Contacts of the helix formed by residues 207 - 222 (chain B) in PDB entry 6FQP
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 207 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B SER* 3.7 2.0 - - - -
206B LEU* 1.3 77.9 - - - +
208B THR* 1.3 65.1 + - - +
209B LEU* 3.3 9.1 + - - +
210B GLN* 2.9 40.4 + - - +
211B VAL* 3.0 21.1 + - - +
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Residues in contact with THR 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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197B LYS* 4.8 18.1 + - + +
198B ALA* 5.7 2.6 - - - -
201B SER* 3.8 12.1 + - - -
207B SER* 1.3 73.8 - - - +
209B LEU* 1.3 58.8 + - - +
211B VAL* 3.0 8.8 + - - +
212B CYS* 2.8 41.7 + - - -
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Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B SER* 3.2 7.9 + - - +
208B THR* 1.3 79.4 - - - +
210B GLN* 1.3 58.9 + - + +
212B CYS* 3.3 10.5 + - + +
213B ASN* 2.8 50.2 + - - +
6M C 4.2 16.6 - - - +
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Residues in contact with GLN 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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171B LEU* 4.0 17.0 - - + +
205B HIS 4.9 0.2 - - - +
206B LEU* 3.7 26.1 - - + +
207B SER* 2.9 43.1 + - - +
209B LEU* 1.3 77.5 - - + +
211B VAL* 1.3 56.4 + - - +
213B ASN* 3.2 4.8 + - - +
214B TRP* 2.9 29.5 + - - +
5M A 2.9 42.3 + - - +
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Residues in contact with VAL 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LEU* 4.5 11.4 - - + -
197B LYS* 4.6 17.9 - - + +
200B LEU* 4.6 10.5 - - + -
201B SER* 3.9 30.7 - - - +
204B THR* 4.3 3.8 - - - +
206B LEU* 4.2 11.9 - - + -
207B SER 3.0 15.4 + - - +
208B THR* 3.0 8.5 + - - +
210B GLN* 1.3 76.2 - - - +
212B CYS* 1.3 65.4 + - - +
214B TRP* 3.1 7.1 + - - +
215B PHE* 3.0 47.3 + - + -
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Residues in contact with CYS 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LYS* 3.3 42.6 - - - +
208B THR* 2.8 27.8 + - - +
209B LEU* 3.7 15.0 - - + +
211B VAL* 1.3 73.5 - - - +
213B ASN* 1.3 65.5 + - - +
215B PHE* 3.0 8.3 + - - +
216B ILE* 2.9 35.2 + - + +
219B ARG* 4.9 0.3 + - - -
7L A 6.1 2.5 - - - -
8L G 5.0 0.7 - - - +
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Residues in contact with ASN 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 2.8 42.7 + - - +
210B GLN* 3.7 6.6 - - - +
212B CYS* 1.3 77.2 - - - +
214B TRP* 1.3 65.1 + - - +
216B ILE* 3.2 16.4 + - - +
217B ASN* 2.9 35.6 + - - +
4M G 5.6 1.3 - - + -
5M A 4.1 32.6 + - + +
6M C 3.5 30.3 + - - +
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Residues in contact with TRP 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LEU* 4.1 15.3 - - + -
176B VAL* 3.9 24.9 - - + +
179B LEU* 3.5 49.8 - - + -
180B ARG* 3.7 22.8 - - - +
183B LEU* 4.2 10.1 - - + -
210B GLN 2.9 14.0 + - - +
211B VAL 3.1 7.4 + - - +
213B ASN* 1.3 76.7 - - - +
215B PHE* 1.3 69.1 + + - +
217B ASN* 3.2 6.7 + - + +
218B ALA* 2.6 58.4 + - + +
222B LEU* 3.7 25.4 - - + -
4M G 3.8 23.9 + - - -
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Residues in contact with PHE 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LEU* 4.1 18.2 - - + -
182B TRP* 3.5 37.5 - + - -
183B LEU* 4.3 16.6 - - + -
190B ALA 4.2 3.8 - - - -
192B PRO* 3.8 17.0 - - + -
197B LYS* 5.9 0.9 - - + -
200B LEU* 3.7 20.6 - - + -
211B VAL* 3.0 43.7 + - + +
212B CYS* 3.0 10.3 + - - +
