Contacts of the strand formed by residues 107 - 113 (chain A) in PDB entry 2WIJ
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 ALA 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A PRO* 3.8 25.8 - - + -
106A ASN* 1.3 77.6 - - - +
108A THR* 1.3 70.7 + - - +
138A ARG 3.8 22.0 - - - +
140A ILE* 4.0 12.1 - - + -
186A GLY 2.9 8.1 + - - +
187A GLY* 3.4 2.6 - - - -
188A ASN* 2.6 30.1 + - - +
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Residues in contact with THR 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ASN 3.7 2.2 + - - -
107A ALA* 1.3 74.6 - - - +
109A VAL* 1.3 70.4 + - - +
110A LEU* 4.2 2.7 - - + -
138A ARG 5.2 0.4 + - - -
139A VAL* 3.5 12.8 - - + +
140A ILE 3.1 22.5 + - - -
191A SER* 2.6 36.5 + - - +
193A THR* 5.0 0.4 - - - +
475A ALA* 4.0 29.2 - - + +
476A LYS* 3.6 29.3 + - + +
2C FUL 5.6 0.3 + - - -
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Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ALA 3.8 9.6 - - - +
108A THR* 1.3 78.6 - - - +
110A LEU* 1.3 61.7 + - - +
111A ILE* 3.9 22.4 - - + -
140A ILE* 3.4 16.6 - - + +
142A VAL* 4.0 18.4 - - + -
178A VAL* 4.3 9.4 - - + -
182A ILE* 3.9 24.9 - - + -
187A GLY* 4.2 0.7 - - - -
188A ASN 4.1 15.0 - - - +
191A SER 2.8 12.9 + - - +
192A VAL* 3.3 9.1 - - + +
193A THR 2.8 30.8 + - - +
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Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A THR* 4.2 5.4 - - + -
109A VAL* 1.3 77.6 - - - +
111A ILE* 1.3 62.6 + - - +
133A LEU* 4.5 22.2 - - + -
139A VAL* 4.0 28.0 - - + -
140A ILE 2.9 12.1 + - - +
141A VAL* 3.2 8.7 - - + +
142A VAL 2.9 25.6 + - - +
193A THR* 3.4 11.0 - - + +
195A PHE* 3.8 23.3 - - + -
221A ILE* 5.9 2.9 - - + -
471A TRP* 5.3 7.0 - - + +
472A ALA* 5.3 8.5 - - + +
475A ALA* 3.3 34.5 - - + -
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Residues in contact with ILE 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A VAL* 3.9 13.9 - - + -
110A LEU* 1.3 74.6 - - - +
112A TRP* 1.3 58.6 + - - +
113A ILE* 3.9 3.4 + - + +
142A VAL* 3.2 19.1 - - + +
144A MET* 3.7 29.4 - - + -
175A LEU* 3.7 26.5 - - + -
178A VAL* 4.1 25.4 - - + -
192A VAL* 3.5 26.5 - - + -
193A THR 2.9 8.5 + - - -
194A LEU* 3.4 11.9 - - + +
195A PHE* 2.8 32.9 + - - +
216A LEU 5.3 0.4 - - - +
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Residues in contact with TRP 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ILE* 1.3 71.3 - - - +
113A ILE* 1.3 67.4 + - - +
114A TYR* 3.5 22.0 + + + +
115A GLY 5.1 0.2 - - - -
123A SER* 5.4 0.7 - - - -
128A TYR* 3.5 54.9 - + + -
141A VAL* 5.2 1.6 - - + -
142A VAL 2.8 14.5 + - - +
143A SER* 3.7 29.6 - - - -
144A MET* 3.8 15.1 + - - +
195A PHE* 3.1 60.2 - + + -
196A GLY* 3.7 12.6 - - - -
197A GLU* 3.6 35.4 - - + -
223A GLN* 4.0 14.6 - - - -
442A ILE* 4.3 4.7 - - + -
446A PHE* 3.5 20.6 - + + -
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Residues in contact with ILE 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ILE* 4.5 5.2 - - + +
112A TRP* 1.3 80.2 - - - +
114A TYR* 1.3 63.2 + - - +
144A MET* 4.3 15.5 - - + -
146A TYR* 3.8 11.0 - - + -
171A GLN* 3.4 48.2 - - + +
175A LEU* 5.3 2.2 - - + -
194A LEU* 4.6 12.1 - - + -
195A PHE 2.8 13.8 + - - +
196A GLY* 3.1 21.5 - - - -
197A GLU 3.6 0.7 + - - -
200A GLY* 3.2 23.4 - - - +
203A SER* 4.0 3.4 - - - +
204A VAL* 4.3 15.3 - - + -
207A HIS* 4.0 17.5 - - + +
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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