Contacts of the strand formed by residues 103 - 108 (chain E) in PDB entry 2W8B
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 VAL 103 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E LEU* 3.8 20.7 - - + +
102E LYS* 1.3 75.8 - - - +
104E THR* 1.3 66.6 + - - +
105E VAL* 4.5 2.9 - - + -
133E LEU* 4.3 9.0 - - + -
142E GLN 2.8 15.6 + - - +
143E ILE* 3.4 18.9 - - + -
144E SER* 2.9 24.8 + - - +
171E LEU* 3.9 17.9 - - + -
172E VAL 3.5 24.7 - - - +
173E TYR* 3.7 29.2 - - + +
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Residues in contact with THR 104 (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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102E LYS* 4.1 3.0 + - - +
103E VAL* 1.3 74.3 + - - +
105E VAL* 1.3 61.9 + - - +
106E GLU* 3.9 20.9 - - + +
144E SER* 3.4 18.6 + - - +
146E VAL* 4.1 22.0 - - + -
170E VAL 3.5 1.7 - - - +
172E VAL* 2.9 38.1 + - - +
174E LEU* 3.9 31.0 + - + +
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Residues in contact with VAL 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E VAL* 4.5 10.3 - - + -
104E THR* 1.3 75.3 - - - +
106E GLU* 1.3 61.8 + - - +
126E ALA* 3.7 35.4 - - + +
129E VAL* 3.8 32.1 - - + -
133E LEU* 4.9 0.4 - - + -
143E ILE* 3.9 26.7 - - + -
144E SER 2.7 12.0 + - - +
145E ILE* 3.4 4.6 - - + -
146E VAL 2.9 24.3 + - - +
169E ALA* 3.8 13.7 - - + -
170E VAL 3.5 6.7 - - - +
171E LEU* 4.5 8.5 - - + -
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Residues in contact with GLU 106 (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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104E THR* 3.9 14.5 - - + +
105E VAL* 1.3 75.1 - - - +
107E GLY* 1.3 59.5 + - - +
108E HIS* 3.4 16.8 + - - +
126E ALA* 4.7 0.4 - - - -
146E VAL* 3.1 8.3 - - + +
148E TYR* 3.9 34.5 + - + -
169E ALA* 3.2 4.4 - - - -
170E VAL* 2.8 44.5 + - + +
172E VAL* 3.4 31.8 - - + +
174E LEU* 3.9 16.1 - - - +
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Residues in contact with GLY 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E VAL 3.9 1.6 + - - -
106E GLU* 1.3 71.2 - - - +
108E HIS* 1.3 68.6 + - - -
122E GLY* 3.3 27.6 - - - -
126E ALA* 4.2 6.3 - - - +
146E VAL 2.8 14.1 + - - -
147E SER* 3.6 0.3 - - - -
148E TYR* 3.0 26.0 + - - +
149E GLY 3.6 1.2 + - - -
168E ARG 3.7 4.7 - - - -
169E ALA* 4.4 2.5 - - - -
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Residues in contact with HIS 108 (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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106E GLU* 3.4 28.5 + - - +
107E GLY* 1.3 78.4 + - - -
109E ALA* 1.3 61.7 + - - +
122E GLY* 3.7 7.7 - - - -
125E ARG* 2.9 27.0 + - - -
148E TYR* 3.8 31.6 - + + +
149E GLY 3.4 8.2 + - - +
152E LYS* 3.5 23.3 + - + -
166E ASN 3.2 20.2 - - - +
168E ARG* 2.9 52.6 + - + +
170E VAL* 4.3 6.9 - - + +
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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