Contacts of the helix formed by residues 194 - 207 (chain T) 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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192T GLY 3.8 0.2 + - - -
193T LYS* 1.3 72.8 - - - +
195T HIS* 1.3 67.2 + - - -
196T GLY 3.2 1.0 + - - -
197T VAL* 3.3 6.4 + - - +
198T TRP* 3.1 22.2 + - - +
190U ARG* 3.3 33.7 - - - +
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Residues in contact with HIS 195 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195S HIS* 3.7 23.6 + + + +
193T LYS 3.7 2.2 + - - -
194T GLY* 1.3 71.2 - - - -
196T GLY* 1.3 62.8 + - - +
198T TRP* 3.3 12.8 + + - +
199T HIS* 2.9 19.5 + - + +
190U ARG 3.7 4.0 + - - -
191U VAL* 3.7 24.3 + - + +
195U HIS* 3.7 43.3 + + - +
196U GLY* 3.8 22.0 + - - -
199U HIS* 2.9 30.4 + - - +
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Residues in contact with GLY 196 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195S HIS* 3.8 15.9 + - - -
191T VAL* 3.4 33.3 + - - +
192T GLY 3.6 9.9 + - - -
193T LYS 4.2 2.6 + - - -
194T GLY 3.2 1.0 - - - -
195T HIS* 1.3 78.9 - - - +
197T VAL* 1.3 56.3 - - - +
199T HIS* 3.1 3.5 + - - +
200T PHE 2.9 25.1 + - - -
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Residues in contact with VAL 197 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77T LEU* 4.2 9.0 - - + -
126T LYS 6.2 0.2 - - - +
128T ASP* 5.1 0.2 - - - +
129T ALA* 3.8 26.9 - - + -
130T LEU* 5.9 2.2 - - + +
188T LEU* 4.1 20.0 - - + +
191T VAL* 4.2 5.2 - - + -
192T GLY 3.1 20.0 + - - +
193T LYS* 3.7 17.0 - - + -
194T GLY 3.3 10.2 + - - +
196T GLY* 1.3 74.4 - - - +
198T TRP* 1.3 59.0 + - - +
200T PHE* 3.3 3.3 + - + +
201T ASP* 2.9 27.8 + - + +
190U ARG* 3.9 22.7 - - - +
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Residues in contact with TRP 198 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76T ALA 5.2 1.6 - - - -
77T LEU* 4.5 6.7 - - + -
194T GLY 3.1 12.6 + - - +
195T HIS* 3.6 13.0 - + - +
197T VAL* 1.3 78.9 - - - +
199T HIS* 1.3 62.7 + - - +
201T ASP* 3.3 9.1 + - - +
202T GLN* 2.9 54.8 + - + +
187U GLN* 2.9 43.5 + - + +
190U ARG* 4.1 14.4 - - - +
191U VAL* 3.5 27.8 - - + -
199U HIS* 3.6 38.6 - + + -
200U PHE* 3.7 28.5 - + - -
203U MET* 3.8 24.0 - - + -
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Residues in contact with HIS 199 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195S HIS* 2.9 25.7 + - + +
198S TRP* 3.6 22.1 - + + -
199S HIS* 3.5 42.5 + + - -
202S GLN* 5.5 1.4 - - - +
195T HIS* 2.9 17.0 + - + +
196T GLY 3.1 4.9 + - - +
198T TRP* 1.3 81.2 - - + +
200T PHE* 1.3 65.3 + - - +
202T GLN* 3.1 9.1 + - + +
203T MET* 3.0 21.5 + - + +
199U HIS* 3.5 32.1 + + + -
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Residues in contact with PHE 200 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198S TRP* 3.8 16.0 - + + -
80T LEU* 4.2 8.7 - - + -
133T MET* 4.7 1.3 - - + -
184T TYR* 3.5 41.3 - + + -
187T GLN* 3.8 33.0 - - + -
188T LEU* 3.5 35.9 - - + -
191T VAL* 4.4 7.4 - - + -
196T GLY 2.9 12.4 + - - +
