Contacts of the helix formed by residues 266 - 271 (chain P) in PDB entry 6CNB
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 GLU 266 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302O THR* 3.3 30.3 - - - +
494O TYR* 3.8 17.4 + - - +
183P TRP* 4.4 6.8 - - + -
251P ASP* 4.2 7.6 - - + +
252P LYS* 5.5 5.8 + - + +
263P VAL* 4.8 1.4 - - - +
264P THR* 3.0 29.9 + - - +
265P LEU* 1.3 79.1 - - - +
267P SER* 1.3 63.2 + - - +
268P ILE* 2.8 23.2 - - - +
269P LEU* 2.7 57.1 + - + +
270P GLN* 3.2 2.9 + - - +
296P TYR* 5.5 0.2 - - - -
297P PHE* 4.2 3.6 - - - -
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Residues in contact with SER 267 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183P TRP* 3.9 30.0 - - - -
187P SER* 5.9 3.6 - - - -
191P PHE* 5.4 4.2 - - - -
194P GLY* 6.4 1.3 - - - -
196P LYS* 3.8 31.3 + - - +
263P VAL* 5.3 2.4 - - - +
265P LEU* 3.0 12.6 + - - +
266P GLU* 1.3 77.1 - - - +
268P ILE* 1.3 57.6 + - - +
270P GLN* 2.9 9.9 + - - +
271P MET* 2.8 25.5 + - - -
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Residues in contact with ILE 268 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302O THR* 6.0 1.6 - - + -
196P LYS* 4.5 17.7 - - + +
265P LEU* 3.0 34.5 - - + +
266P GLU* 2.8 27.4 - - - +
267P SER* 1.3 81.6 + - - +
269P LEU* 1.3 68.3 + - - +
271P MET* 3.4 19.8 - - - +
295P ASN* 5.3 1.8 - - + +
297P PHE* 3.5 23.4 - - + -
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Residues in contact with LEU 269 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494O TYR* 6.4 0.4 - - + -
183P TRP* 6.3 0.7 - - + -
252P LYS* 5.1 18.2 - - + -
266P GLU* 2.7 51.0 + - + +
268P ILE* 1.3 76.1 - - - +
270P GLN* 1.3 76.1 + - + +
271P MET* 4.3 3.6 - - - +
296P TYR* 2.9 31.8 + - + +
297P PHE* 3.0 40.7 - - + +
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Residues in contact with GLN 270 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183P TRP* 3.1 32.9 - - + -
184P ARG* 4.5 21.4 + - - +
266P GLU 3.2 6.3 + - - +
267P SER* 2.9 18.5 + - - +
269P LEU* 1.3 89.0 - - + +
271P MET* 1.3 77.0 + - - +
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Residues in contact with MET 271 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196P LYS* 6.2 5.2 - - - -
267P SER 2.8 12.3 + - - -
268P ILE* 3.4 18.1 + - - +
269P LEU 3.4 3.1 - - - +
270P GLN* 1.3 90.7 - - - +
297P PHE* 5.5 10.8 - - + -
298P LYS* 5.5 20.2 - - + +
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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