Contacts of the helix formed by residues 172 - 186 (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 PRO 172 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170B ASN 3.6 3.5 - - - +
171B LEU* 1.3 94.9 - - + +
173B LYS* 1.3 64.5 + - - +
174B GLU* 4.4 3.6 - - + +
175B SER* 3.0 28.9 + - - +
176B VAL* 3.0 19.9 + - - +
204B THR 5.2 0.9 - - - +
206B LEU* 4.7 6.5 - - + -
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Residues in contact with LYS 173 (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 3.5 4.1 + - - +
172B PRO* 1.3 72.3 - - - +
174B GLU* 1.3 57.1 + - - +
176B VAL* 3.4 6.5 + - - +
177B GLN* 2.9 28.4 + - - +
180B ARG* 5.9 0.3 + - - -
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Residues in contact with GLU 174 (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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172B PRO* 3.2 4.3 - - + +
173B LYS* 1.3 76.6 - - - +
175B SER* 1.3 64.5 + - - +
177B GLN* 3.4 7.2 + - - +
178B ILE* 3.2 32.0 + - + +
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Residues in contact with SER 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LEU* 5.0 0.2 - - - -
172B PRO* 3.0 34.0 + - - +
174B GLU* 1.3 76.8 - - - +
176B VAL* 1.3 64.3 + - - +
178B ILE* 3.4 7.2 + - - +
179B LEU* 3.2 26.5 + - - +
204B THR* 2.7 43.9 + - - +
205B HIS* 5.5 0.2 + - - -
206B LEU* 4.0 11.4 - - - -
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Residues in contact with VAL 176 (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* 3.8 28.9 - - + +
172B PRO 3.0 15.6 + - - +
173B LYS* 3.9 6.1 - - - +
175B SER* 1.3 75.0 - - - +
177B GLN* 1.3 61.3 + - - +
179B LEU* 3.7 5.8 - - - +
180B ARG* 2.8 63.7 + - - +
214B TRP* 3.9 26.9 - - + +
3M T 6.2 0.2 - - - +
4M G 4.3 8.5 - - - +
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Residues in contact with GLN 177 (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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173B LYS 2.9 18.6 + - - +
174B GLU* 3.8 9.0 - - - +
175B SER 3.3 0.2 - - - -
176B VAL* 1.3 76.5 - - - +
178B ILE* 1.3 58.6 + - + +
180B ARG* 3.8 14.5 - - - +
181B ASP* 2.9 56.7 + - - +
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Residues in contact with ILE 178 (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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174B GLU* 3.2 19.0 + - + +
175B SER* 3.5 7.0 - - - +
176B VAL 3.2 0.2 - - - -
177B GLN* 1.3 79.3 - - + +
179B LEU* 1.3 63.0 + - - +
181B ASP* 3.2 9.2 + - - +
182B TRP* 3.0 23.1 + - + +
200B LEU* 3.8 23.3 - - + -
203B GLN* 3.9 43.7 - - + +
204B THR* 3.9 10.3 - - + -
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LEU* 4.9 0.9 - - + -
175B SER 3.2 14.7 + - - +
176B VAL* 3.2 8.3 + - - +
178B ILE* 1.3 76.2 - - - +
180B ARG* 1.3 57.1 + - - +
182B TRP* 3.2 6.1 + - - +
183B LEU* 2.8 30.3 + - - +
200B LEU* 4.4 14.8 - - + -
204B THR* 3.8 17.7 - - + -
206B LEU* 3.9 22.0 - - + -
211B VAL* 4.5 9.4 - - + -
214B TRP* 3.5 56.1 - - + -
215B PHE* 4.1 22.8 - - + -
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Residues in contact with ARG 180 (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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173B LYS 5.9 0.2 + - - -
176B VAL* 2.8 48.3 + - - +
177B GLN* 3.9 14.4 - - - +
179B LEU* 1.3 71.1 - - - +
181B ASP* 1.3 67.7 + - - +
183B LEU* 3.3 3.0 + - - +
184B TYR* 2.9 25.9 + - + +
214B TRP* 3.7 9.9 - - + -
222B LEU* 3.6 38.3 - - + +
226B MET* 4.1 15.5 - - + +
3M T 4.4 17.6 + - - -
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Residues in contact with ASP 181 (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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177B GLN* 2.9 49.0 + - - +
178B ILE* 3.2 7.2 + - - +
180B ARG* 1.3 75.5 - - - +
182B TRP* 1.3 59.2 + - - +
184B TYR* 3.2 6.5 + - - +
185B GLU* 2.9 31.1 + - - +
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Residues in contact with TRP 182 (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 ILE 3.0 16.1 + - - +
179B LEU 3.7 3.8 - - - +
181B ASP* 1.3 77.3 - - - +
183B LEU* 1.3 62.1 + - - +
185B GLU* 3.4 3.5 + - - -
186B HIS* 2.9 79.5 + + + -
189B ASN 4.0 1.6 - - - -
190B ALA* 4.1 10.5 - - - -
191B TYR 3.8 7.0 - - - -
192B PRO* 3.4 32.5 - - + -
196B GLU* 3.5 31.9 - - - +
199B LEU* 6.4 1.8 - - + -
200B LEU* 4.1 30.0 - - + +
215B PHE* 3.5 28.3 - + + -
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Residues in contact with LEU 183 (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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179B LEU 2.8 17.6 + - - +
180B ARG* 3.6 5.2 - - - +
182B TRP* 1.3 84.5 - - - +
184B TYR* 1.3 56.3 + - - +
186B HIS 3.4 1.2 - - - -
187B ARG* 2.8 31.7 + - - +
190B ALA* 3.4 32.3 - - + -
214B TRP* 4.2 9.6 - - + -
215B PHE* 4.3 15.7 - - + -
218B ALA* 3.9 29.2 - - + +
219B ARG* 4.8 4.7 - - + -
222B LEU* 3.9 12.8 - - + -
223B LEU* 4.3 10.3 - - + +
226B MET* 3.9 24.5 - - + -
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Residues in contact with TYR 184 (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 2.9 17.9 + - - +
181B ASP* 3.6 6.7 - - - +
183B LEU* 1.3 77.1 - - - +
185B GLU* 1.3 65.2 + - - +
187B ARG* 3.0 75.5 + - - -
226B MET* 4.0 35.9 - - + +
229B LYS* 5.3 2.7 - - + +
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Residues in contact with GLU 185 (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 ASP 2.9 20.5 + - - +
182B TRP* 3.9 5.5 - - - +
184B TYR* 1.3 77.5 - - - +
186B HIS* 1.3 78.2 + - + +
187B ARG* 3.3 5.5 + - - +
188B TYR* 5.3 1.4 + - - -
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Residues in contact with HIS 186 (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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182B TRP* 2.9 84.4 + + + +
183B LEU 3.4 3.4 - - - -
185B GLU* 1.3 98.3 + - + +
187B ARG* 1.3 54.7 + - - +
188B TYR 3.1 2.9 - - - -
189B ASN* 2.8 39.9 + - + +
190B ALA* 3.1 3.0 + - - -
196B GLU* 4.4 10.1 + - - -
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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