Contacts of the helix formed by residues 194 - 207 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B ARG* 3.3 36.1 - - - +
192I GLY 3.8 0.2 + - - -
193I LYS* 1.3 71.5 - - - +
195I HIS* 1.3 66.2 + - - -
196I GLY 3.2 0.7 - - - -
197I VAL* 3.3 6.6 + - - +
198I TRP* 3.1 22.9 + - - +
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Residues in contact with HIS 195 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ARG 3.7 3.8 + - - -
191B VAL* 3.8 23.2 + - + +
195B HIS* 3.7 46.0 + + - +
196B GLY* 3.8 23.0 + - - -
199B HIS* 2.9 30.3 + - - +
195G HIS* 5.2 0.2 - + - -
199G HIS* 5.3 0.2 - - - -
195H HIS* 3.7 20.2 + + + +
193I LYS 3.7 2.2 + - - -
194I GLY* 1.3 71.2 - - - -
196I GLY* 1.3 63.1 + - - +
198I TRP* 3.3 12.7 + + - +
199I HIS* 2.9 20.9 + - + +
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Residues in contact with GLY 196 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195H HIS* 3.7 17.0 + - - -
191I VAL* 3.4 34.2 + - - +
192I GLY 3.5 10.7 + - - -
193I LYS 4.2 1.8 + - - -
194I GLY 3.2 1.0 - - - -
195I HIS* 1.3 79.3 - - - +
197I VAL* 1.3 56.2 + - - +
199I HIS* 3.2 3.5 + - - +
200I PHE 2.9 25.1 + - - -
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Residues in contact with VAL 197 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ARG* 3.9 20.6 - - - +
77I LEU* 4.3 9.6 - - + -
80I LEU* 6.0 0.2 - - + -
129I ALA* 3.6 28.0 - - + -
130I LEU* 5.8 2.7 - - + +
188I LEU* 4.1 17.7 - - + +
191I VAL* 4.3 5.2 - - + -
192I GLY 3.0 23.0 + - - +
193I LYS* 3.7 18.8 - - + -
194I GLY 3.3 9.7 + - - +
196I GLY* 1.3 74.6 - - - +
198I TRP* 1.3 58.7 + - - +
200I PHE* 3.2 6.5 + - + +
201I ASP* 2.8 27.4 + - + +
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Residues in contact with TRP 198 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLN* 2.8 44.9 + - + +
190B ARG* 4.1 12.8 - - - -
191B VAL* 3.5 26.5 - - + -
199B HIS* 3.6 38.8 - + + -
200B PHE* 3.8 27.4 - + - -
203B MET* 3.8 22.4 - - + -
76I ALA 5.0 1.3 - - - -
77I LEU* 4.5 10.1 - - + -
194I GLY 3.1 16.8 + - - +
195I HIS* 3.7 8.5 - + - +
197I VAL* 1.3 78.1 - - - +
199I HIS* 1.3 63.4 + - - +
201I ASP* 3.2 10.5 + - - +
202I GLN* 2.9 57.4 + - + +
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Residues in contact with HIS 199 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B HIS* 3.5 32.8 + + + -
195H HIS* 2.9 25.3 + - + +
198H TRP* 3.6 22.2 - + + -
199H HIS* 3.5 42.1 + + - -
202H GLN* 5.6 1.4 - - - +
195I HIS* 2.9 17.5 + - + +
196I GLY 3.5 4.0 - - - +
198I TRP* 1.3 81.1 - - + +
200I PHE* 1.3 66.0 + - - +
202I GLN* 3.0 9.7 + - + +
203I MET* 3.0 21.0 + - + +
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Residues in contact with PHE 200 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198H TRP* 3.9 15.8 - + + -
80I LEU* 4.2 8.1 - - + -
133I MET* 4.5 1.8 - - + -
184I TYR* 3.7 36.1 - + + -
187I GLN* 3.8 35.4 - - + -
188I LEU* 3.5 35.7 - - + -
191I VAL* 4.3 7.6 - - + -
196I GLY 2.9 13.1 + - - +
