Contacts of the helix formed by residues 194 - 207 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192H GLY 3.8 0.2 + - - -
193H LYS* 1.3 71.7 - - - +
195H HIS* 1.3 67.8 + - - -
196H GLY 3.2 1.1 - - - -
197H VAL* 3.3 6.7 + - - +
198H TRP* 3.1 22.0 + - - +
190I ARG* 3.3 34.8 - - - +
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Residues in contact with HIS 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195G HIS* 3.7 24.7 + + + +
193H LYS 3.7 2.2 + - - -
194H GLY* 1.3 71.0 - - - -
196H GLY* 1.3 63.0 + - - +
198H TRP* 3.3 13.4 + + - +
199H HIS* 2.9 20.4 + - + +
190I ARG 3.6 3.6 + - - -
191I VAL* 3.6 24.3 + - + +
195I HIS* 3.7 39.7 + + - +
196I GLY* 3.7 21.7 + - - -
199I HIS* 2.9 31.7 + - - +
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Residues in contact with GLY 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195G HIS* 3.8 16.3 + - - -
191H VAL* 3.4 34.3 + - - +
192H GLY 3.6 9.9 + - - -
193H LYS 4.2 2.0 + - - -
194H GLY 3.2 1.0 - - - -
195H HIS* 1.3 79.3 - - - +
197H VAL* 1.3 56.3 + - - +
199H HIS* 3.2 3.6 + - - +
200H PHE 2.9 24.8 + - - -
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Residues in contact with VAL 197 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H LEU* 4.2 9.4 - - + -
80H LEU* 6.0 0.4 - - + -
128H ASP* 5.1 0.2 - - - +
129H ALA* 3.7 27.6 - - + -
130H LEU* 5.7 2.7 - - + +
188H LEU* 4.1 19.1 - - + +
191H VAL* 4.2 5.2 - - + -
192H GLY 3.1 19.9 + - - +
193H LYS* 3.8 17.0 - - + -
194H GLY 3.3 10.6 + - - +
196H GLY* 1.3 74.6 - - - +
198H TRP* 1.3 57.5 + - - +
200H PHE* 3.3 6.2 + - - +
201H ASP* 2.9 28.4 + - + +
190I ARG* 3.9 21.3 - - - +
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Residues in contact with TRP 198 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H ALA 5.0 1.3 - - - -
77H LEU* 4.4 11.9 - - + -
194H GLY 3.1 11.4 + - - +
195H HIS* 3.6 12.8 - + - +
197H VAL* 1.3 77.6 - - - +
199H HIS* 1.3 62.2 + - - +
201H ASP* 3.3 9.8 + - - +
202H GLN* 3.0 57.2 + - + +
187I GLN* 2.9 44.3 + - + +
190I ARG* 4.1 11.9 - - - +
191I VAL* 3.5 30.1 - - + -
199I HIS* 3.6 38.4 - + + -
200I PHE* 3.9 20.2 - + - -
203I MET* 3.8 28.5 - - + -
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Residues in contact with HIS 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195G HIS* 3.0 25.1 + - + +
198G TRP* 3.6 19.6 - + + -
199G HIS* 3.5 47.3 + + - -
202G GLN* 5.7 1.4 - - - +
195H HIS* 2.9 17.7 + - + +
196H GLY 3.5 4.5 - - - +
198H TRP* 1.3 80.5 - - + +
200H PHE* 1.3 65.5 + - - +
202H GLN* 3.1 9.7 + - + +
203H MET* 3.0 20.3 + - + +
199I HIS* 3.5 29.4 + + + -
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Residues in contact with PHE 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198G TRP* 3.8 17.1 - + + -
80H LEU* 4.2 9.0 - - + -
133H MET* 4.8 1.6 - - + -
184H TYR* 3.6 38.8 - + + -
187H GLN* 3.8 34.1 - - + -
188H LEU* 3.5 35.0 - - + -
191H VAL* 4.4 6.7 - - + -
196H GLY 2.9 13.7 + - - +
197H VAL 3.6 6.5 - - - +
