Contacts of the helix formed by residues 187 - 201 (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 ASN 187 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100c ARG* 3.4 5.9 - - - +
101c TYR* 3.7 2.2 - - - -
186c HIS* 1.3 72.7 - - - +
188c LEU* 1.3 60.7 + - - +
189c THR* 3.2 34.8 + - - -
190c GLU* 3.3 30.0 + - + +
191c LEU* 3.0 29.0 + - - +
215c GLY 5.0 2.4 + - - -
217c ASP* 3.0 35.0 + - + +
482c ASP* 2.9 24.4 + - - +
483c ASP 3.3 13.5 + - - -
484c ARG* 3.4 5.3 - - - +
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Residues in contact with LEU 188 (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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101c TYR* 2.9 32.0 + - + +
131c ILE* 4.1 14.4 - - + -
164c PHE* 3.9 22.2 - - + -
165c PRO* 4.0 15.5 - - + -
169c ALA* 4.5 6.7 - - + -
186c HIS 3.7 0.8 + - - -
187c ASN* 1.3 67.7 - - - +
189c THR* 1.3 60.2 + - - +
191c LEU* 3.2 7.6 + - + +
192c ILE* 2.9 48.8 + - + +
476c ILE* 4.4 11.4 - - + +
480c PHE* 3.5 37.5 - - + +
481c GLY* 4.1 6.5 - - - +
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Residues in contact with THR 189 (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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187c ASN* 3.2 10.0 + - - -
188c LEU* 1.3 78.3 - - - +
190c GLU* 1.3 64.3 + - + +
192c ILE* 3.3 1.6 + - - +
193c ASN* 3.0 42.3 + - - +
477c ARG* 3.9 22.2 - - + +
481c GLY* 3.1 23.8 - - - -
482c ASP 3.2 12.2 + - - -
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Residues in contact with GLU 190 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186c HIS* 6.4 0.2 - - + -
187c ASN* 3.3 24.6 + - + +
189c THR* 1.3 76.9 - - + +
191c LEU* 1.3 58.3 + - + +
193c ASN* 3.4 9.4 + - - +
194c GLY 2.9 24.4 + - - -
212c ASP* 3.2 24.7 - - - +
213c ILE* 3.6 15.0 - - + +
214c GLU* 3.1 29.8 + - - +
215c GLY 4.0 2.1 - - - +
484c ARG* 2.8 48.8 + - - +
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Residues in contact with LEU 191 (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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165c PRO* 3.7 25.8 - - + +
168c LEU* 3.8 28.0 - - + -
169c ALA* 3.4 41.3 - - + +
186c HIS* 3.8 18.2 - - + -
187c ASN 3.0 16.7 + - - +
188c LEU* 3.2 11.0 + - - +
190c GLU* 1.3 75.9 - - + +
192c ILE* 1.3 56.6 + - - +
194c GLY* 3.0 4.7 + - - -
195c VAL* 2.9 32.3 + - - +
213c ILE* 3.9 24.4 - - + +
352c LEU* 4.6 4.5 - - + +
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Residues in contact with ILE 192 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165c PRO* 4.2 12.3 - - + -
188c LEU* 2.9 33.5 + - + +
189c THR 4.0 2.7 - - - +
191c LEU* 1.3 72.9 - - - +
193c ASN* 1.3 60.4 + - - +
195c VAL* 3.1 8.6 + - - +
196c LEU* 2.9 39.9 + - + +
473c LEU* 3.4 44.9 - - + +
476c ILE* 3.8 14.4 - - + -
477c ARG* 3.4 43.3 - - + +
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Residues in contact with ASN 193 (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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189c THR* 3.0 32.8 + - - +
190c GLU* 3.6 9.3 - - - +
192c ILE* 1.3 75.1 - - - +
194c GLY* 1.3 55.4 + - - +
196c LEU* 3.4 8.3 + - - +
197c SER* 3.0 33.3 + - - -
212c ASP* 3.6 20.1 + - + +
477c ARG* 2.7 34.7 + - - +
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Residues in contact with GLY 194 (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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190c GLU 2.9 14.6 + - - -
