Contacts of the helix formed by residues 198 - 211 (chain D) in PDB entry 2W3S
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 HIS 198 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196D SER* 2.7 16.1 + - - +
197D GLN* 1.3 73.9 - - - +
199D PRO* 1.3 68.1 - - + +
200D SER 3.8 3.4 - - - -
201D GLU* 3.3 45.6 + - + +
202D ILE* 3.1 20.8 + - - +
231D LYS 4.0 0.4 + - - -
232D GLU* 3.7 20.8 + - - +
236D ASN* 5.4 0.2 + - - -
464D LEU* 6.3 2.2 - - + -
524D THR 3.2 25.3 + - - -
525D SER* 3.8 4.9 - - - -
526D ALA* 3.5 34.2 + - + +
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Residues in contact with PRO 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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196D SER* 3.7 2.0 - - - +
197D GLN 3.7 1.3 - - - +
198D HIS* 1.3 89.8 - - + +
200D SER* 1.3 64.6 + - - +
202D ILE* 2.8 23.4 + - + +
203D GLN* 2.9 13.7 + - - +
219D VAL* 3.9 18.7 - - + +
221D MET* 4.1 18.4 - - + -
484D GLY 5.3 1.1 - - - +
486D THR* 3.7 27.1 - - + -
516D THR* 4.3 13.0 - - + -
518D THR* 3.9 18.6 - - + -
524D THR* 4.9 7.0 - - - +
525D SER 5.5 1.8 - - - +
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Residues in contact with SER 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D HIS* 3.4 1.4 - - - -
199D PRO* 1.3 78.2 - - - +
201D GLU* 1.3 62.3 + - - +
203D GLN* 3.3 12.6 + - - +
204D HIS* 3.1 22.1 + - - +
214D PHE* 6.1 0.2 - - - -
518D THR* 4.0 14.2 - - - +
521D VAL 4.8 1.0 + - - -
522D PRO 4.7 0.2 - - - -
523D ASN* 4.0 9.9 + - - -
524D THR* 2.7 57.3 + - - +
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Residues in contact with GLU 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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77D SER 5.3 0.2 - - - -
78D PRO* 3.4 34.9 - - - +
198D HIS* 3.3 42.3 + - + +
199D PRO 3.3 0.4 - - - -
200D SER* 1.3 74.3 - - - +
202D ILE* 1.3 68.3 + - - +
204D HIS* 3.2 10.6 + - + +
205D LYS* 3.0 30.5 + - + +
232D GLU 4.2 2.6 - - - +
233D SER* 3.9 7.6 - - - -
236D ASN* 3.1 27.5 - - - +
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Residues in contact with ILE 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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192D ILE* 4.0 7.2 - - + -
194D CYS* 4.0 13.9 - - + -
196D SER* 3.7 19.1 - - - +
198D HIS 3.1 16.1 + - - +
199D PRO* 2.8 15.7 + - + +
201D GLU* 1.3 71.6 - - - +
203D GLN* 1.3 65.2 + - - +
205D LYS* 3.6 1.0 - - - +
206D VAL* 2.8 32.3 + - + +
219D VAL* 3.8 21.3 - - + -
235D GLY* 3.9 15.5 - - - +
236D ASN* 3.8 20.6 - - - +
239D ALA* 3.7 32.8 - - + -
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Residues in contact with GLN 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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474B TYR* 3.6 33.8 + - - -
199D PRO 2.9 9.7 + - - +
200D SER* 3.3 15.6 + - - +
202D ILE* 1.3 76.1 - - - +
204D HIS* 1.3 53.5 + - - +
206D VAL* 3.8 0.5 - - - +
207D ALA* 2.7 38.4 + - - +
214D PHE* 2.8 38.5 + - + +
217D VAL* 3.2 32.8 + - + +
219D VAL* 3.6 15.0 - - + +
518D THR* 3.6 21.9 + - + +
523D ASN 5.4 1.2 + - - -
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Residues in contact with HIS 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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475B THR* 4.6 4.3 + - - -
200D SER 3.1 9.7 + - - +
201D GLU* 3.3 17.7 - - + +
203D GLN* 1.3 78.0 - - - +
205D LYS* 1.3 77.1 + - + +
