Contacts of the helix formed by residues 194 - 206 (chain W) in PDB entry 3A68
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 GLY 194 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190P ARG* 3.3 34.9 - - - +
192W GLY 3.8 0.2 + - - -
193W LYS* 1.3 72.2 - - - +
195W HIS* 1.3 66.2 + - - -
196W GLY 3.2 0.9 - - - -
197W VAL* 3.2 6.5 + - - +
198W TRP* 3.0 22.5 + - - +
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Residues in contact with HIS 195 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E HIS* 3.6 23.9 + + + +
190P ARG 3.6 4.2 + - - -
191P VAL* 3.7 24.8 + - + +
195P HIS* 3.7 41.5 + + - +
196P GLY* 3.8 23.1 + - - -
199P HIS* 2.9 30.1 + - - +
193W LYS 3.8 2.2 + - - -
194W GLY* 1.3 71.0 - - - -
196W GLY* 1.3 63.1 + - - +
198W TRP* 3.3 13.9 + + - +
199W HIS* 2.9 20.1 + - + +
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Residues in contact with GLY 196 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E HIS* 3.8 16.5 + - - -
191W VAL* 3.4 33.0 + - - +
192W GLY 3.6 10.1 + - - -
193W LYS 4.3 1.8 + - - -
194W GLY 3.2 1.2 - - - -
195W HIS* 1.3 78.1 - - - +
197W VAL* 1.3 56.8 + - - +
199W HIS* 3.2 3.8 + - - +
200W PHE 2.9 25.1 + - - -
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Residues in contact with VAL 197 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190P ARG* 3.9 20.6 - - - +
77W LEU* 4.3 9.4 - - + -
80W LEU* 5.9 0.2 - - + -
126W LYS 6.1 0.2 - - - +
127W GLY* 6.5 0.4 - - - -
128W ASP* 4.9 0.2 - - - +
129W ALA* 3.7 27.8 - - + -
130W LEU* 5.7 2.5 - - + +
188W LEU* 4.0 18.4 - - + +
191W VAL* 4.2 4.5 - - + -
192W GLY 3.1 19.6 + - - +
193W LYS* 3.8 15.3 - - + -
194W GLY 3.2 10.2 + - - +
196W GLY* 1.3 74.7 - - - +
198W TRP* 1.3 59.2 + - - +
200W PHE* 3.3 6.3 + - + +
201W ASP* 2.9 28.0 + - + +
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Residues in contact with TRP 198 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187P GLN* 2.9 46.2 + - + +
190P ARG* 4.0 15.0 - - - +
191P VAL* 3.5 28.3 - - + -
199P HIS* 3.6 38.4 - + + -
200P PHE* 3.8 26.5 - + - -
203P MET* 3.9 22.4 - - + -
76W ALA 5.0 1.3 - - - -
77W LEU* 4.5 8.1 - - + -
194W GLY 3.0 13.1 + - - +
195W HIS* 3.6 12.1 - + - +
197W VAL* 1.3 76.8 - - - +
199W HIS* 1.3 63.8 + - - +
201W ASP* 3.3 9.4 + - - +
202W GLN* 3.0 57.8 + - + +
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Residues in contact with HIS 199 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E HIS* 2.9 25.1 + - + +
198E TRP* 3.6 20.5 - + + -
199E HIS* 3.5 42.7 + + - -
202E GLN* 5.7 1.6 - - - +
199P HIS* 3.5 33.8 + + + -
195W HIS 2.9 17.1 + - - +
196W GLY 3.5 4.5 - - - +
198W TRP* 1.3 81.0 - - + +
200W PHE* 1.3 65.9 + - - +
202W GLN* 3.1 9.4 + - + +
203W MET* 3.0 21.0 + - + +
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Residues in contact with PHE 200 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E TRP* 3.8 16.2 - + + -
80W LEU* 4.2 9.2 - - + -
133W MET* 4.6 2.0 - - + -
184W TYR* 3.7 36.3 - + + -
187W GLN* 3.8 34.3 - - + -
188W LEU* 3.5 35.2 - - + -
191W VAL* 4.3 7.2 - - + -
196W GLY 2.9 12.9 + - - +
197W VAL 3.6 6.7 - - - +
199W HIS* 1.3 76.2 - - - +
201W ASP* 1.3 62.0 + - - +
203W MET* 3.1 31.1 + - + +
204W LEU* 2.9 44.2 + - + +
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Residues in contact with ASP 201 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76W ALA 4.9 0.3 - - - +
77W LEU* 3.3 28.4 - - + +
78W ARG* 3.1 9.9 + - - +
79W GLY* 2.8 19.3 + - - -
80W LEU* 2.7 40.8 + - + +
197W VAL 2.9 13.8 + - - +
198W TRP* 3.4 11.3 - - - +
200W PHE* 1.3 84.6 - - - +
202W GLN* 1.3 62.9 + - - +
204W LEU* 3.2 4.0 + - - +
205W LEU* 2.8 27.7 + - - +
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Residues in contact with GLN 202 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199P HIS* 5.6 1.8 - - - +
203P MET* 3.4 21.7 - - - +
78W ARG* 3.1 27.2 + - - +
198W TRP* 3.0 53.4 + - + +
199W HIS* 3.4 14.4 - - + +
201W ASP* 1.3 78.4 - - - +
203W MET* 1.3 64.3 + - - +
205W LEU* 3.4 10.1 + - - +
206W HIS* 3.0 52.9 + - - +
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Residues in contact with MET 203 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E ARG* 4.0 12.1 - - - +
198E TRP* 3.9 11.2 - - + -
202E GLN* 3.4 28.9 - - - +
206E HIS* 6.1 0.2 - - + -
184W TYR* 4.9 1.8 - - + -
187W GLN* 3.7 15.9 - - - +
199W HIS* 3.0 13.5 + - + +
200W PHE* 3.3 46.9 - - + +
202W GLN* 1.3 77.6 - - - +
204W LEU* 1.3 61.7 + - + +
206W HIS* 3.1 6.4 + - - +
207W GLU* 3.0 57.3 + - - +
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Residues in contact with LEU 204 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79W GLY* 3.7 14.6 - - - +
80W LEU* 4.0 15.9 - - + -
82W LYS* 4.8 5.7 - - - +
83W PHE* 3.7 28.3 - - + -
133W MET* 3.9 22.4 - - + -
180W ARG* 5.3 1.1 - - - +
184W TYR* 3.4 37.7 - - + +
200W PHE* 2.9 20.2 + - + +
201W ASP* 3.6 8.7 - - - +
203W MET* 1.3 78.5 - - + +
205W LEU* 1.3 63.3 + - - +
207W GLU* 3.2 27.7 + - + +
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Residues in contact with LEU 205 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78W ARG* 3.8 60.8 - - + +
79W GLY* 3.7 7.1 - - - +
82W LYS* 3.7 31.3 - - + +
201W ASP 2.8 17.2 + - - +
202W GLN* 3.5 16.8 - - - +
204W LEU* 1.3 78.2 - - - +
206W HIS* 1.3 80.9 + - + +
207W GLU 3.8 0.2 + - - -
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Residues in contact with HIS 206 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202W GLN* 3.0 42.2 + - - +
203W MET* 3.1 6.8 + - - +
205W LEU* 1.3 95.0 - - + +
207W GLU* 1.3 63.3 + - - +
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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