Contacts of the helix formed by residues 261 - 273 (chain A) in PDB entry 1PBW
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 ALA 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A SER* 3.9 9.7 - - - -
260A ASN* 1.3 72.1 - - - +
262A ARG* 1.3 61.4 + - - +
264A LEU* 4.5 2.5 - - - -
265A SER* 3.0 24.4 + - - -
291A GLU* 3.5 28.4 - - + +
294A ILE* 3.7 30.9 - - + +
295A SER* 4.4 10.3 - - - +
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Residues in contact with ARG 262 (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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260A ASN* 3.0 12.8 + - - +
261A ALA* 1.3 78.1 - - - +
263A VAL* 1.3 64.8 + - + +
265A SER* 3.2 1.0 + - - -
266A GLU* 2.8 54.9 + - - +
284A GLU* 2.8 42.6 + - - -
287A ILE* 3.5 23.5 - - - +
288A LYS* 3.9 10.1 - - - +
291A GLU* 3.0 39.5 + - - +
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Residues in contact with VAL 263 (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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151A ARG* 4.5 9.4 - - - +
258A LEU 4.5 9.0 - - - +
259A LEU* 3.8 26.2 - - + -
260A ASN* 2.6 34.9 + - - +
262A ARG* 1.3 76.7 - - + +
264A LEU* 1.3 62.9 + - - +
266A GLU* 3.2 15.9 + - - +
267A ILE* 3.1 32.7 + - + +
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Residues in contact with LEU 264 (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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150A TYR* 4.4 1.3 - - + -
247A PHE* 3.4 46.8 - - + +
250A LEU* 4.2 15.0 - - + -
251A SER* 4.5 1.1 - - - +
259A LEU* 3.9 39.7 - - + +
260A ASN 3.0 20.7 + - - +
261A ALA* 3.9 6.1 - - - +
263A VAL* 1.3 73.0 - - - +
265A SER* 1.3 59.2 + - - +
267A ILE* 4.6 2.5 - - + +
268A PHE* 3.0 58.3 + - + +
294A ILE* 4.2 10.3 - - + -
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Residues in contact with SER 265 (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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261A ALA 3.0 20.1 + - - -
262A ARG 3.7 3.1 - - - -
264A LEU* 1.3 74.5 - - - +
266A GLU* 1.3 61.7 + - - +
268A PHE* 5.3 0.2 - - - -
269A SER* 2.8 51.2 + - - +
287A ILE* 2.7 34.1 + - - +
290A ILE* 3.5 12.9 - - - +
291A GLU* 3.6 14.4 - - - -
294A ILE* 4.3 1.3 - - - +
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Residues in contact with GLU 266 (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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262A ARG* 2.8 56.4 + - - +
263A VAL* 3.2 15.5 + - - +
265A SER* 1.3 77.0 - - - +
267A ILE* 1.3 59.9 + - + +
270A PRO* 3.3 18.5 - - - +
287A ILE* 4.1 21.4 - - + +
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Residues in contact with ILE 267 (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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150A TYR* 4.0 25.6 - - + +
151A ARG* 4.3 13.7 - - + -
187A LYS* 4.1 18.8 - - - +
259A LEU* 4.4 4.7 - - + -
263A VAL* 3.1 33.5 + - + +
264A LEU* 4.7 2.5 - - - -
265A SER 3.2 0.2 - - - -
266A GLU* 1.3 78.3 - - + +
268A PHE* 1.3 87.6 + - + +
269A SER 3.6 0.2 - - - -
270A PRO* 3.5 10.7 - - - +
271A MET* 3.8 17.0 - - + +
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Residues in contact with PHE 268 (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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150A TYR* 3.5 43.7 - + + -
186A PHE* 3.5 25.6 - + - -
187A LYS* 4.4 11.9 - - + -
190A LEU* 3.9 21.1 - - + -
247A PHE* 3.7 32.3 - + + -
264A LEU* 3.0 33.3 + - + +
265A SER* 5.3 0.4 - - - -
267A ILE* 1.3 91.1 - - + +
269A SER* 1.3 66.0 + - - +
270A PRO* 3.3 3.1 - - - -
271A MET* 3.2 14.8 + - - +
272A LEU* 3.0 29.4 + - + +
290A ILE* 6.2 0.4 - - + -
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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
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265A SER* 2.8 38.7 + - - +
268A PHE* 1.3 69.7 - - - +
270A PRO* 1.3 69.3 - - - +
272A LEU* 3.2 5.9 + - - +
273A PHE* 3.1 36.1 + - - +
275A PHE* 4.0 10.3 - - - -
287A ILE* 3.9 21.0 - - - -
290A ILE* 3.5 19.3 - - - +
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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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266A GLU* 3.3 24.2 - - - +
267A ILE 3.5 7.2 - - - +
268A PHE 3.4 4.0 - - - -
269A SER* 1.3 94.9 - - - +
271A MET* 1.3 56.3 + - + +
274A ARG* 2.9 28.9 + - - +
275A PHE* 3.2 32.0 + - + +
287A ILE* 5.4 2.0 - - + -
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Residues in contact with MET 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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187A LYS* 4.0 53.8 - - + +
190A LEU* 4.1 30.4 - - + +
191A LEU* 3.9 26.5 - - + +
196A PRO* 4.3 8.7 - - - +
197A VAL* 4.9 1.6 + - - +
267A ILE* 3.8 26.9 - - + +
268A PHE* 3.2 19.6 + - + +
270A PRO* 1.3 75.9 - - + +
272A LEU* 1.3 67.0 + - - +
273A PHE 3.4 0.2 - - - -
274A ARG* 3.9 8.6 + - - +
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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
----------------------------------------------------------
190A LEU* 4.7 11.9 - - + -
196A PRO* 3.5 3.5 - - - +
197A VAL* 3.4 32.5 + - + -
198A ILE* 3.0 39.6 + - + -
240A LEU* 4.4 9.9 - - + -
243A LEU* 3.9 21.5 - - + -
244A LEU* 5.9 0.4 - - + -
247A PHE* 4.6 9.9 - - + -
268A PHE* 3.0 31.8 + - + +
269A SER* 3.2 5.1 + - - +
271A MET* 1.3 78.8 - - - +
273A PHE* 1.3 61.4 + - + +
290A ILE* 4.3 33.0 - - + -
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Residues in contact with PHE 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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196A PRO* 4.2 7.3 - - - +
198A ILE* 3.5 48.4 - - + +
200A ALA* 5.6 1.7 - - - -
203A TYR* 3.9 33.5 - + + +
206A MET* 5.2 0.7 - - + -
223A LEU* 4.3 14.1 - - + -
269A SER* 3.1 23.8 + - - +
272A LEU* 1.3 78.6 - - + +
274A ARG* 1.3 70.6 + - - +
275A PHE* 3.5 31.4 - + + -
286A LEU* 3.9 38.8 - - + -
289A VAL* 5.5 0.9 - - + -
290A ILE* 3.7 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