Contacts of the helix formed by residues 191 - 209 (chain D) in PDB entry 4GQS
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 191 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187D PHE* 4.4 15.4 - - - -
188D ASP* 3.2 30.2 + - + +
189D TYR 5.0 0.2 - - - -
190D LYS* 1.3 76.1 - - - +
192D GLN* 1.3 70.2 + - - +
193D GLN* 3.5 28.6 + - - +
194D PHE* 3.0 6.1 + - + +
195D LEU* 2.9 20.9 + - - +
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Residues in contact with GLN 192 (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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190D LYS 3.3 6.3 + - - +
191D ASP* 1.3 75.7 + - - +
193D GLN* 1.3 55.6 + - - +
195D LEU* 3.4 30.1 - - - +
196D ASN* 2.6 56.7 + - - +
199D GLU* 5.5 1.0 + - - -
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Residues in contact with GLN 193 (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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187D PHE* 3.6 32.4 - - + -
191D ASP* 3.2 17.2 + - - +
192D GLN* 1.3 77.2 - - + +
194D PHE* 1.3 57.6 + - - +
196D ASN* 4.0 3.7 - - - +
197D LEU* 3.0 30.0 + - - +
247D LYS* 5.0 6.1 - - - +
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Residues in contact with PHE 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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172D CYS* 3.4 40.8 - - + -
175D CYS* 3.7 18.2 - - - -
176D ASN* 3.2 39.5 - - + -
179D CYS* 4.0 8.3 - - - -
187D PHE* 3.7 25.4 - + + -
188D ASP 3.4 27.4 - - - +
189D TYR* 3.6 29.4 - + - -
191D ASP* 3.0 4.9 + - + +
193D GLN* 1.3 78.4 - - - +
195D LEU* 1.3 59.7 + - - +
197D LEU* 3.4 5.8 + - + +
198D MET* 3.0 33.5 + - + +
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Residues in contact with LEU 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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168D PHE* 4.5 25.1 - - + -
189D TYR 5.1 9.2 - - - +
190D LYS* 5.4 4.9 - - - +
191D ASP 2.9 16.4 + - - +
192D GLN* 3.4 32.1 - - - +
194D PHE* 1.3 78.0 - - - +
196D ASN* 1.3 60.3 + - - +
198D MET* 3.3 6.9 + - + +
199D GLU* 2.8 30.1 + - + +
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Residues in contact with ASN 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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192D GLN* 2.6 34.4 + - - +
193D GLN* 4.1 3.6 - - - +
195D LEU* 1.3 72.1 - - - +
197D LEU* 1.3 66.1 + - - +
199D GLU* 3.0 40.6 + - - +
200D LYS* 3.0 33.9 + - - +
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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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175D CYS* 4.3 7.2 - - - -
179D CYS* 4.0 25.1 - - - -
183D PHE* 5.4 4.0 - - + -
187D PHE* 5.3 8.5 - - + -
193D GLN 3.0 19.5 + - - +
194D PHE* 3.4 11.0 - - + +
196D ASN* 1.3 76.7 - - - +
198D MET* 1.3 54.1 + - + +
200D LYS* 3.9 2.8 - - - +
201D LEU* 2.7 66.0 + - + +
240D MET* 5.0 15.1 - - + +
295D LEU* 4.1 24.0 - - + -
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Residues in contact with MET 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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168D PHE* 4.4 15.9 - - + +
171D GLY* 3.5 8.7 - - - +
172D CYS* 3.4 43.7 - - - +
175D CYS* 3.5 36.6 - - - -
194D PHE* 3.0 26.0 + - + +
195D LEU* 3.5 10.3 - - + +
197D LEU* 1.3 79.3 - - - +
199D GLU* 1.3 55.3 + - - +
201D LEU* 4.1 5.6 - - - -
202D ASN* 2.7 40.5 + - + +
299D THR* 4.4 8.7 - - + -
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Residues in contact with GLU 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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192D GLN* 5.5 0.9 + - - -
195D LEU* 2.8 18.1 + - + +
196D ASN* 3.0 37.6 + - - +
198D MET* 1.3 80.3 - - - +
200D LYS* 1.3 67.2 + - + +
202D ASN* 3.7 4.2 + - - +
203D GLU* 3.1 19.9 + - - +
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Residues in contact with LYS 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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196D ASN* 3.0 29.5 + - - +
197D LEU* 4.1 2.2 - - - +
199D GLU* 1.3 82.7 - - + +
201D LEU* 1.3 67.5 + - - +
203D GLU* 2.8 18.0 + - - +
204D ASN* 3.0 17.0 + - - +
232D LYS* 5.7 4.3 - - - +
