Contacts of the helix formed by residues 268 - 276 (chain A) in PDB entry 4Y6O
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 PRO 268 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A LEU* 3.6 32.1 - - + -
243A PHE* 3.9 19.6 - - + -
244A PHE* 4.2 14.6 - - + -
247A MET* 6.3 0.4 - - - -
267A GLN* 1.3 89.1 - - + +
269A PHE* 1.3 63.9 + - - +
270A ALA 3.3 3.1 - - - -
271A SER* 2.7 30.3 + - - +
272A LEU 4.0 0.7 + - - -
8C PRO* 4.5 8.5 - - + -
9C LYS 3.5 17.0 - - - +
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Residues in contact with PHE 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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82A LEU* 4.1 15.7 - - + -
83A VAL 3.9 8.3 - - - -
165A TYR* 3.4 48.2 - - + -
166A THR 3.9 5.4 - - - -
167A GLN* 3.3 47.8 - - + -
186A ALA* 3.7 20.0 - - + -
187A HIS* 4.3 11.4 - - - +
239A LEU* 4.9 0.8 - - + +
243A PHE* 4.1 9.7 - + + -
264A LEU* 4.0 19.3 - - + +
266A VAL 3.5 7.9 - - - +
267A GLN 3.3 2.8 - - - -
268A PRO* 1.3 78.2 - - - +
270A ALA* 1.3 64.4 + - - +
272A LEU* 3.1 28.7 + - + +
273A ILE* 6.0 0.2 - - - +
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Residues in contact with ALA 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU* 3.3 44.3 - - + +
265A GLN 4.7 0.7 - - - -
266A VAL 2.8 22.8 + - - +
267A GLN* 3.6 20.4 - - + +
268A PRO 3.3 0.4 - - - -
269A PHE* 1.3 73.2 - - - +
271A SER* 1.3 60.4 + - - +
272A LEU 3.3 1.2 + - - -
273A ILE* 4.1 8.3 + - - +
304A GLY 4.0 4.7 - - - +
305A GLY* 3.8 19.8 - - - +
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Residues in contact with SER 271 (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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247A MET* 5.1 3.3 - - - -
267A GLN* 3.4 16.6 + - - +
268A PRO* 2.7 25.8 + - - +
270A ALA* 1.3 76.1 - - - +
272A LEU* 1.3 63.2 + - - +
273A ILE 3.4 0.4 - - - -
274A SER* 2.7 30.2 + - - -
275A LYS* 3.5 23.1 + - - +
305A GLY 6.0 0.2 - - - -
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Residues in contact with LEU 272 (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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82A LEU* 3.7 24.5 - - + -
165A TYR* 3.6 25.6 - - + -
243A PHE* 3.7 27.1 - - + -
247A MET* 3.6 38.8 - - + -
251A PHE* 3.3 26.4 - - + -
268A PRO 4.4 0.7 - - - +
269A PHE* 3.1 28.6 + - + +
270A ALA 3.2 0.2 - - - -
271A SER* 1.3 78.0 + - - +
273A ILE* 1.3 58.1 + - + +
275A LYS* 3.0 27.2 + - - +
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Residues in contact with ILE 273 (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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82A LEU* 3.8 15.9 - - + -
257A LEU* 3.8 25.2 - - + +
259A VAL* 3.8 22.7 - - + -
264A LEU* 3.9 16.4 - - + -
270A ALA 4.1 4.4 + - - +
272A LEU* 1.3 76.7 - - + +
274A SER* 1.3 60.6 + - - +
275A LYS 3.4 0.3 + - - -
276A ALA* 3.6 16.6 + - - +
282A ARG* 3.0 30.1 + - - +
305A GLY* 3.4 41.7 - - - +
307A MET* 3.7 27.4 - - + -
316A ARG* 5.0 1.0 + - - -
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Residues in contact with SER 274 (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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271A SER* 2.7 26.3 + - - -
273A ILE* 1.3 80.5 - - - +
275A LYS* 1.3 66.0 + - - +
276A ALA 3.3 7.3 + - - +
282A ARG* 4.3 6.1 - - - +
305A GLY 4.5 10.3 - - - -
316A ARG* 5.8 2.5 + - - +
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Residues in contact with LYS 275 (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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247A MET* 4.0 37.9 - - + +
251A PHE* 3.2 30.3 - - + +
252A LEU* 6.1 0.5 - - - +
271A SER* 3.5 27.1 + - - +
272A LEU* 3.0 20.5 + - - +
274A SER* 1.3 80.0 + - - +
276A ALA* 1.3 64.4 + - - +
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Residues in contact with ALA 276 (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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251A PHE* 3.6 11.1 - - + -
254A VAL* 4.2 8.7 - - + -
257A LEU* 3.8 21.1 - - + -
273A ILE 3.6 13.7 + - - +
274A SER 3.3 9.2 - - - +
275A LYS* 1.3 81.2 - - - +
277A PRO* 1.4 80.6 - - + +
278A LEU* 3.6 2.9 + - - +
280A THR* 4.2 10.3 - - - -
316A ARG* 4.8 6.5 + - - +
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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