Contacts of the strand formed by residues 184 - 189 (chain W) in PDB entry 3D29
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 184 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218V ILE* 3.4 7.7 - - - +
219V VAL* 2.8 64.2 + - + +
221V ILE* 4.1 24.5 - - + -
42W PHE* 4.0 15.9 - - + -
176W TYR* 4.1 9.0 - - + -
177W ILE 3.3 7.4 - - - +
178W ILE* 3.9 30.5 - - + -
179W LYS 4.6 2.5 - - - +
183W GLU* 1.3 81.6 - - - +
185W VAL* 1.3 63.5 + - - +
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Residues in contact with VAL 185 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216V GLU* 3.9 18.8 - - + +
217V SER 3.5 10.3 - - - +
218V ILE* 4.4 8.1 - - + -
175W VAL 3.7 1.2 - - - +
176W TYR* 3.4 5.2 - - - +
177W ILE* 2.9 41.2 + - + +
179W LYS* 6.0 1.3 - - + -
183W GLU* 3.5 29.8 - - + +
184W VAL* 1.3 76.9 - - - +
186W LYS* 1.3 62.4 + - - +
187W ARG* 3.6 40.0 + - + +
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Residues in contact with LYS 186 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216V GLU* 3.4 2.4 - - - +
217V SER* 2.8 44.7 + - - +
219V VAL* 3.9 17.9 - - + -
32W GLU* 2.8 24.4 + - - -
174W VAL* 3.3 31.4 - - + -
175W VAL 3.4 2.9 - - - -
176W TYR* 3.2 33.2 + - + +
184W VAL 4.2 0.6 + - - -
185W VAL* 1.3 72.4 - - - +
187W ARG* 1.3 66.9 - - - +
188W TYR* 3.1 29.5 + - + -
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Residues in contact with ARG 187 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213V VAL* 4.0 17.7 - - + -
215V LYS 3.4 7.6 - - - +
216V GLU* 3.1 31.7 + - + -
152W PHE* 3.5 55.0 - - + +
174W VAL* 3.2 3.3 - - - -
175W VAL* 2.8 39.4 + - - +
177W ILE* 3.6 19.6 - - - +
185W VAL* 3.6 25.7 + - + +
186W LYS* 1.3 80.7 - - - +
188W TYR* 1.3 65.8 + - - +
189W LEU* 3.7 1.9 + - + -
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Residues in contact with TYR 188 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210K ILE* 5.9 5.8 - - + -
213V VAL* 3.6 1.9 - - - -
214V LEU* 2.6 47.8 + - + +
215V LYS* 3.1 49.1 + - + +
216V GLU* 5.9 0.2 - - - -
217V SER* 5.7 3.1 - - - -
18W LEU* 4.3 20.9 - - + -
32W GLU* 2.7 30.7 + - - -
173W ALA 3.3 13.0 - - - +
174W VAL* 4.4 4.9 - - + -
186W LYS* 3.1 36.0 + - + -
187W ARG* 1.3 77.0 - - - +
189W LEU* 1.3 56.7 - - - +
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Residues in contact with LEU 189 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211V THR* 3.7 11.0 - - + -
212V ALA 3.6 3.8 - - - +
213V VAL* 4.3 5.6 - - + -
214V LEU* 3.4 13.0 - - - +
152W PHE* 3.6 34.8 - - + -
156W SER* 3.4 30.5 - - - +
159W LEU* 4.5 3.1 - - + -
160W LEU* 4.1 25.8 - - + -
172W GLY* 4.9 3.5 - - - -
173W ALA* 3.0 34.1 + - + +
175W VAL* 3.5 20.2 - - + -
187W ARG* 4.5 2.9 - - + +
188W TYR* 1.3 79.7 - - - +
190W LYS* 1.3 62.0 + - - +
191W MET* 3.9 2.2 + - - +
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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