Contacts of the helix formed by residues 237 - 247 (chain v) 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 ASN 237 (chain v).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235v HIS 4.0 0.4 + - - -
236v ASN* 1.3 78.0 - - - +
238v PHE* 1.3 62.3 + - - +
239v VAL* 3.1 8.4 + - + +
240v LYS* 3.2 10.2 + - + +
241v ILE* 2.9 25.3 + - - +
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Residues in contact with PHE 238 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172v ASP* 4.4 23.4 - - + +
176v ALA* 6.2 2.2 - - + +
236v ASN 3.9 0.2 + - - -
237v ASN* 1.3 74.7 - - - +
239v VAL* 1.3 57.5 - - - +
241v ILE* 3.7 7.8 - - - +
242v LYS* 2.9 28.6 + - - +
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Residues in contact with VAL 239 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237v ASN* 3.1 6.3 - - + +
238v PHE* 1.3 76.3 - - - +
240v LYS* 1.3 60.2 + - - +
242v LYS* 3.1 7.8 + - - +
243v LYS* 2.9 26.5 + - - +
110w TYR* 6.0 0.7 - - - +
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Residues in contact with LYS 240 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233v ASN* 5.3 1.1 - - - +
236v ASN* 4.1 17.9 - - + -
237v ASN* 3.2 14.2 + - + +
239v VAL* 1.3 79.5 - - - +
241v ILE* 1.3 57.2 + - - +
243v LYS* 3.3 7.2 + - - +
244v GLU* 2.9 29.6 + - - +
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Residues in contact with ILE 241 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176v ALA* 4.9 19.6 - - + +
230v VAL* 6.3 2.5 - - - -
233v ASN* 4.4 28.3 - - + +
236v ASN* 4.9 1.4 - - - +
237v ASN 2.9 17.0 + - - +
238v PHE* 3.7 9.4 - - - +
240v LYS* 1.3 76.2 - - - +
242v LYS* 1.3 59.3 + - - +
244v GLU* 3.5 2.4 + - - +
245v LEU* 2.9 27.9 + - - +
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Residues in contact with LYS 242 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238v PHE 2.9 18.1 + - - +
239v VAL* 3.1 8.3 + - - +
241v ILE* 1.3 75.7 - - - +
243v LYS* 1.3 59.8 + - - +
245v LEU* 3.3 8.2 + - - +
246v PHE* 2.9 27.0 + - - +
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Residues in contact with LYS 243 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239v VAL 2.9 12.9 + - - +
240v LYS* 3.7 11.7 - - - +
242v LYS* 1.3 75.8 - - - +
244v GLU* 1.3 59.0 + - - +
246v PHE* 3.0 10.6 + - - +
247v SER* 2.9 26.4 + - - -
110w TYR* 5.0 18.4 - - + +
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Residues in contact with GLU 244 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229v ILE* 4.9 16.6 - - + +
233v ASN* 4.8 13.0 - - + -
240v LYS 2.9 17.5 + - - +
241v ILE* 3.8 7.4 - - - +
243v LYS* 1.3 76.1 - - - +
245v LEU* 1.3 61.0 + - - +
247v SER* 3.2 22.3 + - - -
248v ILE* 3.7 5.2 + - - +
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Residues in contact with LEU 245 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176v ALA 6.1 0.9 - - - +
180v GLY* 5.7 9.4 - - - +
229v ILE* 5.5 5.1 - - - +
241v ILE 2.9 18.6 + - - +
242v LYS* 3.4 9.9 - - - +
243v LYS 3.2 0.2 - - - -
244v GLU* 1.3 75.0 - - - +
246v PHE* 1.3 60.0 + - - +
248v ILE* 3.4 20.5 + - - +
249v PHE 4.6 0.7 + - - -
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Residues in contact with PHE 246 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242v LYS 2.9 12.7 + - - +
243v LYS* 3.0 13.2 + - - +
245v LEU* 1.3 71.9 - - - +
247v SER* 1.3 61.0 + - - +
248v ILE 3.1 6.0 + - - -
249v PHE* 3.5 17.8 + - - +
250v SER 4.2 1.4 + - - -
103w LEU* 4.9 8.7 - - - +
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Residues in contact with SER 247 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243v LYS 2.9 11.4 + - - -
244v GLU* 3.2 17.0 + - - -
246v PHE* 1.3 74.6 - - - +
248v ILE* 1.3 58.9 + - - +
249v PHE 3.2 0.7 - - - -
250v SER* 3.3 11.6 + - - +
251v GLU* 3.0 27.5 + - - +
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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