Contacts of the helix formed by residues 266 - 270 (chain A) in PDB entry 5TOL
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 LYS 266 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A ASP* 2.9 22.3 + - - +
265A CYS* 1.3 76.8 - - - +
267A GLU* 1.3 68.5 + - + +
268A TYR 3.2 0.2 - - - -
269A ASN* 3.1 13.7 + - - -
270A TYR* 3.4 13.9 + - - +
429A ASP* 2.8 37.8 + - - +
430A CYS 3.4 13.0 - - - +
431A GLY 3.6 17.3 - - - +
432A TYR* 4.7 19.9 - - + +
433A ASN* 5.3 5.8 - - - +
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Residues in contact with GLU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A MET* 3.9 26.3 - - + +
264A ASP* 2.9 32.3 + - + +
266A LYS* 1.3 81.2 - - + +
268A TYR* 1.3 58.6 + - - +
269A ASN 3.1 1.4 + - - -
270A TYR* 3.5 22.1 + - - +
285A PRO* 3.3 21.0 - - - +
287A LYS* 2.9 36.7 - - + +
288A VAL* 3.4 7.9 - - + +
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Residues in contact with TYR 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ILE* 4.0 17.7 - - + +
252A VAL 4.4 0.2 - - - -
253A ARG* 3.7 27.4 - - - -
254A VAL* 3.5 32.4 + - + -
260A ASP* 4.1 2.6 + - - -
261A LEU* 3.5 24.0 - - + +
262A LYS 4.0 2.4 + - - -
263A MET* 3.6 36.2 + - + -
265A CYS* 3.4 35.9 - - + +
266A LYS 3.2 0.2 - - - -
267A GLU* 1.3 75.5 - - - +
269A ASN* 1.3 61.4 + - - +
270A TYR 3.7 0.4 - - - -
273A SER* 3.0 7.1 + - - -
285A PRO* 4.4 1.8 - - - -
288A VAL* 3.6 28.7 - - + -
379A THR* 3.0 25.6 + - - -
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Residues in contact with ASN 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A ARG* 6.0 0.9 - - - +
248A GLU* 5.8 1.6 - - - +
249A VAL 4.7 1.1 - - - +
250A ILE* 3.7 9.0 - - + +
251A ILE* 2.9 45.5 + - - +
265A CYS 3.2 11.5 + - - -
266A LYS 3.1 7.4 + - - -
268A TYR* 1.3 80.7 - - - +
270A TYR* 1.3 54.9 + - - +
271A ASP* 2.9 5.7 - - - +
272A LYS* 2.8 25.5 + - - -
273A SER* 2.5 31.0 + - - +
430A CYS* 2.9 32.0 + - - +
431A GLY* 4.7 4.9 - - - -
432A TYR* 3.4 10.4 + - - +
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Residues in contact with TYR 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A LYS 3.6 12.3 - - - +
267A GLU* 3.5 27.1 + - - +
268A TYR 3.7 0.8 + - - -
269A ASN* 1.3 76.9 - - - +
271A ASP* 1.3 58.6 + - + +
272A LYS 3.4 1.1 + - - -
285A PRO* 3.5 20.4 - - + +
287A LYS* 6.1 6.1 - - + -
376A SER* 5.6 1.6 - - - -
378A GLY* 3.4 17.7 + - - -
432A TYR* 3.7 44.4 + + + -
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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