Contacts of the helix formed by residues 194 - 207 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190C ARG* 3.3 36.9 - - - +
192M GLY 3.8 0.2 + - - -
193M LYS* 1.3 71.7 - - - +
195M HIS* 1.3 66.6 + - - -
196M GLY 3.2 1.7 + - - -
197M VAL* 3.3 6.6 + - - +
198M TRP* 3.1 22.3 + - - +
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Residues in contact with HIS 195 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C ARG 3.7 3.8 + - - -
191C VAL* 3.7 23.5 + - + +
195C HIS* 3.7 45.8 + + - +
196C GLY* 3.7 22.0 + - - -
199C HIS* 2.9 30.6 + - - +
193M LYS 3.7 2.6 + - - -
194M GLY* 1.3 70.7 - - - -
196M GLY* 1.3 63.0 + - - +
198M TRP* 3.3 12.7 + + - +
199M HIS* 2.9 19.0 + - + +
195V HIS* 3.6 19.9 + + + +
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Residues in contact with GLY 196 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191M VAL* 3.5 33.1 + - - +
192M GLY 3.6 9.8 + - - -
193M LYS 4.3 1.6 + - - -
194M GLY 3.2 0.6 - - - -
195M HIS* 1.3 78.9 - - - +
197M VAL* 1.3 57.0 + - - +
199M HIS* 3.1 3.3 + - - +
200M PHE 2.8 25.6 + - - -
195V HIS* 3.8 17.0 + - - -
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Residues in contact with VAL 197 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C ARG* 3.9 21.1 - - - +
77M LEU* 4.2 10.1 - - + -
80M LEU* 5.9 0.4 - - + -
126M LYS 6.1 0.2 - - - +
127M GLY* 6.6 0.4 - - - -
128M ASP* 5.0 0.2 - - - +
129M ALA* 3.7 27.1 - - + -
130M LEU* 5.8 2.2 - - + +
188M LEU* 4.1 17.9 - - + +
191M VAL* 4.3 4.9 - - + -
192M GLY 3.1 19.3 + - - +
193M LYS* 3.8 17.3 - - + -
194M GLY 3.3 10.6 + - - +
196M GLY* 1.3 74.4 - - - +
198M TRP* 1.3 58.1 + - - +
200M PHE* 3.3 5.9 + - - +
201M ASP* 2.9 27.1 + - + +
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Residues in contact with TRP 198 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C GLN* 2.9 46.9 + - + +
190C ARG* 4.1 11.8 - - - +
191C VAL* 3.5 26.7 - - + -
199C HIS* 3.5 38.4 - + + -
200C PHE* 3.8 27.1 - + - -
203C MET* 3.8 24.0 - - + -
76M ALA 5.0 1.8 - - - -
77M LEU* 4.4 11.2 - - + -
194M GLY 3.1 13.2 + - - +
195M HIS* 3.6 13.2 - + - +
197M VAL* 1.3 77.1 - - - +
199M HIS* 1.3 62.9 + - - +
201M ASP* 3.3 10.0 + - - +
202M GLN* 3.0 54.3 + - + +
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Residues in contact with HIS 199 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C HIS* 3.5 29.6 + + + -
195M HIS* 2.9 17.9 + - + +
196M GLY 3.5 4.3 - - - +
198M TRP* 1.3 81.2 - - + +
200M PHE* 1.3 65.4 + - - +
202M GLN* 3.1 9.8 + - + +
203M MET* 3.0 21.2 + - + +
195V HIS* 2.9 25.2 + - + +
198V TRP* 3.6 20.9 - + + -
199V HIS* 3.5 46.9 + + - -
202V GLN* 5.7 1.4 - - - +
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Residues in contact with PHE 200 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80M LEU* 4.3 9.2 - - + -
133M MET* 4.5 2.5 - - + -
184M TYR* 3.6 40.4 - + + -
187M GLN* 3.8 32.5 - - + -
188M LEU* 3.5 35.7 - - + -
191M VAL* 4.4 6.7 - - + -
196M GLY 2.8 14.4 + - - +
197M VAL 3.6 6.3 - - - +
