Contacts of the strand formed by residues 196 - 202 (chain A) in PDB entry 2WIN
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 PHE 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A GLY 3.5 14.1 - - - -
107A TYR* 3.5 11.9 - + + -
108A LEU* 3.4 67.8 - - + +
109A PHE* 6.4 0.9 - + - -
110A ILE* 4.1 7.4 - - + +
184A ILE 3.7 0.7 - - - +
185A ARG* 3.3 0.3 - - - -
186A ALA 2.8 37.2 + - - +
188A TYR* 4.9 4.7 - + - -
194A GLN* 3.3 47.3 - - + -
195A VAL* 1.3 75.6 - - - +
197A SER* 1.3 66.3 + - - +
597A VAL* 5.4 7.6 - - + -
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Residues in contact with SER 197 (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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110A ILE* 4.4 1.8 - - - +
183A LYS* 3.8 20.4 - - - +
184A ILE 3.2 9.0 - - - -
185A ARG* 3.2 29.5 + - - +
195A VAL* 4.1 3.5 + - - +
196A PHE* 1.3 80.0 + - - +
198A THR* 1.3 66.8 + - - +
199A GLU* 5.8 1.1 - - - -
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Residues in contact with THR 198 (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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110A ILE* 3.3 48.6 + - + +
112A THR* 5.0 13.8 - - + +
183A LYS* 3.8 0.3 - - - -
184A ILE* 3.0 34.7 + - - +
197A SER* 1.3 78.4 + - - +
199A GLU* 1.3 70.6 + - - +
200A PHE* 4.1 1.0 + - - -
587A ASN* 4.0 24.0 - - + +
588A LYS 5.9 0.4 - - - +
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Residues in contact with GLU 199 (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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112A THR* 5.2 1.7 + - - -
115A THR* 4.9 1.6 - - - +
181A GLN* 4.2 24.6 - - - +
182A TRP 3.1 15.5 - - - +
183A LYS* 3.9 28.3 + - + -
197A SER* 5.8 0.7 - - - -
198A THR* 1.3 82.7 - - - +
200A PHE* 1.3 60.9 + - - +
584A ASN* 5.9 0.3 + - - -
587A ASN* 3.2 45.0 + - - +
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Residues in contact with PHE 200 (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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112A THR* 4.7 12.8 - - + +
115A THR* 3.7 8.3 - - - +
117A TYR* 3.4 35.7 - + + -
123A VAL* 4.0 12.8 - - + -
145A ILE* 4.6 3.4 - - + -
171A TRP* 4.5 10.5 - + - -
173A ILE* 4.0 14.1 - - + -
181A GLN* 4.3 1.6 - - - -
182A TRP* 3.0 67.8 + + + +
183A LYS 4.4 0.9 - - - -
184A ILE* 3.5 40.2 - - + -
198A THR 4.5 1.3 - - - -
199A GLU* 1.3 76.6 - - - +
201A GLU* 1.3 60.2 + - - +
202A VAL* 3.8 17.3 - - + -
584A ASN* 5.6 0.4 - - - +
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Residues in contact with GLU 201 (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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115A THR 3.2 7.1 + - - -
116A ILE* 3.1 25.8 - - + +
117A TYR* 2.8 26.3 + - - -
180A GLY* 3.3 17.6 - - - +
181A GLN* 3.7 28.5 + - - +
200A PHE* 1.3 72.9 - - - +
202A VAL* 1.3 67.9 + - - +
203A LYS* 3.9 18.5 - - - +
583A LEU 4.7 3.6 - - - +
584A ASN* 3.7 26.8 + - - +
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Residues in contact with VAL 202 (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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117A TYR* 3.3 10.1 - - + +
119A PRO* 4.1 23.3 - - + -
173A ILE* 3.8 28.9 - - + -
177A VAL* 4.7 9.0 - - + -
178A ASN 4.6 1.8 - - - +
179A MET* 3.2 14.7 - - + +
180A GLY* 2.9 30.1 + - - +
182A TRP* 3.3 36.1 - - + +
200A PHE* 3.8 11.0 + - + -
201A GLU* 1.3 75.9 - - - +
203A LYS* 1.3 64.8 + - - +
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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