Contacts of the helix formed by residues 237 - 246 (chain r) in PDB entry 6QXT
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 r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172r ASP* 5.6 1.3 - - - -
235r HIS 3.9 0.6 + - - -
236r ASN* 1.3 78.5 - - - +
238r PHE* 1.3 62.9 + - - +
239r VAL* 3.1 9.2 - - + +
240r LYS* 3.0 9.5 + - + +
241r ILE* 2.9 25.0 + - - +
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Residues in contact with PHE 238 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172r ASP* 4.2 29.0 - - + +
175r ALA* 5.8 5.2 - - + -
176r ALA* 6.0 1.3 - - + +
236r ASN 3.9 0.4 + - - -
237r ASN* 1.3 74.1 - - - +
239r VAL* 1.3 57.3 + - - +
241r ILE* 3.3 9.7 + - - +
242r LYS* 2.9 27.7 + - - +
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Residues in contact with VAL 239 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237r ASN* 3.1 7.1 - - + +
238r PHE* 1.3 79.2 - - - +
240r LYS* 1.3 57.3 + - - +
242r LYS* 3.1 8.2 + - - +
243r LYS* 2.9 26.2 + - - +
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Residues in contact with LYS 240 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233r ASN* 5.5 0.6 - - - +
236r ASN* 3.7 21.8 - - + -
237r ASN* 3.0 14.2 + - + +
239r VAL* 1.3 78.6 - - - +
241r ILE* 1.3 57.7 + - - +
243r LYS* 3.2 8.1 + - - +
244r GLU* 2.9 29.3 + - - +
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Residues in contact with ILE 241 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172r ASP* 5.5 0.9 - - + +
176r ALA* 4.2 23.7 - - + +
230r VAL* 6.3 2.9 - - - -
233r ASN* 4.9 15.5 - - + +
236r ASN* 4.8 3.9 - - - +
237r ASN 2.9 13.0 + - - +
238r PHE* 3.6 12.8 - - - +
239r VAL 3.2 0.2 - - - -
240r LYS* 1.3 77.3 - - - +
242r LYS* 1.3 55.3 + - - +
244r GLU* 3.8 5.9 - - - +
245r LEU* 2.9 30.1 + - - +
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Residues in contact with LYS 242 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179r TYR* 6.1 6.5 - - + -
238r PHE 2.9 14.7 + - - +
239r VAL* 3.1 10.5 + - - +
241r ILE* 1.3 74.8 - - - +
243r LYS* 1.3 60.5 + - - +
245r LEU* 3.4 5.9 + - - +
246r PHE* 2.9 29.5 + - - +
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Residues in contact with LYS 243 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239r VAL 2.9 13.3 + - - +
240r LYS* 3.2 11.6 + - - +
242r LYS* 1.3 77.9 - - - +
244r GLU* 1.3 60.7 + - - +
246r PHE* 3.4 16.2 + - - +
247r SER* 3.6 7.8 + - - -
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Residues in contact with GLU 244 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229r ILE* 5.4 13.3 - - + +
233r ASN* 4.7 15.3 - - + -
240r LYS 2.9 16.5 + - - +
241r ILE* 3.8 7.4 - - - +
242r LYS 3.3 0.2 - - - -
243r LYS* 1.3 76.4 - - - +
245r LEU* 1.3 61.7 + - - +
247r SER* 3.2 19.0 + - - -
248r ILE* 4.1 2.4 + - - +
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Residues in contact with LEU 245 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176r ALA 5.9 1.3 - - - +
179r TYR* 6.1 3.1 - - + -
180r GLY* 5.3 14.4 - - - +
229r ILE* 5.8 5.6 - - + +
241r ILE 2.9 18.5 + - - +
242r LYS* 3.9 5.8 - - - +
244r GLU* 1.3 76.2 - - - +
246r PHE* 1.3 60.3 + - - +
247r SER 3.2 1.1 + - - -
248r ILE* 3.4 19.8 + - - +
249r PHE 4.9 0.5 + - - -
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Residues in contact with PHE 246 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242r LYS 2.9 18.8 + - - +
243r LYS* 3.6 10.3 - - - +
244r GLU 3.2 0.4 - - - -
245r LEU* 1.3 77.5 - - - +
247r SER* 1.3 59.0 + - - +
248r ILE 3.2 1.5 + - - -
249r PHE* 3.9 14.1 + - - +
250r SER* 4.7 1.0 + - - -
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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