Contacts of the strand formed by residues 176 - 186 (chain A) in PDB entry 1WKB
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 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A PHE* 4.2 15.3 - - + -
170A LEU* 3.8 13.4 + - + -
171A LYS* 3.7 36.9 - - + +
174A GLY* 4.4 5.2 - - - -
175A TYR* 1.3 86.9 - - - +
177A VAL* 1.3 66.5 + - - +
465A TRP* 3.5 33.5 - - + -
466A PHE 3.3 10.3 - - - +
467A ILE* 3.9 19.3 - - + -
508A CYS* 4.6 3.4 - - - -
520A TRP* 3.6 22.2 - - + -
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Residues in contact with VAL 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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174A GLY 4.5 7.9 - - - +
175A TYR 4.1 0.2 + - - -
176A ILE* 1.3 79.7 - - - +
178A LYS* 1.3 75.6 + - - +
465A TRP* 3.5 6.9 - - - -
466A PHE* 2.6 49.6 + - + +
468A ASP* 4.1 25.6 - - + +
505A LYS* 4.7 17.0 - - + -
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Residues in contact with LYS 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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177A VAL* 1.3 88.3 - - - +
179A GLY* 1.3 61.0 - - - +
462A HIS 4.0 4.0 - - - +
463A ASP* 3.6 38.1 - - + +
464A GLN 3.3 3.8 - - - +
465A TRP* 3.3 45.4 - - + +
521A ASP* 5.1 3.2 + - - -
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Residues in contact with GLY 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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177A VAL* 5.2 0.7 - - - -
178A LYS* 1.3 78.2 - - - +
180A ALA* 1.3 62.8 + - - -
181A HIS 4.0 0.2 + - - -
462A HIS 3.1 15.3 - - - -
464A GLN* 2.9 32.5 + - - +
466A PHE* 3.8 10.9 - - - -
505A LYS* 5.2 3.6 - - - -
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Residues in contact with ALA 180 (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 GLY* 1.3 71.3 - - - -
181A HIS* 1.3 64.6 + - - +
460A ILE* 4.7 8.3 - - + -
461A ILE 3.1 13.0 - - - +
462A HIS* 4.0 17.0 - - + +
466A PHE* 3.4 14.2 - - - -
505A LYS* 5.0 4.8 + - - +
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Residues in contact with HIS 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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179A GLY 4.0 0.2 + - - -
180A ALA* 1.3 78.0 - - - +
182A ARG* 1.3 97.8 + - - +
183A VAL* 4.1 7.7 - - + +
460A ILE* 3.2 6.5 - - - +
461A ILE* 2.7 37.9 + - + +
464A GLN* 3.4 41.3 + - + +
466A PHE* 4.0 9.3 - + + -
507A ALA* 3.9 20.9 - - + -
510A ARG* 4.8 5.6 - - - -
905A SO4 4.0 15.2 + - - -
906A SO4 5.8 1.3 + - - -
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Residues in contact with ARG 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 HIS* 1.3 99.0 + - - +
183A VAL* 1.3 64.0 + - - +
206A ILE* 3.0 43.0 + - + +
208A ASP* 3.7 9.9 + - - -
441A TYR* 3.5 46.8 + - + +
458A ILE* 3.6 24.7 - - + -
459A LYS 3.3 6.1 - - - +
460A ILE* 4.3 3.6 - - + -
906A SO4 2.8 39.2 + - - -
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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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181A HIS* 4.1 14.8 - - + +
182A ARG* 1.3 79.5 - - - +
184A ARG* 1.3 74.3 + - - +
185A TRP* 4.2 18.8 - - + -
192A PRO* 4.8 7.2 - - + -
193A LEU 5.9 1.3 - - - +
195A ASP* 6.1 0.4 - - - +
206A ILE* 4.9 3.8 - - - -
458A ILE* 3.4 7.2 - - - -
459A LYS* 2.9 36.7 + - + +
461A ILE* 3.9 33.2 - - + -
464A GLN* 4.2 4.9 - - - +
524A TRP* 6.0 0.2 - - + -
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Residues in contact with ARG 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 82.8 - - - +
185A TRP* 1.3 60.2 + - - +
192A PRO* 3.7 0.7 - - - +
193A LEU* 3.0 40.9 + - + +
195A ASP* 3.1 43.1 + - - +
198A LEU* 4.2 24.7 - - - -
201A GLY 5.8 0.4 + - - -
202A GLU 5.6 2.2 + - - -
204A VAL 3.3 25.1 + - - -
206A ILE* 3.7 22.5 - - + +
443A PHE* 3.6 29.2 - - + -
448A VAL* 4.4 5.8 - - + +
456A ALA* 4.8 1.8 - - + -
457A VAL 3.8 2.7 - - - -
906A SO4 2.5 42.4 + - - -
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Residues in contact with TRP 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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183A VAL* 4.1 10.1 - - + +
184A ARG* 1.3 75.5 - - - +
186A ASP* 1.3 82.4 + - - +
187A PRO* 3.5 1.6 - - - +
190A GLY* 3.5 15.6 - - - -
191A THR 3.6 9.2 - - - -
192A PRO* 3.4 43.1 - - + -
193A LEU* 3.8 6.5 - - - +
275A PHE* 4.2 7.2 - + - -
456A ALA* 3.3 4.4 - - - +
457A VAL* 2.8 51.9 + - + +
459A LYS* 3.6 42.8 - - + -
461A ILE* 4.6 11.4 - - + -
511A LYS* 6.1 1.3 - - - -
908A SO4 2.8 42.9 + - - -
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Residues in contact with ASP 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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185A TRP* 1.3 73.5 - - - +
187A PRO* 1.3 59.4 - - - +
188A VAL* 2.8 35.5 + - - +
189A VAL* 2.9 20.0 + - + -
190A GLY* 2.7 34.1 + - - -
191A THR* 3.0 13.5 + - + +
193A LEU* 3.7 21.1 - - + +
450A SER* 2.5 26.2 + - - +
452A PHE* 3.4 10.7 - - + -
454A ASN* 3.2 17.0 - - - +
456A ALA* 4.9 1.6 - - - +
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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