Contacts of the helix formed by residues 198 - 211 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196B SER* 2.8 10.5 + - - +
197B GLN* 1.3 80.9 - - - +
199B PRO* 1.3 68.1 - - + +
200B SER* 3.8 4.2 - - - -
201B GLU* 3.0 56.1 + - + +
202B ILE* 3.1 12.0 + - - +
231B LYS 4.1 0.6 + - - -
232B GLU* 3.7 17.1 + - - +
236B ASN* 6.3 0.4 - - - +
464B LEU* 6.3 2.9 - - + -
524B THR* 3.0 24.1 + - - -
525B SER* 3.8 4.5 - - - -
526B ALA* 3.3 37.1 + - + +
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Residues in contact with PRO 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B SER* 4.1 3.6 - - - +
197B GLN 3.6 5.8 - - - +
198B HIS* 1.3 89.1 - - + +
200B SER* 1.3 56.3 + - - +
202B ILE* 3.0 10.6 + - + +
203B GLN* 2.9 23.6 + - - +
219B VAL* 3.6 34.1 - - + +
221B MET* 4.3 16.6 - - + -
484B GLY 5.4 1.8 - - - +
486B THR* 3.8 24.9 - - + -
516B THR* 4.5 12.8 - - + -
518B THR* 3.9 13.0 - - + +
524B THR* 5.1 7.2 - - - +
525B SER 5.5 1.6 - - - +
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Residues in contact with SER 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B HIS* 3.2 3.2 - - - -
199B PRO* 1.3 74.5 - - - +
201B GLU* 1.3 61.2 + - - +
203B GLN* 3.3 8.7 + - - +
204B HIS* 3.0 26.2 + - - +
214B PHE* 5.6 0.9 - - - -
518B THR* 3.9 16.8 - - - +
521B VAL 5.1 0.5 + - - -
522B PRO 4.6 0.3 - - - -
523B ASN* 4.0 9.4 + - - -
524B THR* 2.8 55.1 + - - +
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Residues in contact with GLU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B PRO* 3.2 42.2 - - - +
198B HIS* 3.0 40.3 + - + +
200B SER* 1.3 75.8 - - - +
202B ILE* 1.3 62.1 + - - +
203B GLN 3.1 0.2 - - - -
204B HIS* 3.4 8.0 - - + +
205B LYS* 2.9 36.5 + - + +
232B GLU 4.2 4.2 - - - +
233B SER* 3.8 11.3 - - - -
236B ASN* 3.8 20.3 - - - +
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Residues in contact with ILE 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ILE* 4.0 18.4 - - + -
194B CYS* 4.3 6.3 - - + -
196B SER* 3.7 25.8 - - - +
198B HIS 3.1 14.1 + - - +
199B PRO* 3.0 14.8 + - + +
201B GLU* 1.3 75.8 - - - +
203B GLN* 1.3 56.5 + - - +
205B LYS* 3.4 2.3 + - - +
206B VAL* 2.9 33.7 + - + +
219B VAL* 4.0 9.6 - - + -
235B GLY* 3.9 21.5 - - - +
236B ASN* 3.6 23.3 - - - +
239B ALA* 3.7 25.1 - - + -
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Residues in contact with GLN 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B PRO 2.9 11.6 + - - +
200B SER* 3.4 12.9 + - - +
201B GLU 3.1 0.2 - - - -
202B ILE* 1.3 78.1 - - - +
204B HIS* 1.3 63.6 + - - +
207B ALA* 2.9 27.9 + - - +
214B PHE* 3.2 34.1 + - + +
217B VAL* 3.4 40.8 + - + +
219B VAL* 3.8 7.6 - - + -
518B THR* 3.2 27.6 - - + +
523B ASN 5.6 1.0 + - - -
474D TYR* 3.4 35.2 - - - -
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Residues in contact with HIS 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B SER 3.0 14.0 + - - +
201B GLU* 3.4 14.8 - - + +
203B GLN* 1.3 77.4 - - - +
205B LYS* 1.3 77.8 + - + +
