Contacts of the helix formed by residues 194 - 207 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193O LYS* 1.3 72.1 - - - +
195O HIS* 1.3 66.6 + - - -
196O GLY 3.3 0.4 - - - -
197O VAL* 3.3 6.6 + - - +
198O TRP* 3.1 22.5 + - - +
190R ARG* 3.3 35.8 - - - +
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Residues in contact with HIS 195 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A HIS* 3.7 20.8 + + + +
193O LYS 3.7 2.2 + - - -
194O GLY* 1.3 70.3 - - - -
196O GLY* 1.3 63.6 + - - +
198O TRP* 3.3 12.9 + + - +
199O HIS* 2.9 20.0 + - + +
190R ARG 3.7 3.8 + - - -
191R VAL* 3.8 23.6 + - + +
195R HIS* 3.7 45.5 + + - +
196R GLY* 3.8 22.5 + - - -
199R HIS* 2.9 30.4 + - - +
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Residues in contact with GLY 196 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A HIS* 3.8 16.5 + - - -
191O VAL* 3.4 34.6 + - - +
192O GLY 3.6 9.9 + - - -
193O LYS 4.2 2.0 + - - -
194O GLY 3.3 0.6 - - - -
195O HIS* 1.3 78.2 - - - +
197O VAL* 1.3 56.9 + - - +
199O HIS* 3.2 2.9 + - - +
200O PHE 2.9 25.1 + - - -
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Residues in contact with VAL 197 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77O LEU* 4.2 9.9 - - + -
80O LEU* 5.7 0.4 - - + -
126O LYS 6.1 0.7 - - - +
127O GLY* 6.5 0.7 - - - -
129O ALA* 3.7 28.3 - - + -
130O LEU* 5.7 2.0 - - + +
188O LEU* 4.0 18.2 - - + +
191O VAL* 4.3 3.8 - - + -
192O GLY 3.1 23.3 + - - +
193O LYS* 3.7 15.5 - - + -
194O GLY 3.3 10.4 + - - +
196O GLY* 1.3 74.8 - - - +
198O TRP* 1.3 58.3 + - - +
200O PHE* 3.3 6.3 + - - +
201O ASP* 2.9 27.6 + - + +
190R ARG* 3.9 21.3 - - - +
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Residues in contact with TRP 198 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76O ALA 5.0 0.7 - - - -
77O LEU* 4.5 7.4 - - + -
194O GLY 3.1 10.7 + - - +
195O HIS* 3.6 13.0 - + - +
197O VAL* 1.3 78.3 - - - +
199O HIS* 1.3 63.4 + - - +
201O ASP* 3.3 10.1 + - - +
202O GLN* 2.9 57.6 + - + +
187R GLN* 2.9 44.9 + - + +
190R ARG* 4.1 13.9 - - - +
191R VAL* 3.5 30.7 - - + -
199R HIS* 3.6 38.1 - + + -
200R PHE* 3.8 26.5 - + - -
203R MET* 3.9 21.8 - - + -
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Residues in contact with HIS 199 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A HIS* 2.9 26.0 + - + +
198A TRP* 3.6 20.2 - + + -
199A HIS* 3.5 46.2 + + - -
202A GLN* 5.7 1.8 - - - +
195O HIS* 2.9 16.6 + - + +
196O GLY 3.2 4.7 + - - +
198O TRP* 1.3 81.2 - - + +
200O PHE* 1.3 63.7 + - - +
202O GLN* 3.1 9.6 + - + +
203O MET* 3.0 20.2 + - + +
199R HIS* 3.6 29.4 + + + -
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Residues in contact with PHE 200 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A TRP* 3.8 16.9 - + + -
80O LEU* 4.6 6.1 - - + -
133O MET* 4.4 3.8 - - + -
184O TYR* 3.7 37.5 - + + -
187O GLN* 3.8 33.9 - - + -
188O LEU* 3.5 36.6 - - + -
191O VAL* 4.3 6.3 - - + -
196O GLY 2.9 14.2 + - - +
197O VAL 3.6 7.2 - - - +
