Contacts of the strand formed by residues 214 - 218 (chain A) in PDB entry 1WI5
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 GLY 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A GLU* 2.9 33.0 + - - +
212A ASP 3.5 1.2 - - - -
213A HIS* 1.3 83.7 - - - +
215A TYR* 1.3 74.4 + - - -
227A PHE* 3.2 7.3 - - - -
228A LEU 3.1 14.8 - - - -
230A LEU* 3.9 7.6 - - - +
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Residues in contact with TYR 215 (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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207A VAL* 4.8 9.2 - - + -
209A SER 4.1 4.9 - - - +
210A LEU* 3.1 38.6 - - + -
211A GLU 4.5 2.7 - - - +
214A GLY* 1.3 78.5 - - - -
216A LEU* 1.3 68.0 - - - +
217A VAL* 3.7 2.1 + - + +
227A PHE* 3.8 1.9 - - - -
228A LEU* 2.9 40.8 + - + +
230A LEU* 3.6 28.3 - - + +
233A ALA* 3.0 35.9 - - + -
234A GLN* 5.0 4.3 + - - +
237A ILE* 3.3 17.5 - - + +
245A LYS* 5.7 3.4 - - - -
246A LEU* 3.7 22.8 + - + -
252A LEU* 5.4 1.3 - - + -
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Residues in contact with LEU 216 (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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207A VAL* 3.3 9.5 - - - +
208A SER* 3.0 30.5 + - - -
209A SER* 3.4 25.5 + - - +
211A GLU* 3.6 31.4 - - + +
213A HIS* 4.9 2.5 - - + -
215A TYR* 1.3 77.3 - - - +
217A VAL* 1.3 62.7 + - - +
225A ARG* 5.5 7.2 - - + -
226A ALA 3.4 22.2 - - - +
227A PHE* 4.6 13.9 - - + -
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Residues in contact with VAL 217 (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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205A GLY* 3.5 31.6 - - - -
206A THR 3.7 3.4 - - - +
207A VAL* 5.7 1.1 - - + -
208A SER* 5.3 1.6 - - - -
215A TYR* 4.1 10.8 - - + +
216A LEU* 1.3 79.2 - - - +
218A ASP* 1.3 65.8 + - - +
219A ILE* 3.6 6.6 + - + +
226A ALA* 3.3 25.7 + - + +
228A LEU* 4.3 13.0 - - + +
252A LEU* 5.2 5.4 - - + -
254A CYS* 3.9 20.2 - - + -
268A LEU* 3.6 33.0 - - + -
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Residues in contact with ASP 218 (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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204A THR 4.5 1.7 - - - +
205A GLY* 3.4 23.2 - - - -
206A THR* 2.7 35.0 + - - +
208A SER* 4.5 17.1 + - - +
216A LEU 4.2 0.2 + - - -
217A VAL* 1.3 70.6 - - - +
219A ILE* 1.3 64.6 + - - +
220A GLY* 3.3 15.1 + - - -
280A ALA* 5.1 13.7 - - - +
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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