197I VAL 3.5 6.7 - - - +
199I HIS* 1.3 76.4 - - - +
201I ASP* 1.3 61.3 + - - +
203I MET* 3.1 31.4 + - + +
204I LEU* 2.9 46.5 + - + +
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Residues in contact with ASP 201 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76I ALA 4.9 0.3 - - - +
77I LEU* 3.3 28.3 - - + +
78I ARG* 3.2 9.5 + - - +
79I GLY* 2.9 19.4 + - - -
80I LEU* 2.7 41.0 + - + +
197I VAL 2.8 14.2 + - - +
198I TRP* 3.4 11.3 - - - +
199I HIS 3.1 0.2 - - - -
200I PHE* 1.3 83.2 - - - +
202I GLN* 1.3 63.7 + - - +
204I LEU* 3.3 3.4 + - - +
205I LEU* 2.8 27.5 + - - +
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Residues in contact with GLN 202 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B HIS* 5.7 1.1 - - - +
203B MET* 3.3 27.3 - - - +
78I ARG* 3.0 27.2 + - - +
198I TRP* 2.9 46.3 + - + +
199I HIS* 3.0 14.8 + - + +
201I ASP* 1.3 77.0 - - - +
203I MET* 1.3 65.4 + - - +
205I LEU* 3.3 10.3 + - - +
206I HIS* 3.1 52.0 + - + -
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Residues in contact with MET 203 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78H ARG* 3.7 17.7 - - - +
198H TRP* 3.8 11.4 - - + -
202H GLN* 3.4 31.0 - - - +
184I TYR* 4.8 7.2 - - + -
187I GLN* 3.7 15.7 - - - +
199I HIS* 3.0 12.9 + - + +
200I PHE* 3.3 42.6 - - + +
202I GLN* 1.3 76.7 - - - +
204I LEU* 1.3 67.0 + - + +
206I HIS* 3.1 6.0 + - - +
207I GLU* 2.9 38.9 + - - +
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Residues in contact with LEU 204 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79I GLY* 3.8 22.5 - - - +
80I LEU* 3.9 23.8 - - + -
82I LYS* 5.0 4.3 - - - +
83I PHE* 3.9 17.5 - - + -
133I MET* 4.3 11.2 - - + -
184I TYR* 3.4 36.8 - - + +
200I PHE* 2.9 25.6 + - + +
201I ASP* 3.6 9.0 - - - +
203I MET* 1.3 82.7 - - + +
205I LEU* 1.3 64.2 + - - +
206I HIS 3.2 0.7 + - - -
207I GLU* 3.3 32.2 + - - +
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Residues in contact with LEU 205 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I ARG* 3.8 55.4 - - + +
79I GLY* 3.6 8.9 - - - +
82I LYS* 3.8 32.8 - - + -
201I ASP* 2.8 17.3 + - - +
202I GLN* 3.5 20.2 - - - +
203I MET 3.2 0.2 - - - -
204I LEU* 1.3 77.5 - - - +
206I HIS* 1.3 83.4 + - + +
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Residues in contact with HIS 206 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202I GLN* 3.1 44.4 + - + +
203I MET* 3.1 6.8 + - - +
205I LEU* 1.3 94.5 + - + +
207I GLU* 1.3 67.3 + - - +
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Residues in contact with GLU 207 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78H ARG* 5.4 5.6 + - - +
82I LYS* 5.9 3.5 - - - -
83I PHE* 4.9 0.2 - - - -
180I ARG* 2.7 32.6 + - - -
184I TYR* 2.8 25.1 + - - -
203I MET* 2.9 25.6 + - - +
204I LEU* 3.3 25.6 + - - +
205I LEU 3.5 0.7 - - - +
206I HIS* 1.3 82.3 - - - +
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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