Contacts of the helix formed by residues 237 - 246 (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 ASN 237 (chain l).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172l ASP* 5.7 1.1 - - - -
235l HIS 3.9 0.6 + - - -
236l ASN* 1.3 77.9 - - - +
238l PHE* 1.3 61.8 + - - +
239l VAL* 3.1 8.7 - - + +
240l LYS* 3.0 10.0 + - + +
241l ILE* 2.9 24.9 + - - +
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Residues in contact with PHE 238 (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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172l ASP* 4.2 31.2 - - + +
175l ALA* 5.8 4.7 - - + -
176l ALA* 6.0 1.3 - - + +
236l ASN 3.9 0.2 + - - -
237l ASN* 1.3 74.6 - - - +
239l VAL* 1.3 56.5 + - - +
241l ILE* 3.6 9.0 - - - +
242l LYS* 2.9 28.1 + - - +
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Residues in contact with VAL 239 (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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237l ASN* 3.1 6.7 - - + +
238l PHE* 1.3 79.0 - - - +
240l LYS* 1.3 57.5 + - - +
242l LYS* 3.1 8.7 + - - +
243l LYS* 2.9 26.3 + - - +
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Residues in contact with LYS 240 (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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233l ASN* 5.4 0.6 - - - +
236l ASN* 3.7 21.5 - - + -
237l ASN* 3.0 14.3 + - + +
239l VAL* 1.3 78.6 - - - +
241l ILE* 1.3 56.5 + - - +
243l LYS* 3.3 9.1 + - - +
244l GLU* 2.9 28.4 + - - +
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Residues in contact with ILE 241 (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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172l ASP 5.5 0.4 - - - +
176l ALA* 4.2 24.1 - - + +
230l VAL* 6.3 2.7 - - - -
233l ASN* 4.9 15.3 - - + +
236l ASN* 4.8 4.4 - - - +
237l ASN 2.9 12.7 + - - +
238l PHE* 3.6 12.6 - - - +
239l VAL 3.2 0.4 - - - -
240l LYS* 1.3 78.1 - - - +
242l LYS* 1.3 56.2 + - - +
244l GLU* 3.4 6.0 + - - +
245l LEU* 2.9 29.3 + - - +
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Residues in contact with LYS 242 (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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179l TYR* 6.1 6.5 - - + -
238l PHE 2.9 15.3 + - - +
239l VAL* 3.1 10.3 + - - +
241l ILE* 1.3 75.3 - - - +
243l LYS* 1.3 59.8 + - - +
245l LEU* 3.7 5.9 - - - +
246l PHE* 2.9 29.3 + - - +
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Residues in contact with LYS 243 (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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239l VAL 2.9 13.4 + - - +
240l LYS* 3.3 11.9 + - - +
242l LYS* 1.3 78.1 - - - +
244l GLU* 1.3 60.6 + - - +
246l PHE* 3.4 17.5 + - - +
247l SER* 3.7 8.1 + - - -
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Residues in contact with GLU 244 (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* 5.4 13.0 - - + +
233l ASN* 4.7 15.9 - - + -
240l LYS 2.9 16.3 + - - +
241l ILE* 3.8 6.7 - - - +
243l LYS* 1.3 77.5 - - - +
245l LEU* 1.3 61.0 + - - +
247l SER* 3.3 19.5 + - - -
248l ILE* 4.2 2.3 + - - +
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Residues in contact with LEU 245 (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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176l ALA 5.9 2.0 - - - +
179l TYR* 6.1 3.1 - - + -
180l GLY* 5.4 14.1 - - - +
229l ILE* 5.8 4.9 - - + +
241l ILE 2.9 19.1 + - - +
242l LYS* 3.9 6.5 - - - +
244l GLU* 1.3 75.9 - - - +
246l PHE* 1.3 61.0 + - - +
247l SER 3.2 0.9 + - - -
248l ILE* 3.4 20.3 + - - +
249l PHE 4.9 0.5 + - - -
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Residues in contact with PHE 246 (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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242l LYS 2.9 18.0 + - - +
243l LYS* 3.7 10.1 - - - +
244l GLU 3.2 0.8 - - - -
245l LEU* 1.3 76.0 - - - +
247l SER* 1.3 58.9 + - - +
248l ILE 3.2 1.3 + - - -
249l PHE* 3.9 14.1 + - - +
250l 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