Contacts of the helix formed by residues 211 - 226 (chain T) in PDB entry 6FF7
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 PHE 211 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173T VAL 5.5 5.4 - - - +
174T ASN* 6.5 0.2 - - - -
205T GLN* 6.2 0.4 - - - -
208T SER* 2.9 19.1 + - - +
210T ILE* 1.3 79.5 - - + +
212T THR* 1.3 63.3 + - - +
213T HIS* 3.2 3.6 - - - -
214T VAL* 3.0 23.4 + - + +
215T TYR* 3.0 13.7 + - + +
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Residues in contact with THR 212 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205T GLN* 5.2 7.4 - - - -
208T SER 4.0 0.4 + - - -
209T PRO* 3.1 24.4 + - - -
210T ILE 3.4 1.0 - - - -
211T PHE* 1.3 77.5 - - - +
213T HIS* 1.3 57.1 + - - +
215T TYR* 3.2 7.6 + - - +
216T ALA* 2.8 31.3 + - - +
255T THR 5.9 0.4 - - - -
258T LYS* 4.8 25.1 - - - -
259T PHE* 5.0 8.5 - - - -
262T HIS* 4.5 3.7 - - - +
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Residues in contact with HIS 213 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210T ILE 5.2 1.7 + - - +
211T PHE* 3.2 1.3 - - - -
212T THR* 1.3 78.6 - - - +
214T VAL* 1.3 56.6 + - - +
216T ALA* 3.4 8.1 + - - +
217T ALA* 3.1 26.2 + - - +
262T HIS* 4.5 9.2 - - + -
354T LEU* 5.8 8.1 - - + +
357T LEU* 5.2 3.9 - - - +
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Residues in contact with VAL 214 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173T VAL* 5.1 6.6 - - + +
174T ASN* 4.6 27.1 - - - +
175T ILE* 4.8 4.7 - - + +
178T ILE* 5.9 2.1 - - - +
211T PHE* 3.0 19.7 + - + +
213T HIS* 1.3 77.5 - - - +
215T TYR* 1.3 58.6 + - - +
217T ALA* 3.3 7.3 + - - +
218T LEU* 3.0 28.1 + - - +
357T LEU* 6.0 1.1 - - - -
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Residues in contact with TYR 215 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201T VAL* 5.2 11.9 - - + +
204T ALA* 6.3 1.6 - - + -
205T GLN* 4.6 19.3 - - + +
211T PHE 3.0 12.2 + - - +
212T THR* 3.7 10.3 - - - +
214T VAL* 1.3 73.4 - - - +
216T ALA* 1.3 60.7 + - - +
218T LEU* 3.4 7.6 + - - +
219T VAL* 2.9 29.8 + - - +
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Residues in contact with ALA 216 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212T THR 2.8 16.7 + - - +
213T HIS 3.5 5.2 - - - +
215T TYR* 1.3 78.1 - - - +
217T ALA* 1.3 56.9 + - - +
219T VAL* 3.3 6.8 + - - +
220T ALA* 2.8 29.7 + - - +
259T PHE* 5.1 2.2 - - - +
262T HIS* 3.5 41.7 - - + +
263T LEU* 4.1 6.7 - - - +
266T GLN* 4.3 5.2 - - + +
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Residues in contact with ALA 217 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178T ILE* 5.9 7.0 - - + -
213T HIS 3.1 13.5 + - - +
214T VAL* 3.3 9.8 + - - +
216T ALA* 1.3 78.9 - - - +
218T LEU* 1.3 57.2 + - - +
220T ALA* 3.2 8.2 + - - +
221T ILE* 3.0 28.4 + - - +
266T GLN* 5.3 2.7 - - - +
357T LEU* 3.8 37.4 - - + +
359T LEU* 6.2 0.4 - - + +
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Residues in contact with LEU 218 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173T VAL* 5.7 9.4 - - + -
178T ILE* 6.1 6.2 - - + +
214T VAL 3.0 16.6 + - - +
215T TYR* 3.6 9.0 - - - +
217T ALA* 1.3 74.2 - - - +
