Contacts of the strand formed by residues 188 - 193 (chain A) in PDB entry 6WNX
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 THR 188 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A HIS* 3.0 19.8 + - - -
183A GLY* 3.5 3.3 - - - -
184A SER 3.2 23.4 + - - -
186A ASP* 2.5 31.1 + - - +
187A SER* 1.3 81.7 - - - +
189A VAL* 1.3 62.6 + - - +
190A ARG* 3.7 10.0 + - - +
202A THR* 4.0 15.9 - - + -
203A LEU 3.5 7.6 - - - -
204A ILE* 3.9 24.7 - - + -
210A VAL* 3.9 1.0 - - - +
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Residues in contact with VAL 189 (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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181A VAL* 3.5 27.4 - - + -
182A THR 3.0 12.1 - - - +
183A GLY* 4.5 0.7 - - - -
188A THR* 1.3 77.1 - - - +
190A ARG* 1.3 66.9 + - - +
191A VAL* 4.5 1.5 + - + +
202A THR* 3.3 4.5 - - - +
203A LEU* 2.7 52.5 + - + +
206A HIS* 5.2 3.6 - - + -
210A VAL* 3.9 26.0 - - + -
213A LEU* 4.5 3.8 - - + -
220A MET* 4.3 15.3 - - + -
222A THR* 3.9 18.8 - - + -
232A TRP* 6.1 0.7 - - + -
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Residues in contact with ARG 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLY* 3.4 33.0 + - - -
166A HIS* 3.5 32.8 + - + +
167A THR* 5.1 4.9 - - - +
181A VAL* 3.3 4.3 - - - -
182A THR* 2.8 32.9 + - - -
186A ASP* 4.8 2.4 + - - -
188A THR* 3.7 12.1 + - - +
189A VAL* 1.3 76.4 - - - +
191A VAL* 1.3 62.0 + - - +
192A TRP* 3.4 32.4 + - + +
199A VAL* 4.5 18.5 - - + +
201A ASN 3.5 3.8 - - - +
202A THR* 3.6 32.5 + - + +
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Residues in contact with VAL 191 (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 VAL* 3.6 37.2 - - + -
180A ILE 3.3 4.7 - - - +
181A VAL* 4.6 15.9 - - + -
189A VAL* 5.2 4.0 - - + -
190A ARG* 1.3 73.2 - - - +
192A TRP* 1.3 56.1 + - - +
199A VAL* 3.6 3.1 - - - +
200A LEU* 2.7 32.4 + - + -
201A ASN* 3.0 32.0 + - + +
203A LEU* 5.5 3.8 - - + -
220A MET* 5.4 2.0 - - + -
234A MET* 5.1 1.8 - - + -
237A ALA* 3.8 19.1 - - + +
240A ILE* 4.0 19.1 - - + -
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Residues in contact with TRP 192 (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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149A ILE* 3.5 27.2 - - + +
163A LEU* 3.8 24.7 - - + -
164A THR* 3.5 33.9 - - - -
165A GLY* 4.2 4.0 - - - -
166A HIS* 3.8 10.3 - + - -
179A VAL* 3.2 8.7 - - - +
180A ILE* 2.7 58.3 + - + +
182A THR* 3.0 20.1 + - - -
190A ARG* 3.4 39.2 + - + +
191A VAL* 1.3 73.1 - - - +
193A ASP* 1.3 64.8 + - - +
197A GLY 3.6 20.2 - - - +
198A GLU 3.3 8.1 - - - +
199A VAL* 3.6 22.2 - - + -
200A LEU* 4.1 4.5 - - - -
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Residues in contact with ASP 193 (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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178A ARG 4.0 7.6 - - - +
180A ILE* 4.6 2.1 - - - +
192A TRP* 1.3 71.3 - - - +
194A VAL* 1.3 58.3 + - - +
195A ASN* 3.0 42.5 + - - +
196A THR* 3.1 32.7 + - - +
197A GLY* 2.9 28.4 + - - -
198A GLU* 2.8 29.7 + - + +
200A LEU* 3.7 17.8 - - + +
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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