Contacts of the helix formed by residues 205 - 210 (chain c) in PDB entry 6QX2
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 205 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203c ASP 3.6 2.3 + - - -
204c ILE* 1.3 76.2 - - - +
206c ILE* 1.3 63.7 + - - +
207c ALA* 3.5 12.2 + - - +
208c GLU* 3.0 29.4 + - - +
209c LEU* 3.0 23.9 + - - +
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Residues in contact with ILE 206 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204c ILE 4.2 0.2 + - - -
205c SER* 1.3 71.1 - - - +
207c ALA* 1.3 56.8 - - - +
209c LEU* 3.1 9.9 + - + +
210c MET* 2.9 37.2 + - + +
234c TYR* 3.5 44.4 - - + +
235c GLU* 3.8 32.5 - - + +
347c ASN* 3.9 8.3 - - - +
348c LEU* 4.4 4.5 - - + -
349c LYS* 3.6 39.6 - - + +
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Residues in contact with ALA 207 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205c SER* 3.6 10.9 - - - +
206c ILE* 1.3 79.5 - - - +
208c GLU* 1.3 59.3 + - - +
210c MET* 3.3 21.5 + - - +
211c GLU* 3.6 12.3 + - - +
231c ARG* 6.2 2.2 - - - +
235c GLU* 4.8 4.7 + - - +
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Residues in contact with GLU 208 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201c ASN* 4.1 12.6 + - - -
204c ILE* 3.6 25.9 - - + +
205c SER* 3.0 23.4 + - - +
207c ALA* 1.3 72.3 - - - +
209c LEU* 1.3 65.7 + - - +
210c MET 3.1 0.2 - - - -
211c GLU* 3.1 41.8 + - - +
212c ASP* 4.0 6.1 + - - +
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Residues in contact with LEU 209 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194c GLY* 3.5 30.3 - - - +
197c SER* 4.8 0.9 - - - -
198c LEU* 4.5 4.3 - - + -
204c ILE* 4.0 30.5 - - + +
205c SER 3.0 16.5 + - - +
206c ILE* 3.1 15.0 + - + +
208c GLU* 1.3 75.1 - - - +
210c MET* 1.3 56.0 - - - +
212c ASP* 3.0 13.6 + - - +
213c ILE* 2.9 26.3 + - + +
348c LEU* 4.5 11.7 - - + -
349c LYS* 3.9 36.6 - - + +
352c LEU* 3.9 20.0 - - + -
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Residues in contact with MET 210 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206c ILE* 2.9 28.8 + - + +
207c ALA* 3.6 14.6 - - - +
208c GLU 3.1 0.8 - - - -
209c LEU* 1.3 73.1 - - - +
211c GLU* 1.3 62.4 + - - +
212c ASP 3.2 0.9 - - - -
213c ILE* 3.4 21.5 - - - +
214c GLU* 3.7 21.5 + - - +
227c LYS* 3.9 34.3 - - + -
230c ILE* 4.1 11.9 - - + -
231c ARG* 4.2 30.5 - - + +
234c TYR* 3.8 25.4 - - + -
235c GLU* 5.8 0.2 - - - +
348c LEU* 4.7 2.5 - - + -
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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