Contacts of the helix formed by residues 194 - 206 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192C GLY 3.8 0.2 + - - -
193C LYS* 1.3 71.9 - - - +
195C HIS* 1.3 67.3 + - - -
196C GLY 3.2 1.3 + - - -
197C VAL* 3.3 6.6 + - - +
198C TRP* 3.0 22.7 + - - +
190F ARG* 3.3 36.2 - - - +
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Residues in contact with HIS 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C LYS 3.7 2.0 + - - -
194C GLY* 1.3 71.4 - - - -
196C GLY* 1.3 57.2 + - - +
198C TRP* 3.3 12.6 + + - +
199C HIS* 2.9 26.1 + - + +
190F ARG 3.7 3.8 + - - -
191F VAL* 3.7 24.9 + - + +
195F HIS* 3.7 46.0 + + - +
196F GLY* 3.8 22.4 + - - -
199F HIS* 2.9 30.4 + - + +
195M HIS* 3.7 20.0 + + + +
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Residues in contact with GLY 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C VAL* 3.4 28.0 + - - +
192C GLY 3.6 9.5 + - - -
193C LYS 4.3 2.4 + - - -
194C GLY 3.2 0.8 - - - -
195C HIS* 1.3 75.7 - - - +
197C VAL* 1.3 60.5 + - - +
199C HIS* 3.1 2.4 + - - +
200C PHE 2.8 25.6 + - - -
195M HIS* 3.7 21.6 + - - -
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Residues in contact with VAL 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU* 4.2 9.2 - - + -
80C LEU* 6.1 0.4 - - + -
127C GLY* 6.5 0.2 - - - -
128C ASP* 5.0 0.4 - - - +
129C ALA* 3.7 27.8 - - + -
130C LEU* 5.7 2.7 - - + +
188C LEU* 4.0 21.3 - - + +
191C VAL* 4.3 4.5 - - + -
192C GLY 3.1 23.9 + - - +
193C LYS* 3.7 17.9 - - + -
194C GLY 3.3 10.6 + - - +
196C GLY* 1.3 73.1 - - - +
198C TRP* 1.3 58.9 + - - +
200C PHE* 3.3 3.6 + - - +
201C ASP* 2.9 28.2 + - + +
190F ARG* 3.8 22.0 - - - +
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Residues in contact with TRP 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ALA 5.1 0.9 - - - -
77C LEU* 4.5 7.4 - - + -
194C GLY 3.0 13.2 + - - +
195C HIS* 3.6 12.6 - + - +
197C VAL* 1.3 78.5 - - - +
199C HIS* 1.3 63.0 + - - +
201C ASP* 3.3 9.8 + - - +
202C GLN* 3.0 57.8 + - + +
187F GLN* 2.8 45.2 + - + +
190F ARG* 4.1 14.1 - - - +
191F VAL* 3.5 28.0 - - + -
199F HIS* 3.5 37.7 - + + -
200F PHE* 3.8 27.1 - + - -
203F MET* 3.8 22.9 - - + -
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Residues in contact with HIS 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C HIS* 2.9 17.5 + - + +
196C GLY 3.1 4.7 + - - +
198C TRP* 1.3 82.2 - - + +
200C PHE* 1.3 66.8 + - - +
202C GLN* 3.1 9.2 + - + +
203C MET* 3.0 19.9 + - + +
199F HIS* 3.5 32.5 + + + -
195M HIS* 2.9 25.5 + - + +
198M TRP* 3.5 21.1 - + + -
199M HIS* 3.5 42.3 + + - -
202M GLN* 5.6 1.8 - - - +
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Residues in contact with PHE 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C LEU* 4.1 8.5 - - + -
133C MET* 4.8 1.1 - - + -
184C TYR* 3.6 41.1 - + + -
187C GLN* 3.8 31.4 - - + -
188C LEU* 3.6 34.5 - - + -
191C VAL* 4.4 7.2 - - + -
196C GLY 2.8 13.1 + - - +
197C VAL 3.6 7.0 - - - +
199C HIS* 1.3 76.2 - - - +
201C ASP* 1.3 63.0 + - - +
203C MET* 3.1 32.6 + - + +
204C LEU* 2.9 46.3 + - + +
198M TRP* 3.8 15.8 - + + -
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Residues in contact with ASP 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ALA 4.9 0.3 - - - +
77C LEU* 3.3 29.4 - - + +
78C ARG* 3.1 9.5 + - - +
79C GLY* 2.9 19.4 + - - -
80C LEU* 2.7 39.6 + - + +
197C VAL 2.9 14.3 + - - +
198C TRP* 3.4 10.7 - - + +
199C HIS 3.2 0.2 - - - -
200C PHE* 1.3 83.4 - - - +
202C GLN* 1.3 64.0 + - - +
204C LEU* 3.2 3.8 + - - +
205C LEU* 2.8 28.2 + - - +
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Residues in contact with GLN 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C ARG* 3.1 24.7 + - - +
198C TRP* 3.0 48.6 + - + +
199C HIS* 3.1 14.3 + - + +
201C ASP* 1.3 81.5 - - - +
203C MET* 1.3 64.0 + - - +
205C LEU* 3.3 10.7 + - - +
206C HIS* 3.2 51.0 + - + +
187F GLN* 4.2 0.2 - - - +
199F HIS* 5.6 0.9 - - - +
203F MET* 3.3 28.4 - - - +
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Residues in contact with MET 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C TYR* 4.8 6.3 - - + -
187C GLN* 3.7 14.6 - - - +
199C HIS* 3.0 12.7 + - + +
200C PHE* 3.1 44.4 + - + +
202C GLN* 1.3 78.0 - - - +
204C LEU* 1.3 66.4 + - + +
206C HIS* 3.1 4.9 + - - +
207C GLU* 2.9 36.3 + - - +
78M ARG* 3.9 22.4 - - - +
198M TRP* 3.8 11.0 - - + -
202M GLN* 3.3 31.0 - - - +
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Residues in contact with LEU 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C GLY* 3.7 17.8 - - - +
80C LEU* 3.7 28.0 - - + -
82C LYS* 4.3 8.0 + - - -
83C PHE* 3.9 20.4 - - + -
133C MET* 4.0 11.0 - - + -
184C TYR* 3.4 37.7 - - + +
200C PHE* 2.9 23.8 + - + +
201C ASP* 3.6 9.2 - - - +
203C MET* 1.3 82.1 - - + +
205C LEU* 1.3 63.3 + - - +
207C GLU* 3.2 28.3 + - - +
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Residues in contact with LEU 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C ARG* 4.0 58.8 - - + +
79C GLY* 3.6 8.9 - - - +
82C LYS* 3.2 36.7 + - + +
201C ASP* 2.8 17.7 + - - +
202C GLN* 3.4 17.0 - - - +
204C LEU* 1.3 78.3 - - - +
206C HIS* 1.3 80.4 + - + +
207C GLU 5.0 0.2 - - - +
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Residues in contact with HIS 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C GLN* 3.2 37.3 + - + +
203C MET* 3.1 6.4 + - - +
205C LEU* 1.3 98.9 + - + +
207C GLU* 1.3 65.2 + - - +
208C GLY* 3.5 1.9 + - - -
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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