214B TRP* 1.3 91.1 - + - +
216B ILE* 1.3 65.4 + - - +
218B ALA* 4.2 1.1 - - - +
219B ARG* 2.9 55.7 + - - +
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Residues in contact with ILE 216 (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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212B CYS* 2.9 26.3 + - + +
213B ASN* 3.8 18.4 - - - +
215B PHE* 1.3 77.5 - - - +
217B ASN* 1.3 61.2 + - - +
219B ARG* 3.8 19.5 - - - +
220B ARG* 3.5 24.1 + - - +
8L G 4.4 11.7 - - + +
9L C 3.8 40.0 + - + +
10L T 3.5 32.8 - - + +
6M C 5.1 7.0 - - + +
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Residues in contact with ASN 217 (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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213B ASN* 2.9 26.8 + - - +
214B TRP* 3.8 6.1 - - + +
216B ILE* 1.3 75.6 - - - +
218B ALA* 1.3 61.9 + - - +
220B ARG* 2.8 37.0 + - - +
221B ARG* 2.8 55.2 + - - +
4M G 3.9 11.1 + - + +
5M A 3.0 36.7 + - - -
6M C 4.2 3.6 + - - +
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Residues in contact with ALA 218 (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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183B LEU* 3.9 12.6 - - + -
214B TRP* 2.6 60.9 + - + +
215B PHE* 4.0 3.1 - - - +
217B ASN* 1.3 72.9 - - - +
219B ARG* 1.3 60.7 + - - +
221B ARG* 4.7 1.8 - - - -
222B LEU* 2.6 35.6 + - + +
223B LEU 3.0 7.6 + - - -
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Residues in contact with ARG 219 (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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183B LEU* 4.8 4.0 - - + -
190B ALA* 2.9 42.6 + - + +
191B TYR* 3.5 40.2 - - - +
192B PRO* 4.4 2.0 - - - +
212B CYS 4.9 0.2 + - - -
215B PHE* 2.9 41.5 + - - +
216B ILE* 3.7 24.8 - - - +
217B ASN 3.3 0.2 - - - -
218B ALA* 1.3 78.5 - - - +
220B ARG* 1.3 58.4 + - + +
223B LEU* 3.6 18.6 - - + +
224B PRO* 3.3 20.1 - - - +
8L G 3.6 16.0 + - - +
9L C 2.7 33.9 + - - +
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Residues in contact with ARG 220 (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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216B ILE* 3.5 16.9 + - - +
217B ASN* 2.8 33.4 + - - +
219B ARG* 1.3 80.3 - - + +
221B ARG* 1.3 70.5 + - + +
224B PRO* 3.8 15.4 - - - +
9L C 5.9 0.7 - - + -
10L T 3.2 45.1 - - + +
11L G 2.6 48.9 + - - -
12L T 3.7 8.3 + - - +
5M A 3.3 5.9 - - - +
6M C 4.3 1.0 - - - +
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Residues in contact with ARG 221 (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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217B ASN* 2.8 41.7 + - - +
218B ALA* 4.7 0.2 - - - -
220B ARG* 1.3 86.4 - - + +
222B LEU* 1.3 75.8 + - + +
224B PRO* 4.5 2.1 - - - +
225B ASP* 5.3 7.4 + - - +
12L T 3.6 9.1 + - - +
13L C 4.6 0.6 - - - +
3M T 3.7 44.1 + - - +
4M G 2.9 48.9 + - - -
5M A 3.3 14.8 - - - +
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Residues in contact with LEU 222 (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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180B ARG* 3.6 44.4 - - + +
183B LEU* 3.9 11.2 - - + -
214B TRP* 3.7 26.0 - - + -
218B ALA* 2.6 22.0 + - + +
221B ARG* 1.3 90.3 - - + +
223B LEU* 1.3 64.3 + - - +
224B PRO* 3.5 2.2 - - - -
225B ASP* 3.7 7.7 + - - +
226B MET* 3.2 27.6 + - + +
3M T 4.7 11.9 - - - +
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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