236D ASN* 3.1 46.0 - - + +
239D PHE* 3.2 43.7 - - + +
240D MET* 4.4 12.3 - - + +
243D ASP* 5.1 4.8 + - - -
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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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175D CYS* 3.9 7.0 - - - -
197D LEU* 2.7 43.5 + - + +
198D MET* 3.8 6.1 - - - +
200D LYS* 1.3 73.2 - - - +
202D ASN* 1.3 60.2 + - - +
204D ASN* 3.4 26.9 + - - +
205D ILE* 4.1 8.1 + - - +
240D MET* 4.0 21.2 - - + +
295D LEU 3.6 17.5 - - - +
296D GLY* 3.7 16.8 - - - +
299D THR* 3.2 42.4 - - + +
300D GLU* 5.8 2.4 - - + +
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Residues in contact with ASN 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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167D THR* 5.9 2.6 - - - +
198D MET* 2.7 26.9 + - + +
199D GLU* 3.7 4.0 + - - +
201D LEU* 1.3 69.9 - - - +
203D GLU* 1.3 66.0 + - - +
204D ASN 3.1 2.7 + - - -
205D ILE* 3.4 7.3 + - - +
206D ARG* 3.3 23.6 + - - +
300D GLU* 3.9 16.3 - - - +
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Residues in contact with GLU 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 GLU* 3.1 15.0 + - - +
200D LYS* 2.8 9.4 + - - +
202D ASN* 1.3 75.6 - - - +
204D ASN* 1.3 56.0 + - - +
206D ARG* 3.2 39.1 + - - +
207D ILE* 2.8 57.5 + - + +
232D LYS* 3.3 30.9 - - - +
236D ASN* 3.0 23.0 + - - +
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Residues in contact with ASN 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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200D LYS 3.0 14.5 + - - +
201D LEU* 3.4 20.7 + - - +
202D ASN 3.1 0.4 - - - -
203D GLU* 1.3 76.3 - - - +
205D ILE* 1.3 59.2 + - + +
207D ILE* 3.0 5.0 + - - +
208D VAL* 2.7 41.9 + - + +
233D LEU* 3.0 31.7 - - + +
236D ASN* 3.8 15.4 + - - +
237D LEU* 3.7 12.2 - - + +
240D MET* 3.4 28.5 - - - +
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Residues in contact with ILE 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 4.3 9.9 - - - +
202D ASN 3.4 2.8 + - - +
204D ASN* 1.3 81.8 - - + +
206D ARG* 1.3 58.6 + - - +
208D VAL* 4.3 5.8 - - + +
209D SER* 2.8 46.5 + - - +
296D GLY 5.4 3.8 - - - +
300D GLU* 3.3 47.6 - - + +
476D PHE* 5.1 6.5 - - + -
477D ALA* 6.0 1.6 - - + -
502D 0XV 3.7 45.8 - - + -
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Residues in contact with ARG 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 ASN* 3.3 18.3 + - - +
203D GLU* 3.3 42.3 + - - +
205D ILE* 1.3 79.9 - - - +
207D ILE* 1.3 59.5 + - + +
209D SER* 4.7 3.3 - - - -
210D THR* 2.7 26.2 + - - -
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Residues in contact with ILE 207 (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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203D GLU* 2.8 44.2 + - + +
204D ASN* 3.0 6.3 + - - +
206D ARG* 1.3 89.4 - - + +
208D VAL* 1.3 63.7 + - - +
209D SER 3.4 0.2 - - - -
210D THR* 2.9 23.2 + - - +
213D ILE* 3.2 22.7 - - + +
229D THR* 3.0 43.5 - - + +
232D LYS* 5.9 5.2 - - + -
233D LEU* 4.1 20.9 - - + +
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Residues in contact with VAL 208 (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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100D PHE* 4.7 14.6 - - + -
102D LEU* 4.8 4.9 - - + -
204D ASN* 2.7 27.1 + - + +
205D ILE* 4.1 8.1 - - + +
207D ILE* 1.3 69.1 - - - +
209D SER* 1.3 66.8 + - - +
210D THR 3.0 12.7 + - - +
213D ILE* 3.9 18.1 - - + +
214D GLN* 4.1 6.2 + - - +
233D LEU* 3.4 25.8 - - + -
476D PHE* 4.0 21.8 - - + -
502D 0XV 4.5 24.2 - - + -
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Residues in contact with SER 209 (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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205D ILE* 2.8 28.1 + - - -
206D ARG* 4.7 3.1 - - - -
208D VAL* 1.3 73.8 - - - +
210D THR* 1.3 63.4 + - - +
211D PRO* 3.3 3.1 - - - +
214D GLN* 3.8 16.0 + - - -
474D ASN 4.9 1.7 - - - +
475D GLY* 4.2 16.5 - - - -
476D PHE* 4.0 21.7 - - - -
477D ALA* 5.0 4.8 + - - +
479D VAL* 5.7 4.7 - - - +
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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