3.6 0.5 - - - +
89E MET* 3.4 5.5 - - - -
90E TYR* 2.8 36.1 + - - -
111E GLY* 1.3 70.5 + - - -
113E ARG* 1.3 70.3 + - - +
114E LEU* 3.4 3.7 + - + +
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Residues in contact with ARG 113 (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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9E ARG 2.9 8.9 + - - +
10E TYR* 3.2 30.2 - - + +
11E LEU* 2.9 26.5 + - - +
37E GLN 4.4 4.4 + - - -
38E ASP* 5.8 0.2 + - - -
39E PRO* 5.7 5.9 - - - +
87E THR* 5.8 2.8 - - - +
88E SER* 3.6 15.3 + - - +
89E MET* 3.5 58.8 - - + +
112E THR* 1.3 70.4 - - - +
114E LEU* 1.3 60.5 + - - +
115E THR* 4.2 3.5 + - - +
156E ASP 5.0 5.4 - - - -
157E HIS* 3.7 26.4 + - + -
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Residues in contact with LEU 114 (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 LEU* 3.6 28.5 - - + +
13E LYS* 3.9 23.1 - - + -
19E VAL* 4.4 3.1 - - + -
21E LEU* 4.2 16.2 - - + -
79E LEU* 3.6 30.7 - - + -
86E GLN 4.3 2.7 - - - +
87E THR* 3.2 4.7 - - - +
88E SER 2.8 38.5 + - - +
90E TYR* 3.8 27.8 - - + -
112E THR* 3.4 5.1 + - + +
113E ARG* 1.3 75.3 + - - +
115E THR* 1.3 70.6 + - - +
116E VAL* 4.2 9.4 - - + -
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Residues in contact with THR 115 (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 LEU 3.1 7.4 + - - -
12E VAL* 3.5 6.4 - - - +
13E LYS 3.2 23.4 + - - +
87E THR* 3.7 20.0 - - + +
113E ARG* 4.5 3.8 + - - +
114E LEU* 1.3 74.7 + - - +
116E VAL* 1.3 64.7 + - - +
117E VAL* 3.8 15.1 + - + -
154E PHE* 5.5 1.3 - - + -
155E PRO* 3.7 23.9 - - + +
156E ASP 5.4 0.3 + - - -
157E HIS* 2.6 34.8 + - - -
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Residues in contact with VAL 116 (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 LYS* 3.3 11.7 - - + +
14E ARG 4.2 0.2 - - - -
15E THR* 3.9 24.0 - - - +
82E ALA* 4.0 20.6 - - + -
83E SER 3.4 35.7 - - - +
84E THR* 3.7 14.7 - - - +
86E GLN* 4.4 4.7 - - + -
87E THR* 2.9 25.5 + - - +
114E LEU* 4.2 22.4 - - + -
115E THR* 1.3 74.8 - - - +
117E VAL* 1.3 63.0 + - - +
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Residues in contact with VAL 117 (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 VAL* 4.2 11.4 - - + -
13E LYS 2.8 14.6 + - - +
14E ARG* 3.0 10.4 - - - -
15E THR* 3.0 23.2 + - - -
84E THR* 4.9 1.1 - - - -
115E THR* 3.9 18.6 - - + +
116E VAL* 1.3 78.4 - - - +
118E GLU* 1.3 59.5 + - - +
119E ASP 4.0 16.4 - - - +
120E LEU* 3.7 24.9 - - + -
122E LYS* 6.0 0.2 - - + -
123E VAL* 4.9 2.7 - - + -
154E PHE* 3.7 34.8 - - + -
155E PRO* 4.8 1.6 - - + -
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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