Contacts of the helix formed by residues 260 - 264 (chain L) in PDB entry 6Y5D
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 260 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235L PRO* 4.0 24.3 - - - +
253L PHE* 3.1 42.4 - - + -
256L ASN* 4.1 20.9 + - + +
258L LYS 3.3 2.6 + - - +
259L GLU* 1.3 73.0 - - - +
261L PRO* 1.3 63.4 - - - +
262L LEU* 3.2 15.6 + - - +
263L SER* 2.5 43.6 + - - +
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Residues in contact with PRO 261 (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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201L SER 3.7 5.2 - - - +
202L ALA* 4.4 0.4 - - - +
204L ARG* 3.5 48.7 - - + +
235L PRO* 6.3 1.8 - - + -
259L GLU* 3.5 10.5 - - + +
260L ASN* 1.3 90.5 - - - +
262L LEU* 1.3 70.8 + - + +
263L SER* 3.1 2.7 + - - -
264L GLN* 3.0 29.8 + - - +
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Residues in contact with LEU 262 (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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202L ALA 3.0 29.6 - - - +
232L LEU* 3.9 23.8 - - + -
233L GLU 4.4 6.7 - - - +
234L VAL* 3.5 32.1 - - + -
235L PRO* 5.7 0.2 - - + -
253L PHE* 3.9 15.0 - - + -
260L ASN* 3.0 18.6 + - - +
261L PRO* 1.3 82.2 - - + +
263L SER* 1.3 64.5 + - - +
264L GLN 3.0 2.9 - - - -
265L PHE* 2.9 36.7 + - + +
266L LEU* 3.8 2.8 + - - +
271L LEU* 3.9 8.4 - - + +
276L MET* 4.4 7.6 - - + -
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Residues in contact with SER 263 (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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260L ASN* 2.5 33.0 + - - +
261L PRO 3.1 1.2 - - - -
262L LEU* 1.3 77.6 - - - +
264L GLN* 1.3 56.8 + - - +
265L PHE 3.0 0.2 - - - -
266L LEU* 3.0 43.8 + - - +
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Residues in contact with GLN 264 (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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201L SER* 3.6 13.8 + - - -
202L ALA* 3.4 24.8 - - - +
204L ARG* 5.7 0.2 - - - +
261L PRO 3.0 22.4 + - - +
263L SER* 1.3 77.9 - - - +
265L PHE* 1.3 77.7 + - + +
266L LEU 3.4 1.1 + - - -
275L LYS* 4.0 13.2 + - - +
279L LYS* 2.7 30.3 + - - +
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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