Contacts of the helix formed by residues 194 - 207 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192F GLY 3.8 0.4 + - - -
193F LYS* 1.3 71.0 - - - +
195F HIS* 1.3 68.2 + - - -
196F GLY 3.2 1.1 + - - -
197F VAL* 3.3 7.5 + - - +
198F TRP* 3.1 22.3 + - - +
190V ARG* 3.3 35.3 - - - +
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Residues in contact with HIS 195 (chain F).
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* 3.7 21.3 + + + +
193F LYS 3.7 2.4 + - - -
194F GLY* 1.3 71.2 - - - -
196F GLY* 1.3 57.6 + - - +
198F TRP* 3.3 13.2 + + - +
199F HIS* 2.9 26.1 + - + +
190V ARG 3.6 3.6 + - - -
191V VAL* 3.7 24.8 + - + +
195V HIS* 3.7 44.7 + + - +
196V GLY* 3.8 23.1 + - - -
199V HIS* 2.9 30.9 + - - +
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Residues in contact with GLY 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C HIS* 3.8 21.4 + - - -
191F VAL* 3.4 29.7 + - - +
192F GLY 3.7 10.1 + - - -
193F LYS 4.3 2.0 + - - -
194F GLY 3.2 0.8 - - - -
195F HIS* 1.3 77.9 - - - +
197F VAL* 1.3 56.1 + - - +
199F HIS* 3.2 3.1 + - - +
200F PHE 2.9 24.9 + - - -
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Residues in contact with VAL 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F LEU* 4.2 9.0 - - + -
80F LEU* 6.0 0.7 - - + -
126F LYS 6.1 0.7 - - - +
127F GLY* 6.6 0.4 - - - -
128F ASP* 5.0 0.4 - - - +
129F ALA* 3.6 27.8 - - + -
130F LEU* 5.8 2.0 - - + +
188F LEU* 4.1 20.2 - - + +
191F VAL* 4.3 5.4 - - + -
192F GLY 3.1 20.2 + - - +
193F LYS* 3.8 15.9 - - + -
194F GLY 3.3 10.0 + - - +
196F GLY* 1.3 74.2 - - - +
198F TRP* 1.3 58.1 + - - +
200F PHE* 3.3 3.9 + - + +
201F ASP* 2.9 27.3 + - + +
190V ARG* 4.0 21.5 - - - +
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Residues in contact with TRP 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F ALA 5.0 1.1 - - - -
77F LEU* 4.5 11.9 - - + -
194F GLY 3.1 13.0 + - - +
195F HIS* 3.6 12.3 - + - +
197F VAL* 1.3 76.8 - - - +
199F HIS* 1.3 63.0 + - - +
201F ASP* 3.3 10.4 + - - +
202F GLN* 3.0 57.1 + - + +
187V GLN* 2.9 45.5 + - + +
190V ARG* 4.1 11.4 - - - +
191V VAL* 3.5 28.7 - - + -
199V HIS* 3.5 42.2 - + + -
200V PHE* 3.8 26.5 - + - -
203V MET* 3.9 18.2 - - + -
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Residues in contact with HIS 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C HIS* 2.9 25.3 + - + +
198C TRP* 3.5 20.2 - + + -
199C HIS* 3.5 46.8 + + - -
202C GLN* 5.6 1.8 - - - +
195F HIS 2.9 16.8 + - - +
196F GLY 3.5 4.3 - - - +
198F TRP* 1.3 81.2 - - + +
200F PHE* 1.3 64.1 + - - +
202F GLN* 3.1 8.8 + - + +
203F MET* 2.9 21.0 + - + +
199V HIS* 3.5 28.9 + + + -
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Residues in contact with PHE 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C TRP* 3.8 16.0 - + + -
80F LEU* 4.1 8.7 - - + -
133F MET* 4.8 1.3 - - + -
184F TYR* 3.6 40.8 - + + -
187F GLN* 3.9 31.6 - - + -
188F LEU* 3.5 37.5 - - + -
191F VAL* 4.4 7.0 - - + -
196F GLY 2.9 13.1 + - - +
197F VAL 3.6 6.5 - - - +
199F HIS* 1.3 75.3 - - - +
201F ASP* 1.3 61.1 + - - +
203F MET* 3.1 32.5 + - + +
204F LEU* 2.9 44.8 + - + +
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Residues in contact with ASP 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F ALA 4.9 0.5 - - - +
77F LEU* 3.3 28.2 - - + +
78F ARG* 3.1 10.0 + - - +
79F GLY* 2.9 20.2 + - - -
80F LEU* 2.7 43.2 + - + +
197F VAL 2.9 14.2 + - - +
198F TRP* 3.3 12.2 - - + +
199F HIS 3.1 0.2 - - - -
200F PHE* 1.3 83.1 - - - +
202F GLN* 1.3 64.6 + - - +
204F LEU* 3.2 2.0 + - - -
205F LEU* 2.8 27.5 + - - +
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Residues in contact with GLN 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F ARG* 3.0 26.6 + - - +
198F TRP* 3.0 53.0 + - + +
199F HIS* 3.1 14.8 + - + +
201F ASP* 1.3 79.7 + - - +
203F MET* 1.3 63.4 + - - +
205F LEU* 3.2 10.2 + - - +
206F HIS* 3.1 51.6 + - + -
199V HIS* 5.6 1.8 - - - +
203V MET* 3.4 22.4 - - - +
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Residues in contact with MET 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ARG* 3.7 11.0 - - - +
198C TRP* 3.8 10.8 - - + -
202C GLN* 3.3 31.2 - - - +
184F TYR* 4.8 3.8 - - + -
187F GLN* 3.7 14.4 - - - +
199F HIS* 2.9 14.0 + - + +
200F PHE* 3.2 50.9 - - + +
202F GLN* 1.3 75.9 - - - +
204F LEU* 1.3 61.3 + - + +
206F HIS* 3.1 5.5 + - - +
207F GLU* 2.9 56.5 + - - +
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Residues in contact with LEU 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F GLY* 3.8 20.0 - - - +
80F LEU* 3.9 22.2 - - + -
82F LYS* 4.3 7.3 + - - -
83F PHE* 3.8 21.3 - - + -
133F MET* 4.0 15.7 - - + -
180F ARG* 5.1 1.3 - - - +
184F TYR* 3.4 37.5 - - + +
200F PHE* 2.9 19.7 + - + +
201F ASP* 3.6 8.7 - - - +
203F MET* 1.3 82.4 - - + +
205F LEU* 1.3 62.4 + - - +
207F GLU* 3.2 25.5 + - - +
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Residues in contact with LEU 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F ARG* 3.8 54.7 - - + +
79F GLY* 3.6 8.7 - - - +
82F LYS* 3.1 38.7 + - + +
201F ASP 2.8 16.8 + - - +
202F GLN* 3.2 20.6 + - - +
204F LEU* 1.3 76.2 - - - +
206F HIS* 1.3 83.3 + - + +
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Residues in contact with HIS 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F GLN* 3.1 38.3 + - + +
203F MET* 3.1 6.4 + - - +
205F LEU* 1.3 100.8 + - + +
207F GLU* 1.3 65.3 + - - +
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Residues in contact with GLU 207 (chain F).
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 28.5 + - - +
82F LYS* 5.4 6.7 - - - -
180F ARG* 4.1 8.0 + - - -
184F TYR* 2.6 35.4 + - - -
203F MET* 2.9 30.4 + - - +
204F LEU* 3.2 19.9 + - + +
205F LEU 3.5 0.9 - - - -
206F HIS* 1.3 82.5 - - - +
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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