Contacts of the helix formed by residues 213 - 226 (chain A) 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 SER 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A GLY* 1.3 78.2 + - - +
214A ALA* 1.3 59.9 + - - +
215A ALA* 3.6 9.4 + - - +
216A ASP* 3.1 24.7 + - - +
217A ALA* 2.9 28.1 + - - +
236A LEU* 4.2 7.0 - - - +
239A GLU* 6.1 4.5 - - - -
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Residues in contact with ALA 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A SER* 1.3 70.9 - - - +
215A ALA* 1.3 65.8 + - - +
217A ALA* 3.5 1.7 + - - +
218A GLY* 3.1 18.5 + - - -
236A LEU* 3.7 16.8 - - + +
239A GLU* 5.8 6.0 + - - +
242A VAL* 3.8 17.8 - - + +
251A PRO* 5.8 0.3 - - - +
253A HIS* 3.7 37.2 - - + +
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Residues in contact with ALA 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A SER* 3.2 9.9 + - - +
214A ALA* 1.3 78.0 - - - +
216A ASP* 1.3 65.8 + - - +
218A GLY* 3.1 11.3 + - - -
219A GLU* 3.3 14.9 + - - +
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Residues in contact with ASP 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A LEU* 5.1 1.0 - - - +
210A THR* 3.3 32.8 - - - +
211A VAL* 3.6 8.5 - - - +
212A GLY* 2.8 21.5 + - - -
213A SER* 3.1 22.7 + - - +
215A ALA* 1.3 77.3 - - - +
217A ALA* 1.3 58.4 + - - +
219A GLU* 3.2 17.4 + - - +
220A ALA* 3.0 26.7 + - - +
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Residues in contact with ALA 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A VAL* 3.9 13.0 - - + +
213A SER 2.9 16.3 + - - +
214A ALA 3.8 5.6 - - - +
216A ASP* 1.3 76.4 - - - +
218A GLY* 1.3 53.6 + - - +
220A ALA* 4.3 0.7 - - - -
221A ALA* 2.8 36.9 + - - +
234A ILE* 3.4 16.0 - - + +
236A LEU* 3.8 22.4 - - + -
242A VAL* 4.0 16.4 - - + -
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Residues in contact with GLY 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ALA 3.1 13.5 + - - -
215A ALA* 3.1 6.6 + - - -
217A ALA* 1.3 74.3 - - - +
219A GLU* 1.3 63.5 + - - +
221A ALA* 4.0 1.4 - - - +
222A LEU* 3.2 22.2 + - - +
242A VAL* 4.3 4.4 - - - +
244A LEU* 4.0 1.1 - - - +
251A PRO* 3.9 34.9 - - - +
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Residues in contact with GLU 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A LEU* 4.1 20.7 - - + +
210A THR 5.6 1.2 - - - +
215A ALA 3.3 10.1 + - - +
216A ASP* 3.2 17.6 + - - +
218A GLY* 1.3 74.5 - - - +
220A ALA* 1.3 63.5 + - - +
222A LEU* 3.2 10.1 + - - +
223A VAL* 3.2 24.1 + - - +
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Residues in contact with ALA 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ALA* 4.4 1.3 - - + -
207A THR* 3.9 17.2 - - + +
209A LEU* 3.8 13.0 - - + +
211A VAL* 3.6 30.3 - - + -
216A ASP 3.0 9.5 + - - +
217A ALA 3.8 4.0 - - - +
219A GLU* 1.3 73.5 - - - +
221A ALA* 1.3 66.4 + - - +
223A VAL* 3.2 5.9 + - - +
224A LEU* 3.2 26.0 + - - +
234A ILE* 3.8 11.4 - - + -
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Residues in contact with ALA 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ALA 2.8 22.4 + - - +
218A GLY 4.0 0.2 - - - +
220A ALA* 1.3 72.2 - - - +
222A LEU* 1.3 58.1 + - - +
224A LEU* 3.4 2.9 + - - +
225A LEU* 3.0 27.9 + - - +
232A VAL* 3.8 30.6 - - + +
234A ILE* 3.7 9.8 - - + +
242A VAL* 4.9 3.4 - - + +
244A LEU* 3.3 30.3 - - + +
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Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A GLY 3.2 14.8 + - - +
219A GLU* 3.4 12.3 - - - +
220A ALA 3.1 0.2 - - - -
221A ALA* 1.3 74.2 - - - +
223A VAL* 1.3 65.4 + - - +
224A LEU 3.2 0.2 - - - -
225A LEU* 3.3 13.5 + - + -
226A LYS* 3.1 59.6 + - + +
244A LEU* 3.5 19.0 - - + +
249A PRO* 4.0 15.7 - - + +
251A PRO* 6.2 2.7 - - + -
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Residues in contact with VAL 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A THR* 4.2 14.8 - - + +
209A LEU* 4.0 19.7 - - + -
219A GLU 3.2 14.9 + - - +
220A ALA 3.2 7.6 + - - +
222A LEU* 1.3 76.0 - - + +
224A LEU* 1.3 61.1 + - - +
226A LYS* 3.6 12.2 + - + +
227A ARG* 3.5 49.1 + - - +
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Residues in contact with LEU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A TYR* 3.8 25.6 - - + -
196A PHE* 3.7 24.0 - - + -
198A CYS* 4.4 14.1 - - - -
203A ALA* 4.9 1.6 - - + -
206A LEU* 4.2 9.0 - - + -
207A THR* 3.9 23.1 - - + -
220A ALA 3.2 19.9 + - - +
221A ALA* 3.7 7.4 - - - +
222A LEU 3.2 0.2 - - - -
223A VAL* 1.3 72.4 - - - +
225A LEU* 1.3 66.3 + - - +
227A ARG* 3.0 30.1 + - - +
228A GLY 3.8 0.3 + - - -
229A CYS* 3.5 16.5 - - - -
232A VAL* 3.8 26.5 - - + -
234A ILE* 4.6 5.4 - - + -
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Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A ALA 3.0 15.8 + - - +
222A LEU* 3.3 13.0 + - + +
224A LEU* 1.3 76.2 - - - +
226A LYS* 1.3 62.1 + - + +
227A ARG 3.2 0.2 - - - -
228A GLY* 3.3 9.2 + - - -
229A CYS 3.3 20.7 - - - +
230A GLN 3.6 6.3 - - - +
231A VAL 4.2 0.2 - - - +
232A VAL* 3.8 19.0 - - + +
244A LEU* 4.1 14.1 - - + -
245A SER* 3.3 49.8 - - - +
246A GLN* 3.0 33.1 + - - +
249A PRO* 4.1 13.2 - - + -
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Residues in contact with LYS 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LEU* 3.1 50.7 + - + +
223A VAL* 3.8 10.8 - - + +
224A LEU 3.3 0.2 - - - -
225A LEU* 1.3 74.6 - - + +
227A ARG* 1.3 60.7 + - - +
228A GLY 3.3 0.6 + - - -
316B ASP* 5.6 2.3 - - - +
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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