Contacts of the strand formed by residues 202 - 207 (chain F) in PDB entry 2W8B
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 LEU 202 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F VAL* 4.0 21.1 - - + +
180F TYR* 3.8 23.3 - - + +
181F GLU 3.9 3.1 - - - -
182F LEU* 3.7 35.0 - - + +
196F HIS* 3.9 16.6 - - + +
198F SER* 3.7 20.0 - - - -
200F GLN 4.0 1.3 - - - +
201F PRO* 1.3 79.6 - - - +
203F MET* 1.3 64.2 + - - +
216F TYR* 4.4 8.7 - - + -
217F VAL 3.2 5.6 - - - +
218F THR* 3.6 29.4 - - - -
423F PHE* 3.6 17.0 - - - -
151G GLU* 5.0 0.5 - - - +
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Residues in contact with MET 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F VAL* 4.9 1.3 - - - -
202F LEU* 1.3 81.2 - - - +
204F SER* 1.3 69.1 + - - +
205F PRO* 3.5 4.9 - - - -
216F TYR* 3.6 3.9 - - - +
217F VAL* 2.8 42.7 + - + -
219F PHE* 3.8 29.8 - - + -
245F HIS* 4.2 5.6 - - - -
423F PHE* 3.9 8.7 - - + -
115G PRO* 3.8 26.2 - - + +
116G GLU* 3.7 27.8 - - + +
119G ILE* 4.2 12.6 - - + -
151G GLU* 3.7 35.9 - - + +
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Residues in contact with SER 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203F MET* 1.3 77.9 - - - +
205F PRO* 1.3 76.1 - - - +
206F ALA* 4.4 0.2 - - - +
215F ALA 3.5 0.7 - - - +
216F TYR* 4.0 0.2 - - - -
217F VAL* 4.8 0.4 - - - -
248F ALA* 4.4 1.8 - - - -
249F PRO* 3.3 31.7 - - - +
423F PHE* 3.3 20.2 - - - -
116G GLU* 2.8 39.9 + - - +
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Residues in contact with PRO 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F ALA* 4.1 19.7 - - + -
170F VAL* 4.6 3.8 - - + -
182F LEU* 3.9 27.4 - - + -
203F MET 3.5 3.4 - - - -
204F SER* 1.3 92.6 - - - +
206F ALA* 1.3 59.5 + - - +
214F LEU* 4.3 8.1 - - + -
215F ALA 3.0 11.0 - - - +
216F TYR* 4.1 4.5 - - + -
423F PHE* 3.2 36.1 - - + +
424F PRO 5.2 0.4 - - - +
425F ALA* 3.3 18.3 - - + +
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Residues in contact with ALA 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205F PRO* 1.3 76.8 - - - +
207F TRP* 1.3 62.0 + - - +
214F LEU* 3.3 7.1 - - - +
215F ALA* 2.8 32.5 + - + +
249F PRO* 3.5 40.8 - - + +
250F ALA* 4.3 8.5 - - - -
251F PHE* 3.5 5.9 - - + -
425F ALA* 4.8 3.1 - - - -
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Residues in contact with TRP 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F ARG* 3.9 24.0 - - + -
167F ILE 4.0 14.1 - - - -
168F ALA* 3.9 4.5 - - + +
184F VAL* 3.9 30.7 - - + -
206F ALA* 1.3 74.2 - - - +
208F SER* 1.3 61.3 + - - +
209F PRO* 3.8 0.7 - - - +
211F GLY* 3.3 34.1 - - - -
213F LYS 3.5 6.3 - - - -
214F LEU* 3.5 16.8 - - + +
231F LEU* 3.5 15.5 - - + -
251F PHE* 3.3 16.7 + - - +
425F ALA* 3.0 30.2 + - + -
426F TRP 3.4 20.2 - - - +
427F SER* 3.5 24.9 - - - +
428F PRO* 3.6 16.2 - - + -
430F LEU* 5.6 1.1 - - + -
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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