199O HIS* 1.3 76.3 - - - +
201O ASP* 1.3 62.2 + - - +
203O MET* 3.1 31.5 + - + +
204O LEU* 2.9 44.8 + - + +
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Residues in contact with ASP 201 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76O ALA 4.9 0.5 - - - +
77O LEU* 3.4 26.2 - - + +
78O ARG* 3.2 10.0 + - - +
79O GLY* 2.9 18.5 + - - -
80O LEU* 2.7 44.5 + - + +
197O VAL 2.9 14.7 + - - +
198O TRP* 3.4 11.0 - - + +
200O PHE* 1.3 82.3 - - - +
202O GLN* 1.3 64.7 + - - +
204O LEU* 3.2 2.9 + - - +
205O LEU* 2.8 27.9 + - - +
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Residues in contact with GLN 202 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78O ARG* 3.0 26.0 + - - +
198O TRP* 2.9 53.6 + - + +
199O HIS* 3.1 14.3 + - + +
201O ASP* 1.3 81.8 + - - +
203O MET* 1.3 62.3 + - - +
205O LEU* 3.3 11.5 + - - +
206O HIS* 3.1 51.2 + - - +
199R HIS* 5.6 1.3 - - - +
203R MET* 3.4 22.3 - - - +
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Residues in contact with MET 203 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ARG* 3.7 30.5 - - - +
198A TRP* 3.9 10.5 - - + -
202A GLN* 3.4 29.2 - - - +
184O TYR* 4.8 6.7 - - + -
187O GLN* 3.7 3.8 - - - +
199O HIS* 3.0 13.3 + - + +
200O PHE* 3.2 48.0 - - + +
202O GLN* 1.3 75.5 - - - +
204O LEU* 1.3 63.9 + - + +
206O HIS* 3.0 6.5 + - - +
207O GLU* 2.8 41.9 + - - +
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Residues in contact with LEU 204 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79O GLY* 3.8 19.3 - - - +
80O LEU* 3.7 31.6 - - + +
82O LYS* 4.8 5.2 - - - -
83O PHE* 3.9 15.3 - - + -
133O MET* 4.1 6.7 - - + -
184O TYR* 3.4 37.2 - - + +
200O PHE* 2.9 28.0 + - + +
201O ASP* 3.6 7.9 - - - +
203O MET* 1.3 80.5 - - + +
205O LEU* 1.3 63.9 + - - +
206O HIS 3.2 0.7 + - - -
207O GLU* 3.3 36.3 - - - +
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Residues in contact with LEU 205 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78O ARG* 3.8 56.5 - - + +
79O GLY* 3.7 8.7 - - - +
82O LYS* 3.7 32.3 - - + +
201O ASP 2.8 14.4 + - - +
202O GLN* 3.4 23.6 - - - +
203O MET 3.2 0.2 - - - -
204O LEU* 1.3 75.5 - - - +
206O HIS* 1.3 82.5 + - + +
207O GLU 4.0 0.3 + - - +
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Residues in contact with HIS 206 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202O GLN* 3.1 42.1 + - - +
203O MET* 3.0 7.0 + - - +
205O LEU* 1.3 99.0 - - + +
207O GLU* 1.3 64.5 + - - +
203R MET* 6.0 0.2 - - + -
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Residues in contact with GLU 207 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ARG* 5.6 3.3 + - - +
82O LYS* 5.7 5.1 - - - -
83O PHE* 4.8 0.5 - - - -
180O ARG* 2.8 30.4 + - - -
184O TYR* 2.7 24.3 + - - -
203O MET* 2.8 25.3 + - - +
204O LEU* 3.3 29.8 + - + +
205O LEU 3.6 0.9 - - - +
206O HIS* 1.3 82.4 - - - +
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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