Contacts of the helix formed by residues 193 - 203 (chain D) in PDB entry 2OYQ
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 193 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151D LEU* 3.4 7.3 - - - +
153D ASN* 5.6 1.6 - - - +
192D ASP* 1.3 86.5 + - - +
194D GLU* 1.3 65.7 + - - +
195D LYS 3.4 0.9 - - - +
196D GLU* 3.1 31.6 + - + +
197D LEU* 3.3 10.6 + - - +
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Residues in contact with GLU 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D LEU* 3.8 20.9 - - + +
153D ASN* 4.2 16.4 + - - +
154D SER 6.0 0.4 - - - -
155D PRO* 5.4 9.2 - - + -
192D ASP 4.1 0.8 + - - -
193D ASN* 1.3 73.3 - - - +
195D LYS* 1.3 63.9 + - + +
197D LEU* 3.9 10.0 + - - +
198D LEU* 4.4 5.2 + - - +
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Residues in contact with LYS 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D ASN* 3.4 1.2 - - + +
194D GLU* 1.3 80.2 - - + +
196D GLU* 1.3 61.6 + - - +
197D LEU 3.4 0.2 - - - -
198D LEU* 3.6 6.8 + - - +
199D MET* 3.2 22.3 + - - +
233D ILE* 4.6 28.9 - - + -
234D PHE* 4.9 3.6 - - - -
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Residues in contact with GLU 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D PHE* 5.4 2.0 - - + -
192D ASP* 5.2 3.4 - - - +
193D ASN* 3.1 31.1 + - + +
195D LYS* 1.3 77.2 - - - +
197D LEU* 1.3 60.0 + - - +
199D MET* 3.3 8.1 + - - +
200D GLU* 2.8 30.2 + - - +
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Residues in contact with LEU 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ILE* 3.7 28.5 - - + +
134D ASP 5.6 0.2 - - - -
135D ALA 5.7 0.4 - - - +
136D ILE* 5.8 5.6 - - + -
149D PHE* 3.7 35.2 - - + +
150D ASP* 4.1 5.8 - - - +
151D LEU* 4.2 18.2 - - + +
190D PRO 5.2 0.7 - - - +
191D PHE* 3.5 32.9 - - + +
193D ASN 3.3 8.3 + - - +
194D GLU 4.3 5.8 - - - +
195D LYS 3.4 0.4 - - - -
196D GLU* 1.3 78.3 - - - +
198D LEU* 1.3 65.0 + - + +
200D GLU* 3.2 16.4 + - + +
201D TYR* 3.3 14.4 + - + +
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Residues in contact with LEU 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ILE* 6.3 2.9 - - + -
194D GLU 4.4 4.6 + - - +
195D LYS* 3.6 10.2 + - - +
196D GLU 3.4 0.4 - - - -
197D LEU* 1.3 84.6 - - + +
199D MET* 1.3 58.3 + - - +
201D TYR* 3.5 4.2 + - - +
202D LEU* 3.2 29.6 + - - +
229D ARG* 5.7 11.9 - - + +
233D ILE* 6.3 0.9 - - + -
234D PHE* 4.4 17.2 - - + -
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Residues in contact with MET 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D LYS 3.2 16.9 + - - +
196D GLU* 3.5 9.0 - - - +
197D LEU 3.3 0.2 - - - -
198D LEU* 1.3 77.1 - - - +
200D GLU* 1.3 60.3 + - - +
202D LEU* 4.2 4.1 - - - +
203D ASN* 3.7 21.5 + - - +
234D PHE* 3.8 23.5 - - + -
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Residues in contact with GLU 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D PHE* 5.8 8.6 - - + -
191D PHE* 6.0 1.6 - - + -
196D GLU 2.8 16.6 + - - +
197D LEU* 3.4 16.6 - - + +
198D LEU 3.2 0.4 - - - -
199D MET* 1.3 79.2 - - - +
201D TYR* 1.3 56.6 + - - +
203D ASN* 3.9 5.6 - - - +
204D PHE* 3.4 19.9 + - - +
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Residues in contact with TYR 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D PHE* 4.8 22.2 - - + -
197D LEU* 3.3 13.4 + - + +
198D LEU* 3.5 4.2 + - - +
200D GLU* 1.3 76.5 - - - +
202D LEU* 1.3 59.4 + - - +
203D ASN 3.3 2.0 - - - -
204D PHE* 3.1 10.3 + - + +
205D TRP* 2.9 29.8 + - - +
242D LEU* 5.9 0.4 - - - -
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Residues in contact with LEU 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D LEU 3.2 19.6 + - - +
199D MET* 4.6 5.6 - - - +
201D TYR* 1.3 75.1 - - - +
203D ASN* 1.3 57.5 + - - +
204D PHE 3.2 4.3 + - - -
205D TRP* 3.9 14.3 + - - +
206D GLN* 4.6 5.9 + - - +
234D PHE* 5.0 11.9 - - + -
241D ARG* 5.4 12.6 - - + +
242D LEU* 4.8 15.6 - - + +
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Residues in contact with ASN 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D MET 3.7 17.6 + - - +
200D GLU* 3.9 5.2 - - - +
201D TYR 3.3 0.4 - - - -
202D LEU* 1.3 76.3 - - - +
204D PHE* 1.3 57.0 + - - +
206D GLN* 5.0 4.5 - - - -
207D GLN* 4.7 7.5 - - - +
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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