Contacts of the helix formed by residues 226 - 237 (chain A) in PDB entry 6VSU
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 ASN 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A TYR* 3.6 34.7 + - - -
225A ILE* 1.3 74.8 - - - +
227A GLN* 1.3 68.5 + - - +
228A GLU* 3.4 10.9 + - - +
229A GLY* 3.1 19.4 + - - -
230A ARG* 3.1 30.9 + - - +
99B ASN* 4.3 11.4 - - + +
101B ALA* 4.0 20.0 - - + -
105B GLY* 6.4 0.2 - - - -
107B GLU* 5.9 2.2 - - - +
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Residues in contact with GLN 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ASN* 1.3 75.2 - - - +
228A GLU* 1.3 57.5 + - - +
230A ARG* 3.0 10.6 + - + +
231A GLU* 2.8 59.0 + - + +
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Residues in contact with GLU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ILE* 5.4 0.2 - - - -
191A TYR* 3.3 28.3 - - + +
192A ASP* 3.0 34.9 + - - +
193A CYS 4.6 1.0 + - - -
226A ASN* 3.3 13.7 + - - +
227A GLN* 1.3 77.1 - - - +
229A GLY* 1.3 53.3 + - - +
231A GLU* 3.4 12.4 + - - +
232A GLN* 2.8 51.1 + - + +
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Residues in contact with GLY 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A PRO* 4.4 5.6 - - - -
190A ILE* 3.8 17.3 - - - +
191A TYR* 5.6 3.5 - - - -
225A ILE* 3.9 16.8 - - - -
226A ASN* 3.1 18.7 + - - -
228A GLU* 1.3 75.7 - - - +
230A ARG* 1.3 59.2 + - - +
233A GLY 3.2 15.4 + - - -
240A GLN* 3.3 14.7 + - - -
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Residues in contact with ARG 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ILE* 3.6 30.8 + - + +
226A ASN* 3.1 17.2 + - - +
227A GLN* 3.0 11.2 + - + +
229A GLY* 1.3 72.2 - - - +
231A GLU* 1.3 61.5 + - + +
233A GLY* 3.2 2.9 + - - -
234A LYS* 2.9 33.0 + - - +
240A GLN* 3.9 9.4 - - - +
242A GLU* 3.0 39.7 + - - -
244A ARG* 3.9 8.1 - - - +
103B GLU 3.1 20.2 + - - -
104B GLU 4.7 2.3 - - - -
105B GLY* 4.1 20.0 - - - +
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Residues in contact with GLU 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A GLN* 2.8 51.7 + - + +
228A GLU* 3.9 15.1 - - - +
230A ARG* 1.3 72.3 - - + +
232A GLN* 1.3 66.7 + - + +
234A LYS* 3.1 22.5 + - - +
235A ARG* 2.9 24.5 + - - +
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Residues in contact with GLN 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ILE* 2.8 43.6 + - + +
192A ASP* 3.5 28.9 + - - +
206A ALA* 4.0 9.9 - - - +
210A GLU* 5.2 0.2 + - - -
228A GLU* 2.8 36.7 + - + +
231A GLU* 1.3 74.1 - - + +
233A GLY* 1.3 62.8 + - - +
235A ARG* 2.8 40.1 + - - +
236A PHE* 3.0 36.0 + - + -
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Residues in contact with GLY 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ILE* 4.4 2.3 - - - +
229A GLY 3.2 13.9 + - - -
230A ARG 3.2 4.9 + - - -
231A GLU 3.2 0.2 - - - -
232A GLN* 1.3 78.1 - - - +
234A LYS* 1.3 60.3 + - - +
236A PHE 3.3 1.4 + - - -
237A GLY 3.1 3.3 + - - -
238A VAL* 2.9 51.3 + - - +
240A GLN* 4.0 13.5 - - - -
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Residues in contact with LYS 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ARG* 2.9 17.4 + - - +
231A GLU* 3.1 26.4 + - - +
233A GLY* 1.3 72.9 - - - +
235A ARG* 1.3 61.7 + - - +
237A GLY* 3.5 11.6 + - - -
238A VAL 5.5 0.4 - - - -
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Residues in contact with ARG 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ASP* 5.0 7.1 + - - +
210A GLU* 4.4 14.1 + - - +
231A GLU 2.9 12.7 + - - +
232A GLN* 2.8 45.1 + - - +
234A LYS* 1.3 79.4 - - - +
236A PHE* 1.3 94.3 + - + +
237A GLY 3.5 0.2 - - - -
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Residues in contact with PHE 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ILE* 4.1 11.2 - - + -
206A ALA* 4.2 11.0 - - - -
209A MET* 3.5 44.3 - - + +
210A GLU* 3.9 31.2 - - + -
215A ARG 5.4 0.9 - - - +
232A GLN* 3.0 38.9 + - - +
235A ARG* 1.3 125.6 - - + +
237A GLY* 1.3 62.0 + - - +
238A VAL* 3.3 14.7 + - + -
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Residues in contact with GLY 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A MET* 5.8 0.2 - - - -
215A ARG 5.6 1.9 - - - +
216A ARG* 5.8 1.4 - - - -
217A LEU 4.9 3.8 + - - +
233A GLY 3.1 4.6 + - - -
234A LYS 3.5 7.3 + - - -
235A ARG 3.5 2.8 - - - -
236A PHE* 1.3 77.7 - - - +
238A VAL* 1.3 63.7 + - - +
239A GLU* 3.7 10.9 + - - +
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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