Contacts of the strand formed by residues 210 - 215 (chain B) in PDB entry 4LIR
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 TRP 210 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ILE* 3.8 30.3 - - + +
234A GLU 3.6 19.5 - - - -
235A SER 3.7 14.6 - - - -
237A MSE 3.6 27.2 - - + +
177B THR* 4.1 3.1 - - + -
178B VAL 3.2 12.8 - - - +
179B PHE* 3.6 11.4 - - + -
181B PHE* 3.6 8.5 - - - -
204B MSE 4.1 1.9 - - - +
205B SER* 2.9 49.4 + - - -
207B THR* 4.2 6.3 - - - -
208B GLY* 3.1 24.8 + - - +
209B ASN* 1.4 101.9 - - - +
211B MSE 1.3 62.0 + - - +
212B HIS* 3.7 35.1 + + - -
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Residues in contact with MSE 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B THR* 3.3 4.1 - - - +
178B VAL* 2.8 48.8 + - + +
181B PHE* 3.4 29.4 - - + -
186B ALA 3.4 25.6 - - - +
189B ILE* 3.9 14.4 - - + -
190B LEU* 3.9 13.0 - - - +
203B VAL 3.2 12.8 - - - +
204B MSE 3.6 33.7 - - + -
210B TRP* 1.3 76.9 - - - +
212B HIS* 1.3 63.1 + - - +
213B ILE* 3.8 25.0 + - + -
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Residues in contact with HIS 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A MSE 5.4 1.6 - - + -
175B TRP* 3.8 23.1 - - + -
176B VAL 3.4 4.0 - - - +
177B THR* 2.8 30.0 + - + +
202B HIS* 3.1 5.7 - - - +
203B VAL* 2.7 48.0 + - + +
205B SER* 5.9 1.8 - - - -
210B TRP* 3.7 33.4 + + - -
211B MSE 1.3 70.5 - - - +
213B ILE* 1.3 60.4 + - - +
241B LYS* 6.2 0.4 - - - -
243B CYS* 3.5 14.1 - - - -
244B ILE 5.7 0.7 - - - -
245B ASP* 3.9 22.6 + - + -
248B VAL* 4.0 25.6 - - + -
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Residues in contact with ILE 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B SER 3.8 1.4 - - - +
175B TRP* 3.3 4.5 - - - -
176B VAL* 2.8 47.5 + - + +
178B VAL* 3.8 16.8 - - + -
190B LEU* 4.1 13.0 - - + -
193B PHE* 3.8 27.4 - - + -
199B ILE* 3.7 28.9 - - + -
201B LYS 3.7 2.7 - - - -
202B HIS* 4.4 2.2 - - + -
211B MSE 3.8 31.0 - - + -
212B HIS* 1.3 78.1 - - - +
214B ARG* 1.3 64.0 + - - +
215B TYR* 3.7 23.1 + - + +
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Residues in contact with ARG 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B LEU* 4.7 17.0 + - - +
174B SER* 3.7 13.0 + - - +
175B TRP* 3.5 48.6 - - + +
199B ILE* 3.5 4.9 - - - -
200B LEU* 2.8 55.7 + - - +
201B LYS* 2.8 24.0 + - - +
213B ILE* 1.3 71.8 - - - +
215B TYR* 1.3 69.0 + - - +
252B SER* 4.1 23.0 - - - -
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Residues in contact with TYR 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B SER* 2.8 32.2 + - - +
176B VAL* 3.8 10.8 - - + -
193B PHE* 2.7 51.9 + - - +
196B TYR* 4.0 3.9 - - + -
197B GLY 3.9 17.0 - - - -
198B ASN 3.4 13.9 - - - -
199B ILE* 3.9 12.1 - - + -
200B LEU* 3.7 10.9 - - - +
213B ILE* 3.7 18.5 - - + +
214B ARG* 1.3 77.1 - - - +
216B GLN* 1.3 63.6 + - - +
217B SER 3.2 16.2 + - - +
220B GLN* 3.7 19.7 - - + -
221B ALA* 3.7 16.2 - - + +
224B ALA* 3.5 25.4 - - + +
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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