207B ALA* 3.4 2.8 - - - +
208B HIS* 3.0 75.2 + + - -
214B PHE* 3.6 29.7 - + + -
475D THR* 5.1 4.4 + - - -
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Residues in contact with LYS 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASP* 3.6 30.8 + - - +
76B ALA* 4.0 0.7 - - - -
77B SER 2.9 31.5 + - - -
78B PRO* 4.8 1.0 - - - +
79B ALA 5.4 0.6 + - - -
201B GLU* 2.9 27.2 + - + +
202B ILE* 3.8 3.4 - - - +
204B HIS* 1.3 93.2 + - + +
206B VAL* 1.3 61.7 + - + +
208B HIS* 3.3 6.5 + - + +
209B ALA* 2.9 29.5 + - - +
236B ASN* 3.1 32.3 - - + +
240B ILE* 4.0 18.2 - - + +
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Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B VAL* 4.0 1.3 - - + -
192B ILE* 3.9 15.3 - - + -
202B ILE* 2.9 26.8 + - + +
203B GLN 4.1 1.6 - - - +
205B LYS* 1.3 71.2 - - + +
207B ALA* 1.3 66.3 + - - +
209B ALA* 3.4 7.1 + - - +
210B LEU* 3.0 34.1 + - + +
217B VAL* 3.8 19.3 - - + -
239B ALA* 3.7 42.0 - - + +
240B ILE* 3.9 3.6 - - + +
243B ALA* 3.6 20.6 - - + -
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Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B GLN 2.9 20.3 + - - +
204B HIS 3.4 5.4 - - - +
206B VAL* 1.3 77.7 - - - +
208B HIS* 1.3 57.8 + - - +
210B LEU* 3.0 3.0 + - - -
211B GLY 2.8 25.3 + - - -
212B LEU* 3.1 27.7 + - - +
214B PHE* 3.8 21.1 - - + -
217B VAL* 3.8 21.7 - - + +
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Residues in contact with HIS 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B HIS* 3.3 18.4 - - - +
73B ASP* 3.4 33.1 + - + +
204B HIS* 3.0 51.7 + + - +
205B LYS* 3.3 7.4 + - + +
207B ALA* 1.3 76.3 - - - +
209B ALA* 1.3 67.8 + - - +
210B LEU 3.1 0.7 + - - -
211B GLY* 3.3 5.8 + - - +
212B LEU 5.3 2.5 - - - -
214B PHE* 4.0 18.3 - + - -
476D ASP* 6.1 0.8 - - - +
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Residues in contact with ALA 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B PRO* 4.1 8.3 - - - +
72B HIS* 3.3 24.4 + - - +
73B ASP* 3.9 18.0 - - - +
205B LYS 2.9 17.0 + - - +
206B VAL* 3.4 8.3 - - - +
208B HIS* 1.3 77.5 - - - +
210B LEU* 1.3 60.3 + - + +
240B ILE* 3.7 32.3 - - + -
243B ALA* 5.6 0.7 - - + -
244B VAL* 4.1 11.3 - - + +
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Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B PRO* 5.2 0.7 - - + -
72B HIS* 3.3 17.5 + - - -
190B VAL* 3.9 13.0 - - + -
206B VAL* 3.0 25.4 + - + +
207B ALA 3.0 4.9 + - - +
209B ALA* 1.3 80.3 - - + +
211B GLY* 1.3 59.4 + - - +
212B LEU* 3.6 32.9 + - + +
243B ALA* 3.8 33.7 - - + +
244B VAL* 4.1 6.5 - - + +
247B ARG* 3.4 50.8 + - + +
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Residues in contact with GLY 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B HIS* 3.6 26.3 + - - -
207B ALA 2.8 5.1 + - - -
208B HIS* 3.3 9.3 + - - -
210B LEU* 1.3 78.0 - - - +
212B LEU* 1.3 62.9 + - - +
213B ALA 4.1 0.5 + - - -
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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