Contacts of the helix formed by residues 200 - 214 (chain B) in PDB entry 4BLV
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 200 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170B LYS* 6.3 0.4 - - - +
173B TYR* 5.5 1.5 + - - -
198B VAL* 4.8 0.4 - - - -
199B VAL* 1.3 98.8 - - + +
201B ARG* 1.3 67.4 + - - +
202B GLN* 3.1 6.6 + - + +
203B GLN* 3.1 35.9 + - + +
204B ILE* 3.7 7.1 + - - +
230B SER 3.9 1.6 - - - +
231B ASP* 3.9 33.7 - - + +
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Residues in contact with ARG 201 (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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198B VAL* 3.8 26.3 - - - +
199B VAL 4.0 1.8 + - - -
200B LEU* 1.3 73.1 - - - +
202B GLN* 1.3 62.2 + - - +
204B ILE* 3.1 9.8 + - - +
205B LYS* 2.9 49.8 + - - +
223B GLU* 2.9 43.2 + - - -
229B ASP* 2.7 51.1 + - + +
230B SER 5.4 1.2 + - - -
237B ALA* 4.8 1.8 - - - +
271B HIS* 4.2 6.5 - - - -
1283B EDO 2.9 41.9 + - - -
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Residues in contact with GLN 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B LEU* 3.1 4.1 + - + -
201B ARG* 1.3 80.8 - - + +
203B GLN* 1.3 61.2 + - + +
205B LYS* 3.7 37.8 - - - +
206B ARG* 2.9 39.0 + - - +
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Residues in contact with GLN 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LYS* 3.0 44.6 - - - +
173B TYR* 3.6 48.7 - - + +
200B LEU* 3.1 30.2 + - + +
202B GLN* 1.3 77.6 - - + +
204B ILE* 1.3 60.4 + - + +
206B ARG* 3.6 19.2 + - - +
207B MET* 3.0 27.7 + - - +
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Residues in contact with ILE 204 (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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173B TYR* 3.6 23.6 - - + +
196B TYR* 3.8 31.4 - - + -
197B PRO 3.3 27.1 - - - +
198B VAL* 4.4 9.6 - - + -
199B VAL 5.4 0.2 - - - +
200B LEU 4.2 9.4 - - - +
201B ARG* 3.1 12.7 + - - +
203B GLN* 1.3 75.4 - - - +
205B LYS* 1.3 65.7 + - - +
207B MET* 3.6 15.1 - - + +
208B ILE* 2.9 45.1 + - + +
1283B EDO 3.9 11.9 - - - +
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Residues in contact with LYS 205 (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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201B ARG* 2.9 36.0 + - + +
202B GLN* 3.7 36.4 - - - +
204B ILE* 1.3 75.7 - - - +
206B ARG* 1.3 59.2 + - - +
208B ILE* 3.5 4.9 + - - +
209B HIS* 3.0 28.5 + - - +
1283B EDO 3.9 16.8 - - - +
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Residues in contact with ARG 206 (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 GLN* 6.0 6.1 - - - +
202B GLN* 2.9 23.2 + - - +
203B GLN* 3.8 19.8 - - - +
205B LYS* 1.3 75.6 - - - +
207B MET* 1.3 66.3 + - - +
209B HIS* 3.1 9.5 + - + +
210B ASP* 3.0 36.7 + - - +
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Residues in contact with MET 207 (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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167B TYR* 4.3 12.3 - - - -
173B TYR* 3.8 43.1 - - + +
176B VAL* 4.3 14.1 - - - -
177B VAL* 3.8 11.3 - - + +
194B LEU* 4.1 10.1 - - + -
196B TYR* 4.2 17.3 - - + -
203B GLN 3.0 18.9 + - - +
204B ILE* 3.2 12.8 + - + +
206B ARG* 1.3 76.3 - - - +
208B ILE* 1.3 66.8 + - + +
210B ASP* 3.3 10.5 + - - +
211B LEU* 2.9 28.7 + - + +
241B ILE* 3.9 26.9 - - + -
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Residues in contact with ILE 208 (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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204B ILE* 2.9 27.8 + - + +
205B LYS* 3.9 4.3 - - - +
207B MET* 1.3 75.2 - - + +
209B HIS* 1.3 61.8 + - - +
211B LEU* 3.1 8.9 + - + +
212B GLU* 2.8 34.6 + - - +
221B GLN* 3.7 14.1 - - - +
241B ILE* 4.2 20.2 - - + -
277B ILE* 3.8 23.3 - - + -
1283B EDO 3.5 33.0 - - - +
1296B EDO 3.6 24.9 - - - -
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Residues in contact with HIS 209 (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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205B LYS 3.0 15.2 + - - +
206B ARG* 3.2 13.9 - - + +
208B ILE* 1.3 77.7 - - - +
210B ASP* 1.3 70.4 + - - +
212B GLU* 3.1 16.8 + - + +
213B ALA* 3.0 25.4 + - + +
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Residues in contact with ASP 210 (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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173B TYR 5.7 0.3 - - - +
174B GLN* 5.3 11.6 + - - +
177B VAL* 3.8 19.3 - - + +
206B ARG* 3.0 33.2 + - - +
207B MET* 3.5 9.4 - - - +
209B HIS* 1.3 85.0 + - - +
211B LEU* 1.3 63.3 + - - +
213B ALA* 3.2 17.4 + - - +
214B THR* 3.4 15.8 + - - +
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Residues in contact with LEU 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 VAL* 3.9 22.8 - - + +
180B ILE* 4.3 34.8 - - + -
194B LEU* 5.4 2.7 - - + -
207B MET* 2.9 16.3 + - + +
208B ILE* 3.1 11.6 + - + +
210B ASP* 1.3 78.0 - - - +
212B GLU* 1.3 56.2 + - + +
214B THR* 2.5 33.2 + - + +
216B ILE* 4.9 1.0 + - + -
219B ILE* 4.1 26.0 - - + +
241B ILE* 3.7 39.9 - - + -
243B ILE* 4.7 6.7 - - + -
277B ILE* 5.1 5.6 - - + -
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Residues in contact with GLU 212 (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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208B ILE* 2.8 18.3 + - - +
209B HIS* 3.5 17.6 - - + +
211B LEU* 1.3 76.9 - - - +
213B ALA* 1.3 60.5 + - - +
214B THR 3.4 0.7 + - - -
215B GLY* 3.4 12.5 + - - -
216B ILE 5.1 1.3 - - - +
277B ILE* 3.5 40.1 - - + +
278B VAL* 3.7 18.0 - - + +
1296B EDO 3.7 14.3 + - - -
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Residues in contact with ALA 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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209B HIS* 3.0 18.0 + - + +
210B ASP* 3.6 13.9 - - - +
211B LEU 3.2 0.6 - - - -
212B GLU* 1.3 74.2 - - - +
214B THR* 1.3 64.1 + - - +
215B GLY* 3.0 3.6 + - - -
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Residues in contact with THR 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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177B VAL* 3.8 19.7 - - + -
181B ALA* 4.4 8.1 - - + -
210B ASP 3.4 14.7 + - - +
211B LEU* 2.5 22.3 + - + +
213B ALA* 1.3 78.6 - - - +
215B GLY* 1.1 63.0 + - - +
216B ILE* 3.3 28.4 + - + +
1294B EDO 3.2 42.9 + - - +
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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