Contacts of the helix formed by residues 200 - 208 (chain B) in PDB entry 2FV7
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 GLU 200 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B ASN* 1.3 75.9 - - - +
201B SER* 1.3 58.0 + - - +
203B ALA* 3.6 2.7 + - - +
204B GLU* 3.1 33.1 + - - +
211B VAL* 3.6 31.3 - - + +
212B GLY* 6.0 0.4 - - - -
213B SER 6.0 0.4 - - - +
234B ILE* 4.2 4.7 - - + -
235B THR 3.3 6.0 + - - +
236B LEU* 3.2 40.2 - - + -
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Residues in contact with SER 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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199B ASN* 3.1 12.7 + - - -
200B GLU* 1.3 75.5 - - - +
202B GLU* 1.3 67.4 + - - +
204B GLU* 3.3 16.0 + - - +
205B ILE* 3.1 30.8 + - - +
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Residues in contact with GLU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LYS* 4.6 5.9 + - - -
177B ASN* 4.3 1.6 + - - -
178B PRO 3.8 5.6 - - - +
179B ALA* 3.5 28.0 - - - +
180B PRO* 4.8 2.3 - - + +
181B ALA* 3.5 31.4 - - + +
198B CYS* 3.4 18.7 - - + +
199B ASN* 2.9 46.6 + - - +
201B SER* 1.3 76.1 - - - +
203B ALA* 1.3 56.3 + - - +
205B ILE* 3.1 5.2 + - + +
206B LEU* 2.8 37.6 + - + +
402B ADP 4.9 2.9 + - - -
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Residues in contact with ALA 203 (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 CYS* 3.9 10.6 - - - -
199B ASN 3.0 18.1 + - - +
200B GLU* 3.7 6.5 - - - +
201B SER 3.3 0.2 - - - -
202B GLU* 1.3 74.7 - - - +
204B GLU* 1.3 55.5 + - - +
206B LEU* 4.5 5.6 - - - +
207B THR* 2.7 38.4 + - - +
211B VAL* 4.3 11.4 - - + -
220B ALA* 4.3 3.6 - - + -
224B LEU* 4.9 3.6 - - + -
234B ILE* 3.8 28.7 - - + -
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Residues in contact with GLU 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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200B GLU 3.1 20.5 + - - +
201B SER* 3.5 16.2 + - - +
202B GLU 3.2 0.2 - - - -
203B ALA* 1.3 76.1 - - - +
205B ILE* 1.3 57.9 + - + +
208B GLY* 2.7 33.1 + - - -
209B LEU 3.2 22.4 - - - +
210B THR* 3.5 12.2 - - - +
211B VAL* 2.9 34.4 + - + +
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Residues in contact with ILE 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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181B ALA* 3.8 33.4 - - + +
182B ILE 3.9 0.4 - - - -
183B ALA* 3.6 41.8 - - + +
201B SER* 3.1 18.5 + - - +
202B GLU* 3.1 8.0 + - + +
204B GLU* 1.3 80.1 - - + +
206B LEU* 1.3 62.1 + - - +
207B THR 3.5 0.2 + - - -
208B GLY* 4.1 3.3 + - - -
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Residues in contact with LEU 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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178B PRO* 3.8 27.8 - - + -
181B ALA* 4.2 6.3 - - + -
182B ILE 3.2 31.4 - - - +
183B ALA 4.3 10.4 - - - +
185B LEU* 4.0 14.4 - - + -
190B TYR* 3.8 15.5 - - - +
196B PHE* 3.9 18.2 - - + -
198B CYS* 4.4 5.2 - - - -
202B GLU 2.8 26.2 + - - +
203B ALA* 4.1 2.9 - - - +
204B GLU 3.3 0.2 - - - -
205B ILE* 1.3 77.0 - - - +
207B THR* 1.3 58.6 + - - +
224B LEU* 4.0 17.0 - - + -
227B ARG* 3.0 23.7 + - - -
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Residues in contact with THR 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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203B ALA 2.7 22.1 + - - +
206B LEU* 1.3 81.5 - - - +
208B GLY* 1.3 59.3 + - - +
209B LEU* 3.1 35.8 + - - +
220B ALA* 3.7 28.9 - - + +
223B VAL* 4.0 15.6 - - + +
224B LEU* 3.8 20.0 - - + -
227B ARG* 4.2 9.0 + - - +
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Residues in contact with GLY 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 GLU 2.7 22.2 + - - -
205B ILE 4.1 2.5 + - - -
206B LEU 3.8 1.0 - - - -
207B THR* 1.3 71.6 - - - +
209B LEU* 1.3 62.8 + - - +
210B THR* 4.1 0.7 + - - -
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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