Contacts of the helix formed by residues 268 - 276 (chain A) in PDB entry 1PS9
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A LEU* 4.0 14.1 - - + -
220A LEU* 5.1 1.6 - - + -
247A THR* 5.4 0.3 - - - +
249A ILE* 4.0 45.1 - - + +
257A PRO 4.2 9.4 - - - -
258A THR* 3.5 25.6 - - + -
263A VAL* 4.1 10.3 - - + -
266A GLY 3.0 1.0 + - - -
267A ALA* 1.3 86.4 - - + +
269A SER* 1.3 64.4 + - - +
270A TRP* 3.1 10.3 - + - +
271A VAL* 3.1 22.3 + - + +
272A THR* 3.7 4.2 + - - -
285A THR* 3.9 7.1 + - - -
286A THR 4.2 9.6 + - - +
287A ASN* 3.8 19.3 + - + -
527A PHE* 4.1 21.3 - + - -
528A CYS* 5.2 0.7 - - - -
533A ILE* 4.0 24.2 - - + -
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Residues in contact with SER 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLY* 3.2 16.3 + - - -
267A ALA 3.6 0.2 - - - -
268A PHE* 1.3 78.3 - - - +
270A TRP* 1.3 63.2 + - - +
271A VAL 3.1 0.3 + - - -
272A THR* 3.2 5.4 + - - -
273A ARG* 3.0 22.2 + - - +
285A THR* 3.4 16.9 + - - -
286A THR 5.2 0.4 + - - -
289A ILE* 4.8 1.2 - - - +
298A ILE* 3.0 31.7 - - - +
301A ARG* 5.3 1.8 - - - -
303A ASP* 3.7 29.5 - - - +
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Residues in contact with TRP 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LEU* 4.5 3.1 - - + -
266A GLY 5.2 0.7 - - - -
267A ALA 2.8 30.0 + - - -
268A PHE* 3.9 4.9 - + - +
269A SER* 1.3 80.4 - - - +
271A VAL* 1.3 94.6 + - + +
273A ARG* 3.4 9.8 + - - +
274A LYS* 3.2 30.6 + - + +
303A ASP* 5.6 1.6 - - - -
524A ILE* 3.9 14.1 - - + -
528A CYS* 3.9 27.3 - - - -
533A ILE* 3.9 15.3 - - + -
535A SER* 3.3 42.4 - - - -
537A LEU* 3.7 25.8 - - + -
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Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A MET* 3.5 37.5 - - + +
218A LEU* 4.1 14.8 - - + -
227A PHE* 4.9 1.7 - - - -
247A THR* 5.0 0.2 - - + -
249A ILE* 4.2 12.3 - - + -
268A PHE* 3.3 17.3 - - + +
269A SER 3.1 0.4 - - - -
270A TRP* 1.3 116.8 - - + +
272A THR* 1.3 66.5 + - - +
274A LYS* 3.1 19.5 + - - +
275A LEU* 3.8 2.4 + - - +
537A LEU* 3.9 16.6 - - + +
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Residues in contact with THR 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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217A MET* 4.1 12.3 - - + -
247A THR* 2.6 34.0 + - - +
268A PHE 3.7 1.1 + - - -
269A SER 3.2 3.9 + - - -
271A VAL* 1.3 77.2 - - - +
273A ARG* 1.3 61.8 + - - +
275A LEU* 3.2 17.3 + - - +
276A LYS* 3.7 4.3 + - - +
283A LEU* 3.9 20.8 - - + +
284A VAL 3.8 10.3 - - - +
285A THR* 3.0 29.9 + - - -
303A ASP 3.9 2.5 - - - +
304A ALA* 4.0 15.5 - - + -
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Residues in contact with ARG 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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269A SER 3.0 13.7 + - - +
270A TRP* 3.5 13.7 - - - +
271A VAL 3.2 0.2 - - - -
272A THR* 1.3 78.2 - - - +
274A LYS* 1.3 63.0 + - + +
276A LYS* 3.2 39.5 + - - +
301A ARG 5.2 3.0 + - - -
302A GLY 3.4 24.4 + - - -
303A ASP* 3.4 27.2 + - - +
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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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227A PHE* 3.2 39.8 - - + -
270A TRP* 3.2 21.6 + - + +
271A VAL 3.1 10.6 + - - +
273A ARG* 1.3 81.0 + - + +
275A LEU* 1.3 58.4 + - - +
276A LYS 3.4 1.6 - - - +
278A HIS* 3.4 11.3 + - - -
535A SER 3.6 17.7 + - - +
536A SER* 3.4 28.4 + - - +
537A LEU* 3.8 19.5 - - + -
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Residues in contact with LEU 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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215A LEU* 3.7 28.9 - - + -
217A MET* 4.1 21.5 - - + -
227A PHE* 4.0 5.1 - - + -
230A THR* 4.6 6.1 - - + -
231A VAL* 3.7 31.9 - - + +
234A ALA* 4.0 20.6 - - + -
245A ILE* 4.8 1.1 - - + -
271A VAL 3.8 1.2 + - - -
272A THR 3.2 11.7 + - - +
274A LYS* 1.3 75.9 - - - +
276A LYS* 1.3 69.5 + - - +
277A GLY 3.3 0.2 + - - -
278A HIS* 2.9 31.0 + - + +
279A VAL* 4.1 5.5 + - + +
283A LEU* 3.8 23.9 - - + +
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Residues in contact with LYS 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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272A THR 3.7 3.8 + - - +
273A ARG* 3.2 52.0 + - - +
274A LYS 4.3 1.9 - - - +
275A LEU* 1.3 78.5 - - - +
277A GLY* 1.3 62.2 + - - +
278A HIS* 3.4 8.5 + - - -
283A LEU* 3.8 12.5 - - + +
302A GLY* 3.7 25.2 + - - +
303A ASP 5.5 1.3 - - - +
304A ALA 5.9 1.8 + - - -
305A ASP* 5.2 7.7 + - - -
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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