219T VAL* 1.3 66.2 + - - +
221T ILE* 3.2 7.3 + - - +
222T ILE* 3.1 22.8 + - - +
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Residues in contact with VAL 219 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215T TYR 2.9 17.6 + - - +
216T ALA* 3.7 6.3 - - - +
218T LEU* 1.3 75.4 - - - +
220T ALA* 1.3 58.4 + - - +
222T ILE* 3.2 6.5 + - - +
223T ASN* 2.8 34.4 + - + +
230T GLY* 5.3 5.1 - - - -
233T ILE* 5.6 10.1 - - + -
263T LEU* 6.2 4.3 - - + -
268T VAL* 5.6 0.9 - - - -
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Residues in contact with ALA 220 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216T ALA 2.8 19.0 + - - +
217T ALA* 3.4 8.1 - - - +
219T VAL* 1.3 76.3 - - - +
221T ILE* 1.3 61.6 + - - +
223T ASN* 3.8 5.8 - - - +
224T SER* 3.2 22.9 + - - -
266T GLN* 3.8 28.9 - - + +
268T VAL* 4.9 8.3 - - + +
360T VAL* 4.7 12.5 - - + +
365T GLN* 6.0 1.0 - - - +
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Residues in contact with ILE 221 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182T ILE* 5.1 15.3 - - + -
217T ALA 3.0 13.7 + - - +
218T LEU* 3.2 7.8 + - - +
220T ALA* 1.3 77.4 - - - +
222T ILE* 1.3 63.8 + - - +
224T SER* 3.2 19.2 + - - -
225T LYS* 3.6 6.9 + - - +
359T LEU* 5.8 9.4 - - + -
360T VAL* 5.3 6.0 - - + +
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Residues in contact with ILE 222 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218T LEU 3.1 16.1 + - - +
219T VAL* 3.8 6.3 - - - +
221T ILE* 1.3 75.0 - - - +
223T ASN* 1.3 52.8 + - - +
225T LYS* 3.0 7.3 + - - +
226T PHE* 2.6 40.1 + - + +
229T ILE* 5.6 8.3 - - + -
230T GLY* 6.1 0.9 - - - +
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Residues in contact with ASN 223 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219T VAL 2.8 21.8 + - - +
220T ALA* 3.8 6.7 - - - +
222T ILE* 1.3 73.0 - - - +
224T SER* 1.3 62.0 + - - +
226T PHE 3.6 11.0 - - - -
227T PRO* 3.0 29.7 - - + +
230T GLY* 4.0 22.1 - - - +
268T VAL* 5.1 11.0 - - + -
366T PHE* 4.7 14.0 - - - +
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Residues in contact with SER 224 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220T ALA 3.2 12.7 + - - -
221T ILE* 3.2 13.4 + - - -
222T ILE 3.2 1.0 - - - -
223T ASN* 1.3 76.6 - - - +
225T LYS* 1.3 58.6 + - - +
360T VAL* 4.7 11.4 - - - -
364T ASP* 3.7 32.5 - - - +
365T GLN* 4.7 7.6 - - - +
366T PHE* 5.1 3.0 - - - +
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Residues in contact with LYS 225 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221T ILE 3.6 6.6 + - - +
222T ILE* 3.0 8.3 + - - +
224T SER* 1.3 81.7 - - - +
226T PHE* 1.3 58.4 + - + +
227T PRO 4.0 1.5 - - - -
405T ILE* 5.2 14.1 - - + -
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Residues in contact with PHE 226 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222T ILE* 2.6 14.6 + - + +
223T ASN* 3.3 7.9 - - - -
225T LYS* 1.3 75.6 - - + +
227T PRO* 1.3 64.5 - - - +
228T GLN* 3.2 4.3 - - + -
229T ILE* 3.0 26.7 + - + +
230T GLY 3.4 7.6 + - - -
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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