207D ALA* 3.4 2.9 - - - +
208D HIS* 2.9 58.1 + + - -
214D PHE* 3.2 39.1 - + + -
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Residues in contact with LYS 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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73D ASP* 5.6 1.4 + - - -
75D ASP* 3.2 49.6 + - - +
76D ALA* 3.9 16.8 - - - +
77D SER 4.0 11.5 + - - +
201D GLU* 3.0 25.4 + - + +
202D ILE* 3.7 2.7 - - - +
204D HIS* 1.3 99.0 + - - +
206D VAL* 1.3 66.1 + - + +
208D HIS* 3.2 15.0 + - - +
209D ALA* 3.0 23.4 + - - +
236D ASN* 3.6 23.6 - - - +
240D ILE* 3.7 18.3 - - + +
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Residues in contact with VAL 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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190D VAL* 3.9 15.3 - - + -
192D ILE* 3.9 16.2 - - + -
202D ILE* 2.8 29.2 + - + +
203D GLN 3.8 2.7 - - - +
205D LYS* 1.3 70.0 - - + +
207D ALA* 1.3 64.3 + - - +
209D ALA* 3.0 14.1 + - - +
210D LEU* 3.0 16.8 + - + +
217D VAL* 3.9 7.6 - - + -
239D ALA* 3.7 38.1 - - + -
240D ILE* 4.2 8.5 - - + +
243D ALA* 3.7 22.9 - - + -
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Residues in contact with ALA 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 GLN 2.7 22.2 + - - +
204D HIS 3.4 5.6 - - - +
206D VAL* 1.3 72.8 - - - +
208D HIS* 1.3 57.1 + - - +
210D LEU* 3.3 1.1 + - - -
211D GLY* 3.0 8.3 + - - -
212D LEU* 2.9 47.8 + - - +
213D ALA 4.5 1.3 - - - +
214D PHE* 3.6 21.5 - - + -
217D VAL* 3.8 19.4 - - + +
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Residues in contact with HIS 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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476B ASP* 6.1 0.2 - - - +
72D HIS* 3.3 18.7 - - - +
73D ASP* 3.4 34.9 + - + +
75D ASP 6.1 0.2 - - - +
204D HIS* 2.9 60.3 + + - +
205D LYS* 3.2 15.3 + - - +
207D ALA* 1.3 76.0 - - - +
209D ALA* 1.3 61.0 + - - +
211D GLY* 3.6 3.8 + - - +
212D LEU 5.1 2.5 - - - -
214D PHE* 3.8 16.8 - + - -
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Residues in contact with ALA 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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71D PRO* 3.6 17.0 - - - +
72D HIS* 3.5 15.0 + - - +
73D ASP* 3.9 17.1 - - - +
205D LYS 3.0 11.8 + - - +
206D VAL* 3.0 10.2 + - - +
208D HIS* 1.3 78.0 - - - +
210D LEU* 1.3 62.9 + - + +
240D ILE* 3.6 33.2 - - + -
243D ALA* 5.9 0.4 - - + -
244D VAL* 4.2 10.5 - - + +
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Residues in contact with LEU 210 (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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71D PRO* 5.0 2.7 - - + -
72D HIS* 3.3 16.3 + - - -
190D VAL* 3.2 38.1 - - + -
206D VAL* 3.0 16.7 + - + +
207D ALA 4.1 0.4 - - - +
209D ALA* 1.3 84.5 - - + +
211D GLY* 1.3 62.1 + - - +
212D LEU* 3.6 30.2 - - + +
243D ALA* 3.4 39.5 - - + +
244D VAL* 4.0 12.1 - - + +
247D ARG* 4.1 30.9 + - + +
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Residues in contact with GLY 211 (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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72D HIS* 3.5 27.1 + - - -
207D ALA 3.0 5.6 + - - -
208D HIS* 3.6 5.8 + - - -
209D ALA 3.4 3.4 - - - -
210D LEU* 1.3 79.6 - - - +
212D LEU* 1.3 63.5 + - - +
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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