197T VAL 3.6 6.3 - - - +
199T HIS* 1.3 75.8 - - - +
201T ASP* 1.3 62.0 + - - +
203T MET* 3.1 31.2 + - + +
204T LEU* 2.9 44.3 + - + +
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Residues in contact with ASP 201 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76T ALA 4.9 0.5 - - - +
77T LEU* 3.2 29.4 - - + +
78T ARG* 3.1 10.0 + - - +
79T GLY* 2.9 20.3 + - - -
80T LEU* 2.8 39.6 + - + +
197T VAL* 2.9 15.0 + - + +
198T TRP* 3.4 11.5 - - + +
200T PHE* 1.3 83.3 - - - +
202T GLN* 1.3 63.0 + - - +
204T LEU* 3.2 3.8 + - - +
205T LEU* 2.8 27.7 + - - +
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Residues in contact with GLN 202 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78T ARG* 3.0 27.5 + - - +
198T TRP* 2.9 47.4 + - + +
199T HIS* 3.1 14.8 + - + +
201T ASP* 1.3 79.8 - - - +
203T MET* 1.3 63.2 + - - +
205T LEU* 3.2 9.6 + - - +
206T HIS* 3.1 52.3 + - - +
187U GLN* 4.2 0.2 - - - +
199U HIS* 5.7 1.3 - - - +
203U MET* 3.3 27.5 - - - +
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Residues in contact with MET 203 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78S ARG* 3.7 17.9 - - - +
198S TRP* 3.8 10.3 - - + -
202S GLN* 3.4 31.0 - - - +
184T TYR* 4.8 7.0 - - + -
187T GLN* 3.7 15.3 - - - +
199T HIS* 3.0 15.3 + - + +
200T PHE* 3.2 45.8 - - + +
202T GLN* 1.3 76.4 - - - +
204T LEU* 1.3 67.4 + - + +
206T HIS* 3.2 5.7 + - - +
207T GLU* 2.9 37.8 + - - +
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Residues in contact with LEU 204 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79T GLY* 3.8 20.6 - - - +
80T LEU* 3.8 23.6 - - + -
82T LYS* 5.0 4.7 + - - +
83T PHE* 3.9 19.3 - - + -
133T MET* 4.0 14.1 - - + -
184T TYR* 3.3 37.0 - - + +
200T PHE* 2.9 22.2 + - + +
201T ASP* 3.6 7.9 - - - +
203T MET* 1.3 82.6 - - + +
205T LEU* 1.3 62.9 - - - +
206T HIS 3.2 0.5 + - - -
207T GLU* 3.3 36.3 - - - +
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Residues in contact with LEU 205 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78T ARG* 3.9 56.1 - - + +
79T GLY* 3.7 9.1 - - - +
82T LYS* 4.0 32.9 + - + +
201T ASP* 2.8 15.2 + - - +
202T GLN* 3.4 23.6 - - - +
203T MET 3.2 0.4 - - - -
204T LEU* 1.3 78.6 - - - +
206T HIS* 1.3 80.3 + - + +
207T GLU 5.1 0.2 - - - +
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Residues in contact with HIS 206 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202T GLN* 3.1 40.9 + - - +
203T MET* 3.2 6.1 + - - +
205T LEU* 1.3 97.3 - - + +
207T GLU* 1.3 65.3 - - - +
203U MET* 6.0 0.7 - - + -
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Residues in contact with GLU 207 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78S ARG* 5.7 3.1 + - - +
82T LYS* 5.2 8.5 + - - +
83T PHE* 4.9 0.2 - - - -
180T ARG* 2.5 32.9 + - - -
184T TYR* 3.0 21.5 + - - -
203T MET* 2.9 24.5 + - - +
204T LEU* 3.3 27.0 + - - +
205T LEU 5.1 0.9 - - - +
206T HIS* 1.3 83.4 - - - +
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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