Contacts of the helix formed by residues 188 - 203 (chain D) in PDB entry 6Q2N
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 188 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177D PRO* 3.7 12.0 + - + +
180D THR 5.1 0.2 + - - -
182D VAL* 5.0 7.2 - - + +
185D ASP* 5.3 1.1 - - - +
187D CYS* 1.3 78.1 - - - +
189D ARG* 1.3 71.5 + - - +
190D ARG* 2.9 30.1 + - - +
191D LYS* 3.4 40.2 - - + +
192D CYS* 3.2 22.7 + - - +
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Residues in contact with ARG 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D CYS* 4.0 4.5 + - - -
188D ASN* 1.3 74.5 + - - +
190D ARG* 1.3 60.2 + - - +
192D CYS* 3.6 3.7 + - - +
193D HIS* 3.0 55.0 + - + +
233D CYS 4.1 14.1 + - - +
234D SER* 2.6 36.5 + - - +
235D TYR* 3.8 15.8 + - - +
236D GLU 4.0 2.4 + - - -
237D GLU* 3.3 35.4 + - - +
246D LEU* 6.4 0.2 - - - +
296D VAL* 4.2 22.0 + - - +
298D THR* 5.3 3.0 + - - -
312D TRP* 6.3 0.2 - - - +
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Residues in contact with ARG 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D ASN* 2.9 17.2 + - - +
189D ARG* 1.3 79.2 - - - +
191D LYS* 1.3 98.8 + - - +
193D HIS* 3.3 5.0 + - - +
194D LYS* 3.0 41.1 + - + +
197D ARG* 5.6 0.3 + - - -
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Residues in contact with LYS 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D PRO* 3.6 27.4 - - + +
188D ASN* 3.4 17.8 - - + +
190D ARG* 1.3 107.8 - - - +
192D CYS* 1.3 58.1 + - - +
194D LYS* 3.4 12.9 + - + +
195D ALA* 3.0 30.5 + - - +
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Residues in contact with CYS 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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177D PRO* 3.7 5.7 - - - +
178D CYS* 2.0 56.6 - - + +
188D ASN 3.2 20.4 + - - +
189D ARG* 3.7 5.4 - - - +
190D ARG 3.3 0.4 - - - -
191D LYS* 1.3 78.1 - - - +
193D HIS* 1.3 57.0 + - - +
195D ALA* 3.3 3.2 + - - +
196D LEU* 2.9 32.1 + - - +
230D VAL* 6.4 0.4 - - - -
233D CYS* 4.3 4.7 - - - -
234D SER* 4.1 25.6 - - - -
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Residues in contact with HIS 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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189D ARG* 3.0 53.8 + - + +
190D ARG* 3.9 4.2 - - - +
192D CYS* 1.3 78.1 - - - +
194D LYS* 1.3 66.1 + - - +
196D LEU* 3.4 12.6 + - + +
197D ARG* 3.0 25.2 + - - +
234D SER* 2.7 50.4 + - - -
294D GLY* 3.2 31.5 + - - +
295D THR* 4.6 13.1 + - - -
296D VAL* 5.2 5.6 - - - +
298D THR* 4.8 4.8 + - - +
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Residues in contact with LYS 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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190D ARG* 3.0 33.4 + - + +
191D LYS* 3.4 13.0 - - + +
193D HIS* 1.3 76.4 - - - +
195D ALA* 1.3 58.0 + - + +
197D ARG* 3.2 25.0 + - - +
198D GLN* 3.1 50.3 + - + +
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Residues in contact with ALA 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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170D TYR 5.0 0.2 - - - +
173D ALA* 3.2 31.8 - - + +
174D TYR* 3.4 18.4 + - - +
177D PRO* 4.5 6.5 - - + -
191D LYS 3.0 16.9 + - - +
192D CYS 3.7 3.4 - - - +
194D LYS* 1.3 76.3 - - + +
196D LEU* 1.3 65.3 + - - +
198D GLN* 3.4 6.6 + - - +
199D PHE* 3.1 18.0 + - - +
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Residues in contact with LEU 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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174D TYR* 3.5 40.1 - - + +
178D CYS* 5.5 0.2 - - - -
192D CYS* 2.9 21.9 + - - +
