Contacts of the helix formed by residues 193 - 206 (chain D) in PDB entry 3G1Q
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 ASP 193 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180D CYS* 5.9 0.2 - - - -
189D ARG* 3.2 16.6 + - - +
190D LYS 4.8 4.9 - - - +
191D ARG 3.8 2.4 + - - -
192D LEU* 1.3 77.3 - - - +
194D ALA* 1.3 67.8 + - - +
195D ARG* 3.7 23.0 + - - +
196D ARG* 3.0 25.6 + - - +
197D PHE* 2.8 21.6 + - - +
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Residues in contact with ALA 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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176D ILE* 4.1 20.9 - - + +
177D ASN* 3.2 31.2 - - - +
180D CYS* 5.0 8.6 - - + +
192D LEU 4.0 0.4 + - - -
193D ASP* 1.3 72.7 - - - +
195D ARG* 1.4 54.1 + - - +
197D PHE* 3.8 5.2 - - - +
198D ALA* 2.8 37.5 + - - +
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Residues in contact with ARG 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 ASP* 3.7 18.2 + - - +
194D ALA* 1.4 76.2 - - - +
196D ARG* 1.3 58.7 + - + +
198D ALA* 3.6 4.6 + - - +
199D GLN* 3.0 47.4 + - - +
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Residues in contact with ARG 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 ARG* 3.4 33.9 + - - +
192D LEU* 4.3 9.4 - - + -
193D ASP* 3.0 24.5 + - - +
195D ARG* 1.3 76.3 - - + +
197D PHE* 1.3 57.8 + - - +
199D GLN* 3.4 14.7 + - - +
200D LEU* 3.0 36.4 + - + +
239D ILE* 3.6 31.9 - - - +
242D GLU* 5.6 0.8 + - - -
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Residues in contact with PHE 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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176D ILE* 4.8 2.7 - - + -
180D CYS* 3.9 19.5 - - - -
184D PHE* 3.2 34.3 - + - -
192D LEU* 3.8 31.7 - - + +
193D ASP 2.8 18.2 + - - +
194D ALA* 3.8 4.9 - - - +
196D ARG* 1.3 73.6 - - - +
198D ALA* 1.3 58.9 + - - +
200D LEU* 3.3 6.7 + - + -
201D LEU* 2.9 54.0 + - + +
236D LEU* 3.6 32.8 - - + -
285D ILE* 4.3 8.5 - - + -
286D VAL* 6.2 0.2 - - - -
289D MET* 4.0 26.7 - - + -
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Residues in contact with ALA 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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176D ILE* 3.8 24.1 - - + +
194D ALA 2.8 21.8 + - - +
195D ARG* 3.8 5.2 - - - +
197D PHE* 1.3 72.7 - - - +
199D GLN* 1.3 55.9 + - + +
201D LEU* 3.8 4.7 - - - +
202D ALA* 2.8 32.8 + - - +
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Residues in contact with GLN 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 ARG* 3.0 41.7 + - - +
196D ARG* 3.5 14.7 - - - +
197D PHE 3.4 0.2 - - - -
198D ALA* 1.3 72.3 - - - +
200D LEU* 1.3 56.8 + - + +
202D ALA* 3.4 5.5 + - - +
203D LYS* 2.9 28.8 + - - +
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Residues in contact with LEU 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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192D LEU* 4.2 14.6 - - + -
196D ARG* 3.0 20.8 + - + +
197D PHE* 3.8 6.7 - - + +
199D GLN* 1.3 74.7 - - + +
201D LEU* 1.3 59.0 + - + +
203D LYS* 3.3 9.9 + - + +
204D MET* 3.1 34.2 + - - +
232D ALA* 3.7 20.3 - - + +
235D GLU* 3.5 34.1 - - + +
236D LEU* 4.1 21.8 - - + +
239D ILE* 4.1 26.5 - - + -
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Residues in contact with LEU 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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176D ILE* 4.5 13.7 - - + -
197D PHE* 2.9 53.6 + - + +
198D ALA* 3.9 3.8 - - - +
200D LEU* 1.3 75.3 - - + +
202D ALA* 1.3 59.9 + - - +
204D MET* 3.2 12.9 + - - +
205D GLU* 2.8 30.0 + - - +
236D LEU* 5.2 0.9 - - + -
286D VAL* 4.4 13.7 - - + -
289D MET* 3.9 33.0 - - + -
290D PHE* 3.9 25.5 - - + -
293D GLN* 6.1 4.5 - - + -
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Residues in contact with ALA 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 ALA 2.8 20.4 + - - +
199D GLN* 3.8 5.8 - - - +
201D LEU* 1.3 74.7 - - - +
203D LYS* 1.3 62.1 + - - +
205D GLU* 3.7 17.0 - - - +
206D SER* 2.8 31.0 + - - -
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Residues in contact with LYS 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 GLN 2.9 16.8 + - - +
200D LEU* 3.5 13.2 - - + +
202D ALA* 1.3 78.5 - - - +
204D MET* 1.3 61.2 + - - +
206D SER* 3.5 10.1 + - - -
207D SER* 3.1 19.6 + - - -
228D ARG* 3.6 35.8 - - + +
229D CYS* 5.1 0.3 - - - -
231D GLU* 3.1 25.7 + - - +
232D ALA* 3.8 18.2 - - + +
235D GLU* 4.6 8.8 + - - +
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Residues in contact with MET 204 (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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109D VAL* 3.7 41.4 - - + +
200D LEU* 3.1 17.6 + - - +
201D LEU* 3.2 18.1 + - - +
203D LYS* 1.3 75.0 - - - +
205D GLU* 1.3 64.3 + - - +
207D SER* 3.1 17.5 + - - -
208D LEU* 3.6 10.4 + - - +
229D CYS* 4.3 14.4 - - - +
232D ALA* 3.7 14.6 - - + +
233D ARG* 3.3 45.3 - - + +
236D LEU* 5.0 5.2 - - - -
286D VAL* 4.3 20.6 - - + -
290D PHE* 4.0 5.8 - - + -
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Residues in contact with GLU 205 (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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201D LEU 2.8 15.9 + - - +
202D ALA* 3.7 17.3 - - - +
204D MET* 1.3 78.0 - - - +
206D SER* 1.3 60.7 + - - +
207D SER 3.0 0.2 - - - -
208D LEU* 3.1 29.9 + - + +
290D PHE* 3.7 26.1 - - + -
294D HIS* 2.7 38.7 + - - -
460D MET* 4.8 14.9 - - + +
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Residues in contact with SER 206 (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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202D ALA 2.8 23.1 + - - -
203D LYS* 3.5 8.7 + - - -
204D MET 3.2 0.2 - - - -
205D GLU* 1.3 78.9 - - - +
207D SER* 1.3 58.9 + - - +
208D LEU 3.4 3.6 + - - +
225D GLN* 4.9 4.0 - - - +
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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