Contacts of the strand formed by residues 180 - 186 (chain A) in PDB entry 4GWR
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 VAL 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A GLU 5.7 0.2 - - - +
179A ASP* 1.3 73.9 - - - +
181A TRP* 1.3 67.7 + - - +
214A LYS 3.0 11.5 + - - +
215A VAL* 3.3 13.8 - - + +
216A LYS* 2.9 25.6 + - - +
242A ILE* 4.1 6.5 - - + -
243A PHE 3.5 12.8 - - - +
244A GLN* 4.0 17.9 - - + +
245A LYS 6.0 0.2 - - - +
268A LEU* 3.7 43.7 - - + +
272A ASN* 3.6 30.7 - - + -
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Residues in contact with TRP 181 (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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163A ILE* 3.6 34.5 - - + -
165A LEU* 4.1 9.0 - - + -
173A ASN* 3.3 42.1 + - + -
174A VAL* 3.7 37.9 - - + -
177A SER* 3.1 22.5 + - - -
179A ASP* 3.3 19.3 + - - +
180A VAL* 1.3 77.1 - - - +
182A MET* 1.3 60.8 + - - +
183A VAL* 4.0 8.3 - - + -
216A LYS* 3.4 32.3 - - + -
218A ALA* 3.8 28.9 - - + -
241A LYS 3.7 1.2 - - - +
242A ILE* 3.4 3.5 - - - +
243A PHE* 2.8 38.5 + - + +
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Residues in contact with MET 182 (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 TRP* 1.3 75.6 - - - +
183A VAL* 1.3 60.8 + - - +
200A TRP* 3.5 21.1 - - + -
215A VAL* 4.2 7.6 - - + -
216A LYS 2.8 10.1 + - - +
217A LEU* 3.3 16.9 - - + -
218A ALA 2.9 23.7 + - - -
240A ILE* 4.7 1.8 - - + -
241A LYS 3.6 4.7 - - - +
242A ILE* 4.2 18.6 - - + +
252A TYR* 4.4 11.0 - - + -
261A ILE* 4.2 17.7 - - + +
264A ARG* 3.9 30.5 - - + -
265A ALA* 4.1 29.6 - - - -
268A LEU* 4.1 11.9 - - + -
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Residues in contact with VAL 183 (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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165A LEU* 4.4 2.0 - - + -
170A PHE* 4.3 11.0 - - + -
181A TRP* 4.1 14.8 - - + -
182A MET* 1.3 78.1 - - - +
184A GLU* 1.3 62.4 + - - +
185A PHE* 3.6 27.8 + - + -
218A ALA* 3.5 21.3 - - + +
220A VAL* 3.7 25.6 - - + +
239A THR 3.7 1.2 - - - +
240A ILE* 3.3 5.5 - - - +
241A LYS 2.8 40.9 + - - +
243A PHE* 3.8 22.9 - - + -
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Residues in contact with GLU 184 (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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183A VAL* 1.3 70.7 - - - +
185A PHE* 1.3 68.9 + - - +
186A TYR* 3.6 24.6 - - - +
193A CYS* 4.0 16.1 - - - +
196A LEU* 3.7 31.1 - - + +
197A GLU* 5.4 3.9 - - - -
200A TRP* 3.6 39.3 - - + +
218A ALA 3.0 7.8 + - - +
219A ALA* 3.2 11.7 - - + +
220A VAL 2.9 24.5 + - - +
238A PRO* 4.0 6.1 - - + +
239A THR 3.7 3.6 - - - -
240A ILE* 4.0 10.8 - - + -
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Residues in contact with PHE 185 (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 PHE* 4.4 8.5 - + - -
183A VAL* 3.6 31.4 - - + -
184A GLU* 1.3 72.9 - - - +
186A TYR* 1.3 58.7 + - - +
220A VAL* 3.4 39.3 - - + +
222A ALA* 4.7 6.3 - - + -
228A LEU* 4.3 16.2 - - + -
229A ALA* 5.4 0.9 - - - -
232A TYR* 4.0 20.0 - + - -
234A ILE* 3.7 44.2 - - + -
237A PHE* 4.0 4.9 - - - -
238A PRO* 3.5 5.9 - - - +
239A THR* 2.8 40.8 + - - +
241A LYS* 4.1 20.0 - - + -
243A PHE* 4.3 3.1 - + - -
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Residues in contact with TYR 186 (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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164A GLU* 2.9 23.7 + - - -
184A GLU* 3.6 31.6 - - - +
185A PHE* 1.3 73.5 - - - +
187A ALA* 1.3 71.8 + - - +
188A PRO* 4.5 9.4 - - + -
193A CYS* 3.6 16.4 - - + -
219A ALA* 3.8 20.2 - - + -
220A VAL 3.0 37.0 + - - -
221A ASP* 3.4 28.3 + - + +
222A ALA* 3.0 27.6 + - - +
223A THR 4.3 0.2 + - - -
237A PHE* 3.6 8.7 - - - -
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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