191c LEU 3.0 5.3 + - - -
193c ASN* 1.3 75.7 - - - +
195c VAL* 1.3 56.2 + - - +
197c SER* 3.3 4.7 + - - -
198c LEU* 3.0 24.6 + - - +
209c LEU* 3.5 20.3 - - - +
212c ASP* 3.6 16.5 - - - +
213c ILE* 4.4 8.7 - - - -
352c LEU* 4.5 3.1 - - - -
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Residues in contact with VAL 195 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165c PRO* 4.7 5.8 - - + -
191c LEU 2.9 20.5 + - - +
192c ILE* 3.1 9.2 + - - +
194c GLY* 1.3 71.5 - - - +
196c LEU* 1.3 55.5 + - - +
198c LEU* 3.3 9.5 + - + +
199c SER* 2.8 33.0 + - - -
352c LEU* 3.7 25.1 - - + +
355c TYR* 4.3 20.2 - - + -
356c LEU* 3.9 26.6 - - + +
473c LEU* 3.5 30.1 - - + -
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Residues in contact with LEU 196 (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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192c ILE* 2.9 27.4 + - + +
193c ASN* 3.6 8.5 - - - +
195c VAL* 1.3 73.0 - - - +
197c SER* 1.3 64.4 + - - +
199c SER* 2.8 21.2 + - - -
200c LYS* 3.2 20.6 + - + +
470c ARG* 3.7 47.3 - - + +
473c LEU* 4.7 9.0 - - + -
474c THR* 3.6 16.6 - - - +
477c ARG* 3.7 23.6 - - - +
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Residues in contact with SER 197 (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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193c ASN 3.0 8.6 + - - -
194c GLY 3.4 6.7 - - - -
196c LEU* 1.3 73.6 - - - +
198c LEU* 1.3 62.5 + - - +
200c LYS* 3.2 12.1 + - - +
201c ASN* 3.1 22.5 + - - +
204c ILE* 3.8 21.2 - - - +
209c LEU* 4.8 0.2 - - - -
212c ASP* 2.7 30.1 + - - -
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Residues in contact with LEU 198 (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 3.0 13.8 + - - +
195c VAL* 3.5 9.4 - - - +
197c SER* 1.3 74.7 - - - +
199c SER* 1.3 57.3 + - - +
200c LYS 3.1 0.2 - - - -
201c ASN 3.1 31.3 + - - +
202c PRO* 3.4 10.7 - - + +
204c ILE* 3.6 26.8 - - + +
209c LEU* 4.5 5.6 - - + -
349c LYS* 4.0 12.3 - - + -
352c LEU* 3.7 18.6 - - + +
353c VAL* 3.7 49.6 - - + +
356c LEU* 4.1 16.8 - - + +
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Residues in contact with SER 199 (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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195c VAL* 2.8 19.2 + - - -
196c LEU* 2.8 16.8 + - - -
198c LEU* 1.3 72.2 - - - +
200c LYS* 1.3 52.9 + - - +
202c PRO* 5.2 2.4 - - - +
356c LEU* 3.7 29.6 - - - -
466c LEU* 3.5 16.1 - - - +
470c ARG* 2.9 52.5 + - - +
473c LEU* 6.5 0.2 - - - -
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Residues in contact with LYS 200 (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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196c LEU* 3.2 20.7 + - + +
197c SER* 3.6 10.1 - - - +
198c LEU 3.1 0.6 - - - -
199c SER* 1.3 78.2 - - - +
201c ASN* 1.3 58.7 + - + +
202c PRO* 4.0 6.4 - - - +
470c ARG* 3.7 27.4 - - - +
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Residues in contact with ASN 201 (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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197c SER 3.1 10.1 + - - +
198c LEU* 3.1 10.2 + - - +
200c LYS* 1.3 80.1 - - + +
202c PRO* 1.3 67.6 - - - +
203c ASP* 3.0 21.1 + - - +
204c ILE* 3.1 44.4 + - + +
208c GLU* 4.1 13.7 + - - -
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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