Contacts of the strand formed by residues 228 - 234 (chain A) in PDB entry 4WNC
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 LEU 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A LEU* 4.8 7.2 - - + -
161A ALA* 4.7 6.5 - - + -
170A ILE* 4.3 14.8 - - + -
173A GLY* 3.3 28.0 - - - +
175A MET* 6.5 0.2 - - + -
214A ALA* 3.7 15.9 - - + +
215A LYS* 3.7 19.6 + - - +
217A VAL* 3.7 36.1 - - + -
218A GLY 5.2 0.9 - - - +
224A LEU* 4.0 23.5 + - + +
226A GLY* 3.5 4.3 - - - +
227A LYS* 1.3 91.8 + - + +
229A THR* 1.3 66.4 + - - +
245A LEU* 4.3 13.5 - - + -
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Residues in contact with THR 229 (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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173A GLY 3.3 5.1 + - - -
174A LEU* 3.3 25.3 - - + -
175A MET* 2.9 21.0 + - - +
211A THR 5.1 3.5 + - - -
214A ALA* 3.3 17.2 - - - +
215A LYS* 4.3 22.8 + - - +
228A LEU* 1.3 77.5 - - - +
230A GLY* 1.3 70.0 + - - +
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Residues in contact with GLY 230 (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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174A LEU* 4.9 3.4 - - - -
175A MET* 3.0 22.0 - - - -
210A SER* 5.5 0.2 - - - -
211A THR* 3.8 20.6 + - - +
214A ALA* 3.7 3.4 - - - +
229A THR* 1.3 87.4 + - - +
231A MET* 1.3 65.5 + - - +
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Residues in contact with MET 231 (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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175A MET* 3.0 10.7 + - - +
176A THR* 3.3 20.2 - - - +
177A THR 3.1 20.4 + - - -
208A PRO* 4.2 10.5 - - + -
209A ALA 3.8 9.6 - - - +
210A SER* 5.0 3.1 - - - -
211A THR* 3.6 11.9 - - - +
230A GLY* 1.3 76.8 - - - +
232A ALA* 1.3 79.8 + - - +
233A PHE* 3.6 39.3 - - + -
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Residues in contact with ALA 232 (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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177A THR* 3.3 26.0 - - + +
179A HIS* 5.1 5.8 - - + -
208A PRO* 3.3 5.0 - - - +
209A ALA* 2.9 45.8 + - + +
210A SER 5.1 0.2 - - - +
211A THR* 4.1 10.1 - - + -
231A MET* 1.3 82.3 - - - +
233A PHE* 1.3 66.1 + - - +
234A ARG* 4.2 4.3 - - - +
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Residues in contact with PHE 233 (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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176A THR* 3.7 22.7 - - + -
177A THR 2.8 10.4 + - - +
178A VAL* 3.5 10.1 - - + -
179A HIS 2.8 26.9 + - - -
206A ILE* 3.8 28.3 - - + -
207A ILE 3.4 1.6 - - - -
208A PRO* 4.0 23.8 - - + -
231A MET* 3.6 29.8 - - + -
232A ALA* 1.3 74.3 - - - +
234A ARG* 1.3 61.6 + - - +
235A VAL* 3.8 6.5 + - + +
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Residues in contact with ARG 234 (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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179A HIS* 3.3 25.1 + - - +
180A ALA 3.5 13.5 - - - -
181A ILE* 5.4 0.4 - - - -
182A THR* 2.8 42.8 + - - +
184A THR* 4.4 4.9 + - - -
185A GLN* 3.1 47.7 + - + +
198A ASP* 5.7 2.5 - - - +
205A ASN 3.6 3.2 - - - +
206A ILE* 3.4 6.4 - - - -
207A ILE* 2.8 42.7 + - + +
209A ALA* 4.8 15.2 - - + +
232A ALA* 5.5 4.3 - - + +
233A PHE* 1.3 71.9 - - - +
235A VAL* 1.3 61.6 + - - +
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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