Contacts of the helix formed by residues 193 - 205 (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 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191B TYR 3.5 2.4 + - - -
192B PRO* 1.3 74.2 - - - +
194B GLU* 1.3 56.7 + - - +
195B GLN* 3.3 10.6 + - - +
196B GLU* 2.8 38.6 + - - +
197B LYS* 2.6 34.8 + - - +
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Residues in contact with GLU 194 (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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192B PRO 4.0 0.2 + - - -
193B SER* 1.3 72.2 - - - +
195B GLN* 1.3 64.5 + - + +
197B LYS* 3.5 14.4 + - + +
198B ALA* 3.0 23.6 + - - +
7L A 6.1 1.3 - - - -
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Residues in contact with GLN 195 (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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193B SER* 3.0 9.7 + - - +
194B GLU* 1.3 81.4 - - + +
196B GLU* 1.3 62.6 + - + +
198B ALA* 3.4 7.4 + - - +
199B LEU* 3.2 20.4 + - - +
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Residues in contact with GLU 196 (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* 3.5 24.5 + - - +
186B HIS* 4.4 10.7 + - - -
191B TYR 4.2 1.7 - - - +
192B PRO* 3.2 17.8 - - + +
193B SER* 2.8 41.7 + - - +
195B GLN* 1.3 74.6 - - + +
197B LYS* 1.3 66.3 + - - +
198B ALA 3.1 1.6 - - - -
199B LEU* 3.0 12.5 + - + +
200B LEU* 3.0 26.3 + - + +
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Residues in contact with LYS 197 (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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192B PRO* 3.5 38.5 - - + +
193B SER 2.6 22.2 + - - +
194B GLU* 3.8 11.0 - - + +
196B GLU* 1.3 71.6 - - - +
198B ALA* 1.3 62.4 + - - +
200B LEU* 3.8 5.8 - - - +
201B SER* 3.0 24.9 + - - -
208B THR* 4.8 15.7 + - + -
211B VAL* 4.5 15.0 - - + +
212B CYS* 3.3 36.7 - - - +
215B PHE* 6.3 0.9 - - - -
7L A 4.2 9.7 + - - +
8L G 2.5 31.2 + - - -
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Residues in contact with ALA 198 (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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194B GLU 3.0 17.2 + - - +
195B GLN* 3.7 7.4 - - - +
196B GLU 3.1 0.4 - - - -
197B LYS* 1.3 78.5 - - - +
199B LEU* 1.3 61.8 + - - +
201B SER* 3.4 6.0 + - - -
202B GLN* 3.0 22.2 + - - +
208B THR* 5.7 2.9 - - - -
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Residues in contact with LEU 199 (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* 6.4 1.6 - - + -
195B GLN 3.2 10.7 + - - +
196B GLU* 3.0 14.0 + - + +
198B ALA* 1.3 80.0 - - - +
200B LEU* 1.3 60.3 + - + +
202B GLN* 3.2 8.5 + - + +
203B GLN* 2.9 58.9 + - + +
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Residues in contact with LEU 200 (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* 3.8 26.9 - - + -
179B LEU* 4.4 13.7 - - + -
182B TRP* 4.1 37.2 - - + +
192B PRO* 4.4 9.6 - - + -
196B GLU 3.0 19.2 + - - +
197B LYS* 3.8 3.4 - - - +
199B LEU* 1.3 76.3 - - + +
201B SER* 1.3 58.3 + - - +
203B GLN* 3.0 13.1 + - - +
204B THR* 2.6 42.0 + - - +
211B VAL* 4.6 5.8 - - + -
215B PHE* 3.7 36.1 - - + -
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Residues in contact with SER 201 (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 3.0 18.2 + - - -
198B ALA* 3.5 7.2 - - - -
200B LEU* 1.3 77.7 - - - +
202B GLN* 1.3 57.9 + - - +
204B THR* 3.6 4.3 - - - -
205B HIS* 2.9 26.0 + - - -
206B LEU 2.2 34.8 + - - +
207B SER* 3.7 5.4 - - - -
208B THR* 3.8 12.3 + - - -
211B VAL* 3.9 12.2 - - - +
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Residues in contact with GLN 202 (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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198B ALA 3.0 14.3 + - - +
199B LEU* 3.2 11.9 + - + +
201B SER* 1.3 77.5 - - - +
203B GLN* 1.3 63.7 + - + +
205B HIS* 3.5 24.1 + - - -
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Residues in contact with GLN 203 (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* 3.9 39.8 - - + +
199B LEU* 2.9 47.2 + - + +
200B LEU* 3.0 19.9 + - - +
202B GLN* 1.3 79.7 - - + +
204B THR* 1.3 61.1 + - - +
205B HIS* 3.6 13.0 + - - -
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Residues in contact with THR 204 (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* 5.2 1.0 - - - +
175B SER* 2.7 51.0 + - - +
178B ILE* 3.9 15.7 - - + -
179B LEU* 3.8 20.9 - - + -
200B LEU 2.6 27.3 + - - +
201B SER* 3.5 4.2 + - - -
203B GLN* 1.3 73.7 - - - +
205B HIS* 1.3 68.9 + - - +
206B LEU* 3.2 36.4 + - - +
211B VAL* 4.3 1.6 - - - +
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Residues in contact with HIS 205 (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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175B SER* 5.5 0.2 + - - -
201B SER 2.9 9.7 + - - -
202B GLN* 3.5 20.6 + - - +
203B GLN 3.3 11.3 + - - -
204B THR* 1.3 80.6 + - - +
206B LEU* 1.3 64.5 + - - +
207B SER 4.4 0.2 + - - -
210B GLN* 4.9 0.7 - - - +
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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