199H HIS* 1.3 74.1 - - - +
201H ASP* 1.3 67.1 + - - +
203H MET* 3.1 30.9 + - + +
204H LEU* 3.0 41.2 + - + +
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Residues in contact with ASP 201 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H ALA 5.0 0.3 - - - +
77H LEU* 3.3 28.0 - - + +
78H ARG* 3.1 9.2 + - - +
79H GLY* 2.8 22.3 + - - -
80H LEU* 2.7 42.3 + - + +
197H VAL 2.9 14.9 + - - +
198H TRP* 3.4 11.5 - - + +
200H PHE* 1.3 82.5 - - - +
202H GLN* 1.3 64.4 + - - +
204H LEU* 3.2 2.4 + - - +
205H LEU* 2.8 27.5 + - - +
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Residues in contact with GLN 202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78H ARG* 3.0 27.0 + - - +
198H TRP* 3.0 53.3 + - + +
199H HIS* 3.1 14.8 + - + +
201H ASP* 1.3 80.8 - - - +
203H MET* 1.3 63.5 + - - +
205H LEU* 3.3 8.7 + - - +
206H HIS* 3.1 51.8 + - - +
199I HIS* 5.6 1.3 - - - +
203I MET* 3.4 22.3 - - - +
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Residues in contact with MET 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G ARG* 3.8 18.4 - - - +
198G TRP* 3.9 11.0 - - + -
202G GLN* 3.4 29.6 - - - +
206G HIS* 6.1 0.2 - - + -
184H TYR* 4.8 6.7 - - + -
187H GLN* 3.7 15.9 - - - +
199H HIS* 3.0 13.1 + - + +
200H PHE* 3.1 46.2 + - + +
202H GLN* 1.3 75.3 - - - +
204H LEU* 1.3 58.4 + - + +
206H HIS* 3.1 5.0 + - - +
207H GLU* 2.7 48.9 + - - +
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Residues in contact with LEU 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H GLY* 3.9 12.1 - - - +
80H LEU* 3.9 25.8 - - + -
82H LYS* 4.2 8.7 + - - -
83H PHE* 3.9 25.3 - - + +
133H MET* 4.0 12.3 - - + -
184H TYR* 3.4 38.8 - - + +
200H PHE* 3.0 26.7 + - + +
201H ASP* 3.6 8.1 - - - +
203H MET* 1.3 80.8 - - + +
205H LEU* 1.3 63.0 + - - +
206H HIS 3.3 0.3 + - - -
207H GLU* 3.3 28.1 + - + +
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Residues in contact with LEU 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78H ARG* 3.8 54.7 - - + +
79H GLY* 3.7 8.5 - - - +
82H LYS* 3.1 40.3 + - + +
201H ASP* 2.8 17.2 + - - +
202H GLN* 3.4 19.5 - - - +
203H MET 3.2 0.2 - - - -
204H LEU* 1.3 77.7 - - - +
206H HIS* 1.3 80.7 + - + +
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Residues in contact with HIS 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202H GLN* 3.1 35.9 + - - +
203H MET* 3.1 6.6 + - - +
205H LEU* 1.3 100.7 - - + +
207H GLU* 1.3 65.8 + - - +
203I MET* 6.1 0.2 - - + -
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Residues in contact with GLU 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78G ARG* 5.2 9.1 + - - +
82H LYS* 5.6 4.5 - - - -
83H PHE* 5.3 0.3 - - - -
180H ARG* 3.2 23.4 + - - +
184H TYR* 2.5 32.0 + - - -
203H MET* 2.7 26.6 + - - +
204H LEU* 3.3 22.4 + - - +
205H LEU 3.5 0.6 - - - -
206H HIS* 1.3 83.0 - - - +
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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