Contacts of the helix formed by residues 223 - 233 (chain L) in PDB entry 6QY3
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 ARG 223 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184L LEU* 6.4 2.0 - - - -
219L MET 3.5 6.0 + - - +
220L GLU* 3.1 21.2 + - - +
221L PRO 3.4 0.2 - - - -
222L PHE* 1.3 78.0 - - - +
224L PRO* 1.3 64.1 - - - +
226L ILE* 3.0 22.3 + - - +
227L ASP* 3.5 4.4 + - - +
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Residues in contact with PRO 224 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113L LYS 5.4 1.8 - - - +
116L ASN* 4.5 30.7 - - + +
117L GLN* 4.7 9.2 - - + +
120L TYR* 5.0 9.7 - - + +
220L GLU 4.8 0.4 - - - -
221L PRO 4.8 1.7 - - - +
222L PHE 3.4 1.0 - - - -
223L ARG* 1.3 77.4 - - - +
225L ILE* 1.3 62.7 + - - +
226L ILE 3.1 0.2 - - - -
227L ASP* 3.0 12.2 + - + +
228L ARG* 2.9 24.1 + - - +
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Residues in contact with ILE 225 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222L PHE* 3.5 14.9 + - + +
223L ARG 3.1 1.0 + - - -
224L PRO* 1.3 78.9 - - - +
226L ILE* 1.3 60.2 + - - +
228L ARG* 3.7 12.3 + - - +
229L ILE* 3.8 11.8 + - - +
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Residues in contact with ILE 226 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177L LEU* 5.9 4.3 - - - +
180L GLY* 4.7 23.6 - - - +
181L TYR 5.4 0.4 - - - +
222L PHE 4.3 1.7 + - - +
223L ARG* 3.0 12.9 + - - +
225L ILE* 1.3 78.5 - - - +
227L ASP* 1.3 58.7 + - - +
228L ARG 3.2 0.4 + - - -
229L ILE* 3.4 5.8 + - - +
230L VAL* 2.9 30.0 + - - +
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Residues in contact with ASP 227 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160L LEU* 5.4 6.2 - - + +
223L ARG 3.5 3.6 + - - +
224L PRO* 3.0 18.5 + - + +
226L ILE* 1.3 78.2 - - - +
228L ARG* 1.3 58.2 + - - +
230L VAL* 3.8 7.9 - - - +
231L TYR* 2.9 28.8 + - - +
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Residues in contact with ARG 228 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120L TYR* 6.1 5.2 - - + -
224L PRO 2.9 13.5 + - - +
225L ILE* 3.9 9.2 - - - +
226L ILE 3.2 0.4 - - - -
227L ASP* 1.3 74.7 - - - +
229L ILE* 1.3 61.8 + - - +
231L TYR* 3.0 8.6 + - - +
232L GLN* 2.9 27.1 + - - +
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Residues in contact with ILE 229 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225L ILE 3.8 8.3 + - - +
226L ILE* 3.4 7.0 + - - +
228L ARG* 1.3 79.1 - - - +
230L VAL* 1.3 58.1 + - - +
232L GLN* 3.8 7.3 - - - +
233L ASN* 2.9 33.6 + - - +
244L GLU* 5.4 16.4 - - + +
245L LEU* 5.8 4.0 - - + +
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Residues in contact with VAL 230 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173L ILE* 5.4 9.1 - - + +
176L ALA* 5.0 17.5 - - + -
177L LEU* 5.5 6.5 - - + +
226L ILE 2.9 18.6 + - - +
227L ASP* 3.9 9.0 - - - +
229L ILE* 1.3 76.5 - - - +
231L TYR* 1.3 57.8 + - - +
233L ASN* 3.9 3.1 - - - +
234L ARG* 3.1 30.0 + - - +
241L ILE* 6.3 2.5 - - - -
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Residues in contact with TYR 231 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160L LEU* 4.7 22.9 - - + +
227L ASP 2.9 19.0 + - - +
228L ARG* 3.0 7.8 + - - +
230L VAL* 1.3 77.3 - - - +
232L GLN* 1.3 63.8 + - - +
234L ARG* 3.8 13.1 + - - +
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Residues in contact with GLN 232 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228L ARG 2.9 15.1 + - - +
229L ILE* 3.3 7.2 + - - +
231L TYR* 1.3 78.9 - - - +
233L ASN* 1.3 57.9 + - + +
234L ARG 3.3 1.2 + - - -
235L HIS* 4.9 2.6 + - - +
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Residues in contact with ASN 233 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229L ILE 2.9 18.6 + - - +
230L VAL* 3.9 2.7 - - - +
232L GLN* 1.3 74.4 - - + +
234L ARG* 1.3 54.6 + - - +
235L HIS 3.1 3.1 - - - -
236L ASN* 2.8 41.4 + - + +
240L LYS 5.4 0.4 - - - +
241L ILE* 4.9 15.5 - - + +
244L GLU* 4.7 19.3 - - + -
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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