199M HIS* 1.3 76.0 - - - +
201M ASP* 1.3 62.2 + - - +
203M MET* 3.1 29.6 + - + +
204M LEU* 2.9 45.6 + - + +
198V TRP* 3.8 16.0 - + + -
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Residues in contact with ASP 201 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76M ALA 4.9 0.3 - - - +
77M LEU* 3.3 28.4 - - + +
78M ARG* 3.1 10.0 + - - +
79M GLY* 2.9 19.1 + - - -
80M LEU* 2.7 40.7 + - + +
197M VAL 2.9 13.2 + - - +
198M TRP* 3.3 11.6 - - + +
200M PHE* 1.3 81.7 - - - +
202M GLN* 1.3 63.6 + - - +
204M LEU* 3.2 2.8 + - - -
205M LEU* 2.8 27.4 + - - +
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Residues in contact with GLN 202 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C HIS* 5.6 1.6 - - - +
203C MET* 3.3 28.1 - - - +
78M ARG* 3.1 27.3 + - - +
198M TRP* 3.0 47.6 + - + +
199M HIS* 3.1 14.5 + - + +
201M ASP* 1.3 77.1 - - - +
203M MET* 1.3 65.3 + - - +
205M LEU* 3.2 10.8 + - - +
206M HIS* 3.2 51.2 + - + -
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Residues in contact with MET 203 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184M TYR* 4.8 2.9 - - + -
187M GLN* 3.9 11.7 - - - +
199M HIS* 3.0 13.4 + - + +
200M PHE* 3.2 47.6 - - + +
202M GLN* 1.3 77.3 - - - +
204M LEU* 1.3 63.1 + - + +
206M HIS* 3.1 5.8 + - - +
207M GLU* 2.8 55.1 + - - +
78V ARG* 3.7 10.5 - - - +
198V TRP* 3.8 10.5 - - + -
202V GLN* 3.3 30.7 - - - +
206V HIS* 6.0 0.7 - - + -
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Residues in contact with LEU 204 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79M GLY* 3.8 22.2 - - - +
80M LEU* 3.9 23.1 - - + -
82M LYS* 4.4 7.3 + - - -
83M PHE* 3.9 23.8 - - + -
133M MET* 4.3 4.9 - - + -
180M ARG* 5.1 1.6 - - - +
184M TYR* 3.5 36.1 - - + +
200M PHE* 2.9 28.0 + - + +
201M ASP* 3.5 8.5 - - - +
203M MET* 1.3 83.6 - - + +
205M LEU* 1.3 64.5 + - - +
207M GLU* 3.2 23.6 + - + +
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Residues in contact with LEU 205 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78M ARG* 3.8 62.6 - - + +
79M GLY* 3.6 8.7 - - - +
82M LYS* 3.1 39.4 + - + +
201M ASP* 2.8 14.1 + - - +
202M GLN* 3.4 19.3 - - - +
203M MET 3.2 0.2 - - - -
204M LEU* 1.3 77.2 - - - +
206M HIS* 1.3 79.5 + - + +
207M GLU 4.8 0.3 - - - +
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Residues in contact with HIS 206 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78M ARG* 5.9 0.2 + - - -
202M GLN* 3.2 38.5 + - + +
203M MET* 3.1 6.2 + - - +
205M LEU* 1.3 99.2 + - + +
207M GLU* 1.3 68.2 + - - +
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Residues in contact with GLU 207 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82M LYS* 4.9 7.8 + - - -
180M ARG* 4.1 7.4 + - - -
184M TYR* 2.7 37.5 + - - -
203M MET* 2.8 30.4 + - - +
204M LEU* 3.2 18.8 + - - +
205M LEU 4.8 1.6 - - - +
206M HIS* 1.3 84.5 - - - +
78V ARG* 3.2 27.9 + - - +
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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