Contacts of the helix formed by residues 210 - 225 (chain F) in PDB entry 3DV0
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 GLY 210 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F PHE* 5.4 1.3 - - - -
146F ILE* 4.4 20.9 + - - -
147F PRO 4.5 1.8 - - - -
148F SER* 3.4 24.4 - - - -
172F HIS* 4.6 6.7 - - - -
175F LEU* 3.9 11.6 - - - +
209F TYR* 1.3 72.5 - - - +
211F ALA* 1.3 59.6 + - - -
212F MET 3.0 9.8 + - - -
213F VAL* 3.1 13.2 + - - +
214F HIS 4.3 1.2 + - - -
234F ASP* 5.3 0.2 + - - -
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Residues in contact with ALA 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172F HIS* 3.3 40.4 - - + +
174F LYS* 4.6 17.9 + - + +
175F LEU* 4.0 14.8 - - + +
209F TYR 3.7 0.4 + - - -
210F GLY* 1.3 71.3 - - - -
212F MET* 1.3 66.5 + - + +
213F VAL 3.3 0.4 - - - -
214F HIS* 3.6 8.5 + - - +
215F GLU* 3.3 23.9 + - - +
261F GLU* 3.7 10.0 + - - +
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Residues in contact with MET 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174F LYS* 6.2 0.9 - - - +
208F ALA* 4.0 9.0 - - + -
209F TYR 3.4 13.0 - - - +
210F GLY 3.0 1.0 - - - -
211F ALA* 1.3 88.7 - - + +
213F VAL* 1.3 59.9 + - - +
214F HIS 3.2 0.4 - - - -
215F GLU* 3.5 27.0 - - + +
216F SER* 2.8 34.8 + - - -
259F VAL* 3.8 26.9 - - + +
260F GLN* 3.7 6.1 - - - -
261F GLU* 3.5 42.0 - - + +
309F PRO* 3.5 34.1 - - - +
310F ASN* 5.0 0.4 - - - -
314F VAL* 5.5 0.4 - - - -
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Residues in contact with VAL 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148F SER* 3.7 11.9 - - - +
149F THR* 5.9 1.1 - - + -
198F LYS* 3.9 28.5 - - + -
208F ALA* 3.8 7.0 - - + +
209F TYR* 3.6 25.4 - - - +
210F GLY 3.1 8.2 + - - +
212F MET* 1.3 76.8 - - - +
214F HIS* 1.3 59.0 + - - +
216F SER* 3.3 7.0 + - - -
217F LEU* 3.0 34.0 + - + +
232F VAL* 5.0 4.7 - - + -
233F VAL 5.3 0.2 - - - +
234F ASP* 3.3 39.3 - - + +
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Residues in contact with HIS 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148F SER* 5.8 0.2 - - - -
174F LYS* 5.8 3.4 - - - -
175F LEU* 5.5 9.0 - - + -
179F PHE* 5.6 14.3 - + + -
210F GLY 4.3 0.8 + - - +
211F ALA* 3.6 11.0 + - - +
212F MET 3.2 0.4 - - - -
213F VAL* 1.3 75.9 - - - +
215F GLU* 1.3 90.4 + - - +
216F SER 3.0 1.6 - - - -
217F LEU* 3.2 13.2 + - - +
218F LYS* 3.0 39.6 + - + +
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Residues in contact with GLU 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174F LYS* 4.0 19.1 + - - +
211F ALA 3.3 16.4 + - - +
212F MET* 3.5 29.4 - - + +
214F HIS* 1.3 97.2 - - - +
216F SER* 1.3 58.0 + - - +
218F LYS* 3.8 6.0 - - - +
219F ALA* 3.2 9.5 + - - +
309F PRO 4.9 0.4 - - - -
310F ASN* 3.2 18.5 - - - +
311F PHE* 2.9 65.5 + - - +
314F VAL* 4.6 4.0 - - + +
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Residues in contact with SER 216 (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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206F ILE* 3.4 24.2 - - - +
208F ALA* 3.8 8.4 - - - +
212F MET 2.8 22.6 + - - -
213F VAL* 3.4 6.1 - - - -
215F GLU* 1.3 74.9 - - - +
217F LEU* 1.3 52.8 + - - +
218F LYS 2.9 4.5 - - - -
219F ALA* 2.9 3.8 + - - +
220F ALA* 2.8 35.8 + - - +
232F VAL* 3.7 22.2 - - - +
259F VAL* 4.2 4.7 - - - +
314F VAL* 4.1 13.9 - - - +
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Residues in contact with LEU 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198F LYS* 3.5 43.1 - - + -
199F ARG* 3.8 26.4 - - + -
213F VAL* 3.0 27.9 + - + +
214F HIS* 3.7 10.3 - - - +
216F SER* 1.3 73.9 - - - +
218F LYS* 1.3 59.3 - - - +
220F ALA* 3.7 7.9 - - - +
221F ALA* 3.4 19.8 + - - +