193D HIS* 3.8 15.9 - - + +
195D ALA* 1.3 77.1 - - - +
197D ARG* 1.3 56.6 + - - +
199D PHE* 3.2 2.6 + - - +
200D PHE* 2.9 41.2 + - + +
228D THR 5.6 0.9 - - - +
229D ILE* 3.7 44.6 - - + +
234D SER* 4.8 3.6 - - - +
293D ILE* 4.2 12.5 - - + +
294D GLY* 4.2 14.4 - - - -
298D THR* 6.6 0.2 - - + -
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Residues in contact with ARG 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D ARG 5.6 0.4 + - - -
193D HIS* 3.0 14.5 + - - +
194D LYS* 3.2 26.9 + - - +
196D LEU* 1.3 76.7 - - - +
198D GLN* 1.3 59.7 + - + +
200D PHE* 3.4 3.5 + - - -
201D ASP* 2.9 29.8 + - - +
253D ASN* 4.5 10.8 + - - +
255D ILE* 3.7 33.7 - - - +
259D ARG* 4.4 10.5 + - - +
293D ILE 4.0 8.7 - - - +
294D GLY* 2.9 40.8 + - - +
295D THR* 3.6 29.5 - - - +
296D VAL* 5.9 0.6 - - - +
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Residues in contact with GLN 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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170D TYR* 5.4 7.3 - - + +
173D ALA* 6.2 3.4 - - + -
194D LYS* 3.1 40.9 + - + +
195D ALA* 4.1 6.1 - - - +
196D LEU 3.3 0.4 - - - -
197D ARG* 1.3 74.8 - - + +
199D PHE* 1.3 60.3 + - - +
201D ASP* 4.5 4.5 - - + -
202D LYS* 3.0 48.5 + - + +
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Residues in contact with PHE 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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161D CYS* 5.2 1.8 - - - -
167D CYS* 4.1 30.7 - - - -
170D TYR* 3.8 22.2 - - - +
171D ARG* 4.5 0.9 - - + -
173D ALA* 6.2 0.8 - - - +
174D TYR* 3.3 51.1 - + + -
195D ALA 3.1 11.4 + - - +
196D LEU* 3.5 6.7 - - + +
198D GLN* 1.3 79.2 - - - +
200D PHE* 1.3 97.7 + + - +
201D ASP 3.1 1.6 + - - -
203D VAL* 3.5 33.6 + - + +
208D SER* 3.9 22.2 - - - -
211D MET* 6.3 2.0 - - - -
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Residues in contact with PHE 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 LEU* 2.9 22.9 + - + +
197D ARG* 3.6 4.7 - - - +
199D PHE* 1.3 107.3 - + - +
201D ASP* 1.3 58.7 + - - +
203D VAL 5.3 4.0 - - - +
208D SER* 3.7 26.0 - - - -
209D TYR* 4.0 22.7 - + - -
212D LEU* 4.0 19.3 - - + -
228D THR* 5.9 2.5 - - + -
229D ILE* 5.1 2.9 - - + -
259D ARG* 5.4 8.7 + - - +
287D LEU* 5.4 7.3 - - - +
290D SER* 3.9 21.6 - - - +
291D GLY* 6.0 0.9 - - - -
293D ILE* 3.8 43.5 - - + +
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Residues in contact with ASP 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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197D ARG 2.9 15.9 + - - +
198D GLN* 4.1 5.2 - - + +
199D PHE 3.1 0.2 - - - -
200D PHE* 1.3 81.6 - - - +
202D LYS* 1.3 84.4 + - + +
203D VAL 3.7 2.6 - - - +
259D ARG* 5.4 9.2 + - - +
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Residues in contact with LYS 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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170D TYR* 4.9 23.1 + - + -
198D GLN* 3.0 34.6 + - + +
201D ASP* 1.3 93.7 - - + +
203D VAL* 1.3 70.0 + - + +
204D PRO* 3.7 7.4 - - - +
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Residues in contact with VAL 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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164D ASP* 5.2 0.9 - - - +
166D ILE* 3.8 28.3 - - + +
167D CYS* 3.8 35.9 - - + +
170D TYR* 4.0 23.8 - - + -
199D PHE* 3.5 26.8 + - + +
200D PHE* 5.3 2.8 - - - -
201D ASP 4.7 3.8 - - - +
202D LYS* 1.3 76.3 - - + +
204D PRO* 1.3 84.6 - - + +
207D HIS* 4.0 6.1 - - + +
208D SER* 4.9 4.1 + - - -
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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