Contacts of the helix formed by residues 268 - 276 (chain A) in PDB entry 1A8H
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 PHE 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A MET* 3.4 39.0 - - + -
198A ILE* 5.6 1.1 - - + -
201A LEU* 3.9 20.2 - - + -
227A TRP* 3.7 39.7 - + - -
231A LEU* 4.6 2.5 - - + -
263A LYS* 3.4 38.1 + - + -
264A PRO* 3.4 24.5 - - + +
267A VAL* 1.3 80.7 - - + +
269A TRP* 1.3 65.1 + - - +
271A THR* 2.8 22.0 + - - -
272A MET* 3.1 22.0 + - - +
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Residues in contact with TRP 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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231A LEU* 3.5 35.2 - - + -
232A LEU* 3.6 31.6 - - + -
234A TYR* 3.8 15.1 - + + -
235A VAL* 4.9 5.8 - - + -
250A TRP* 4.1 10.5 - + - -
255A HIS* 3.2 25.9 - + - -
264A PRO 2.8 22.4 + - - +
265A HIS* 3.5 16.8 - + - +
268A PHE* 1.3 71.5 - - - +
270A PRO* 1.3 65.9 - - + +
272A MET* 3.2 27.7 + - + -
273A LEU* 3.0 51.1 + - + +
281A TYR* 3.3 28.3 - + - -
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Residues in contact with PRO 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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169A TRP* 3.4 14.6 - - + -
170A LEU* 3.8 20.9 - - + -
180A LEU* 5.8 0.4 - - + -
265A HIS 3.3 20.9 - - - +
266A ALA 3.2 19.1 - - - +
267A VAL 3.2 16.4 - - - +
269A TRP* 1.3 90.7 - - + +
271A THR* 1.3 55.8 + - - +
273A LEU* 3.5 5.0 + - + +
274A LYS 3.1 20.6 + - - -
280A MET* 3.4 27.3 - - + +
281A TYR* 3.6 12.6 - - + +
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Residues in contact with THR 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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161A PHE* 3.6 10.6 - - - -
163A MET* 3.3 29.9 - - + +
166A TYR* 3.7 33.6 - - + +
169A TRP* 4.1 6.1 - - + -
170A LEU* 4.1 19.3 - - + -
198A ILE* 4.9 4.0 - - + -
267A VAL 3.3 13.6 + - - +
268A PHE 2.8 16.9 + - - -
270A PRO* 1.3 75.7 - - - +
272A MET* 1.3 60.0 + - - +
274A LYS* 3.4 3.6 + - - +
275A ALA* 3.0 28.8 + - - +
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Residues in contact with MET 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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107A VAL* 5.4 1.1 - - + +
111A VAL* 4.9 1.7 - - - +
161A PHE* 3.9 22.9 - - + -
201A LEU* 4.7 2.7 - - + -
227A TRP* 3.8 24.7 - - - +
228A PHE* 4.0 41.2 - - + -
231A LEU* 3.7 21.5 - - + -
232A LEU* 4.8 4.9 - - + -
268A PHE* 3.1 27.4 + - - +
269A TRP* 3.2 30.7 + - + +
271A THR* 1.3 74.7 - - - +
273A LEU* 1.3 60.8 + - - +
275A ALA* 3.5 1.4 + - - +
276A ALA* 2.9 32.7 + - - +
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Residues in contact with LEU 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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235A VAL* 4.9 0.9 - - + -
250A TRP* 4.0 15.7 - - + -
269A TRP* 3.0 70.9 + - + +
270A PRO* 3.7 8.3 - - + +
272A MET* 1.3 78.4 - - - +
274A LYS* 1.3 60.1 + - - +
276A ALA* 3.2 2.5 + - - -
277A GLY 2.9 4.5 + - - -
278A ILE* 2.8 75.4 + - + +
279A PRO 4.1 6.1 - - - +
280A MET* 4.4 7.6 - - + -
281A TYR* 4.2 9.9 - - + -
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Residues in contact with LYS 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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166A TYR* 3.9 23.1 - - + -
169A TRP* 3.4 53.9 - - + +
270A PRO 3.1 17.3 + - - +
271A THR* 3.5 7.0 - - - +
273A LEU* 1.3 76.7 - - - +
275A ALA* 1.3 62.9 + - - +
277A GLY* 3.1 14.5 + - - -
278A ILE 4.6 2.9 - - - +
280A MET* 6.2 0.2 - - - +
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Residues in contact with ALA 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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110A LYS* 3.7 13.5 - - - -
111A VAL* 4.0 12.0 - - + +
114A ALA* 5.0 4.3 - - - +
116A ASP* 3.3 13.3 - - - +
161A PHE* 3.6 19.1 - - + -
166A TYR* 3.3 29.6 - - + +
271A THR 3.0 17.6 + - - +
272A MET* 4.0 2.2 - - - +
274A LYS* 1.3 76.1 - - - +
276A ALA* 1.3 60.7 + - - +
277A GLY* 3.5 0.3 + - - -
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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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107A VAL* 3.9 27.8 - - + -
110A LYS* 3.2 25.3 - - + +
111A VAL* 3.9 8.9 - - + +
240A TYR* 4.2 6.1 + - - +
272A MET 2.9 18.8 + - - +
273A LEU 3.7 4.3 - - - +
274A LYS 3.1 0.2 - - - -
275A ALA* 1.3 76.9 - - - +
277A GLY* 1.3 61.9 + - - +
278A ILE* 3.7 21.4 + - + +
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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