232F VAL* 3.9 9.6 - - + -
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Residues in contact with LYS 218 (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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214F HIS* 3.0 32.9 + - + +
215F GLU* 3.6 9.4 - - - +
216F SER 2.9 0.8 - - - -
217F LEU* 1.3 76.5 - - - +
219F ALA* 1.3 65.2 + - - +
221F ALA* 3.4 7.5 + - - +
222F GLU* 3.3 25.5 + - + +
311F PHE* 3.0 55.6 - - + -
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Residues in contact with ALA 219 (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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215F GLU 3.2 8.5 + - - +
216F SER 2.9 7.5 + - - +
218F LYS* 1.3 77.8 - - - +
220F ALA* 1.3 53.5 + - - +
222F GLU* 3.2 2.6 + - - -
223F LEU* 2.8 42.5 + - + +
311F PHE* 3.6 14.6 - - - +
314F VAL* 3.8 18.8 - - + -
315F ILE* 3.2 33.0 - - + +
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Residues in contact with ALA 220 (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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199F ARG* 3.6 33.9 + - - -
206F ILE* 5.3 0.6 - - + +
216F SER 2.8 15.2 + - - +
217F LEU 3.7 4.5 - - - +
219F ALA* 1.3 78.5 - - - +
221F ALA* 1.3 61.7 + - - +
223F LEU* 3.3 14.4 + - - +
224F GLU* 3.0 22.2 + - - +
228F ILE 4.3 1.4 - - - +
230F ALA* 3.9 9.8 - - + +
232F VAL* 3.9 15.9 - - + -
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Residues in contact with ALA 221 (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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199F ARG* 4.9 5.6 - - - +
217F LEU 3.4 11.2 + - - +
218F LYS* 3.4 12.0 + - - +
219F ALA 3.2 0.6 - - - -
220F ALA* 1.3 79.6 - - - +
222F GLU* 1.3 69.5 + - - +
224F GLU* 3.2 21.5 + - - +
225F LYS* 3.4 14.4 + - - +
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Residues in contact with GLU 222 (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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218F LYS* 3.3 15.5 + - + +
219F ALA 3.2 1.4 + - - +
221F ALA* 1.3 81.0 - - - +
223F LEU* 1.3 61.7 + - - +
225F LYS* 3.4 33.6 + - - +
226F GLU* 3.1 27.8 - - - +
311F PHE* 5.2 8.3 - - + -
315F ILE* 3.5 28.9 - - + -
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Residues in contact with LEU 223 (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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204F ILE* 5.1 0.4 - - + -
206F ILE* 4.3 4.9 - - + -
219F ALA* 2.8 30.6 + - + +
220F ALA* 3.4 9.4 - - - +
221F ALA 3.1 0.2 - - - -
222F GLU* 1.3 76.9 - - - +
224F GLU* 1.3 55.8 + - - +
226F GLU* 2.6 33.6 + - - +
227F GLY 3.1 0.5 + - - -
228F ILE* 3.0 48.5 + - + +
230F ALA* 3.7 25.4 - - + -
314F VAL 5.0 0.2 - - - +
315F ILE* 4.4 30.1 - - + +
318F ALA* 4.3 22.0 - - + -
319F LYS* 5.0 7.0 - - + +
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Residues in contact with GLU 224 (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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199F ARG* 3.4 24.7 + - - +
220F ALA 3.0 12.2 + - - +
221F ALA* 3.3 12.3 - - - +
223F LEU* 1.3 71.3 - - - +
225F LYS* 1.3 55.7 + - + +
226F GLU 2.7 14.6 + - - -
227F GLY* 2.8 15.8 + - - -
228F ILE 3.3 18.0 + - - +
229F SER* 4.4 8.8 + - - -
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Residues in contact with LYS 225 (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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221F ALA* 3.4 11.4 + - - +
222F GLU* 3.6 37.2 - - - +
223F LEU 3.2 0.8 - - - -
224F GLU* 1.3 79.3 - - + +
226F GLU* 1.3 62.2 + - + +
227F GLY 3.6 0.4 - - - -
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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