Contacts of the strand formed by residues 170 - 179 (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 ILE 170 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ALA* 3.8 38.6 - - + +
164A ILE* 4.0 24.0 - - + -
165A HIS* 3.1 21.4 + - + +
169A GLY* 1.3 70.9 - - - -
171A VAL* 1.3 64.5 + - - +
172A GLU* 3.7 26.7 - - - +
173A GLY 4.2 2.2 - - - +
224A LEU* 4.0 17.7 - - + +
227A LYS* 3.7 16.5 - - + +
228A LEU* 4.3 12.8 - - + -
245A LEU* 4.8 11.4 - - + -
247A CYS* 4.2 8.3 - - + -
248A ARG 3.7 4.9 - - - +
249A LEU* 4.3 4.0 - - + -
250A GLU* 5.7 0.4 - - - -
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Residues in contact with VAL 171 (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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170A ILE* 1.3 73.7 - - - +
172A GLU* 1.3 63.8 + - + +
227A LYS* 3.5 25.5 + - - +
248A ARG* 2.8 50.2 + - + +
249A LEU 3.9 3.8 - - - +
250A GLU* 3.7 41.3 - - + +
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Residues in contact with GLU 172 (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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170A ILE* 3.5 6.9 - - - -
171A VAL* 1.3 82.1 - - - +
173A GLY* 1.3 59.3 + - - +
227A LYS* 3.3 14.8 - - - +
247A CYS* 3.3 2.8 - - - +
248A ARG* 2.9 72.1 + - + +
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Residues in contact with GLY 173 (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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172A GLU* 1.3 76.1 - - - +
174A LEU* 1.3 66.4 + - - +
227A LYS 2.8 9.2 + - - +
228A LEU* 3.3 39.7 - - - +
229A THR 3.3 3.9 + - - -
245A LEU* 4.5 1.6 - - - -
246A THR 3.2 11.0 - - - -
247A CYS* 4.0 5.8 - - - -
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Residues in contact with LEU 174 (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* 1.3 77.0 - - - +
175A MET* 1.3 62.1 + - - +
229A THR* 3.3 37.2 - - + +
230A GLY* 4.6 3.4 - - - +
244A ASP 3.9 0.9 - - - +
245A LEU* 3.8 2.0 - - - -
246A THR* 2.8 41.2 + - + +
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Residues in contact with MET 175 (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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153A THR* 3.8 23.8 - - + -
157A LEU* 3.8 25.4 - - + -
174A LEU* 1.3 76.3 - - - +
176A THR* 1.3 71.1 + - - +
177A THR* 3.9 14.4 - - + +
211A THR* 4.2 11.0 - - + -
214A ALA* 4.2 14.8 - - + +
229A THR 2.9 12.4 + - - +
230A GLY* 3.0 26.3 - - - -
231A MET* 3.0 37.3 + - - +
243A VAL* 4.0 20.2 - - + -
244A ASP 3.4 9.9 - - - +
245A LEU* 4.6 6.1 - - + -
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Residues in contact with THR 176 (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* 1.3 78.9 + - - +
177A THR* 1.3 70.2 + - - +
178A VAL* 4.2 8.6 + - + -
231A MET* 3.3 17.9 - - - +
233A PHE* 3.7 35.4 - - + -
242A VAL 4.1 0.2 - - - +
243A VAL* 3.6 0.9 - - - -
244A ASP* 2.7 49.7 + - + +
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Residues in contact with THR 177 (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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153A THR* 4.2 16.2 - - + +
175A MET* 3.9 10.5 - - + +
176A THR* 1.3 76.5 - - - +
178A VAL* 1.3 66.2 + - - +
179A HIS* 3.7 8.2 + - + +
211A THR* 4.8 2.7 - - + -
231A MET 3.1 6.9 + - - +
232A ALA* 3.4 24.0 - - + -
233A PHE 2.8 28.1 + - - +
242A VAL 3.1 13.4 + - - -
243A VAL* 4.2 10.8 - - - -
314A TYR* 2.8 24.3 + - - +
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Residues in contact with VAL 178 (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* 4.6 12.3 - - + +
177A THR* 1.3 72.9 - - - +
179A HIS* 1.3 61.3 + - - +
233A PHE* 3.5 11.9 - - + +
235A VAL* 3.9 31.4 - - + -
240A VAL 4.8 0.2 - - - +
241A SER* 3.4 3.8 - - - -
242A VAL* 2.8 53.2 + - + +
244A ASP* 6.0 3.8 - - + -
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Residues in contact with HIS 179 (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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152A CYS* 3.9 22.3 - - - -
153A THR* 3.8 7.9 - - - -
177A THR* 4.1 13.7 - - + +
178A VAL* 1.3 74.7 - - - +
180A ALA* 1.3 91.4 + - - +
182A THR* 3.9 20.0 - - + -
232A ALA* 5.1 2.7 - - + -
233A PHE 2.8 15.8 + - - +
234A ARG* 3.3 24.9 + - - +
235A VAL* 3.0 27.0 + - - -
240A VAL 4.9 0.2 - - - -
241A SER* 3.3 14.5 + - - -
314A TYR* 3.3 24.9 + - - -
316A ASN* 3.9 16.4 - - + +
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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