Contacts of the helix formed by residues 260 - 272 (chain A) in PDB entry 1W5A
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 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A SER* 4.3 2.0 - - - -
259A GLU* 1.3 107.6 + - + +
261A ARG* 1.3 59.3 + - - +
262A ALA 3.3 3.1 - - - -
263A LYS* 2.9 25.2 + - + -
264A GLU* 2.8 37.2 + - + +
302A GLU* 5.7 2.5 - - - +
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Residues in contact with ARG 261 (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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256A SER* 3.4 31.9 - - - +
257A ASP* 4.0 2.2 - - - +
258A SER 3.0 17.7 + - - +
259A GLU 3.3 3.9 + - - +
260A LYS* 1.3 74.4 - - - +
262A ALA* 1.3 66.9 + - - +
265A ALA* 2.9 32.8 + - - +
292A PRO* 3.5 14.5 - - - +
294A ASP* 2.6 45.8 + - - -
295A LEU* 3.8 3.2 - - - +
299A GLU* 2.8 39.5 + - - +
329A ASN* 3.6 22.6 + - - +
331A VAL* 3.2 20.4 - - + +
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Residues in contact with ALA 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 LYS 3.3 0.4 - - - -
261A ARG* 1.3 83.2 - - - +
263A LYS* 1.3 62.6 + - - +
265A ALA* 3.9 0.8 - - - +
266A VAL* 3.1 26.6 + - - +
299A GLU* 3.7 46.4 - - + +
302A GLU* 4.2 10.5 - - - +
303A VAL* 3.8 12.5 - - + +
331A VAL* 4.4 13.7 - - + -
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Residues in contact with LYS 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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260A LYS* 2.9 28.5 + - + +
262A ALA* 1.3 80.7 - - - +
264A GLU* 1.3 63.2 + - + +
266A VAL* 3.4 7.4 - - + +
267A SER* 3.2 22.3 + - - -
302A GLU* 2.9 47.1 + - + +
306A THR* 4.2 16.3 + - + +
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Residues in contact with GLU 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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256A SER* 3.0 26.3 + - - +
258A SER* 3.1 24.1 + - - -
260A LYS* 2.8 30.6 + - + +
263A LYS* 1.3 73.8 - - + +
265A ALA* 1.3 54.8 + - - +
267A SER* 3.0 7.6 + - - -
268A MET* 2.7 36.7 + - - +
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Residues in contact with ALA 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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254A GLY* 3.4 19.4 - - - +
255A GLU* 3.8 7.4 - - - +
256A SER* 3.9 1.2 - - - +
261A ARG 2.9 19.7 + - - +
262A ALA* 3.9 3.6 - - - +
264A GLU* 1.3 75.8 - - - +
266A VAL* 1.3 59.0 + - - +
268A MET* 3.0 6.9 + - - +
269A ALA* 2.8 23.7 + - - +
331A VAL* 3.7 21.5 - - + +
333A VAL* 3.6 21.3 - - + -
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Residues in contact with VAL 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 ALA 3.1 18.1 + - - +
263A LYS* 3.4 11.4 - - + +
265A ALA* 1.3 78.4 - - - +
267A SER* 1.3 60.1 + - - +
269A ALA* 3.6 6.7 - - - +
270A LEU* 2.8 36.2 + - + +
302A GLU 4.9 0.4 - - - +
303A VAL* 3.6 37.0 - - + +
306A THR* 4.3 16.4 - - + +
307A VAL* 3.6 32.1 - - + -
333A VAL* 3.9 7.5 - - + +
335A LEU* 4.7 1.1 - - + -
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Residues in contact with SER 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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263A LYS 3.2 20.5 + - - -
264A GLU* 3.0 9.7 + - - -
266A VAL* 1.3 78.8 - - - +
268A MET* 1.3 62.8 + - - +
270A LEU* 3.5 7.5 + - - +
271A ASN* 3.0 37.3 + - - +
306A THR* 5.7 1.8 - - - -
310A ARG* 5.8 4.0 + - - +
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Residues in contact with MET 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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198A ILE* 6.0 6.5 - - + -
253A ILE* 3.7 11.4 - - + +
254A GLY* 3.5 18.8 - - - -
255A GLU* 3.6 32.5 - - + +
264A GLU 2.7 13.0 + - - +
265A ALA* 3.2 8.7 - - - +
267A SER* 1.3 78.2 - - - +
269A ALA* 1.3 51.4 + - - +
271A ASN* 3.1 5.7 + - - +
272A SER* 2.7 35.9 + - - -
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Residues in contact with ALA 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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252A GLY* 3.4 20.2 - - - +
253A ILE 3.7 11.9 - - - +
254A GLY* 3.9 12.3 - - - +
265A ALA 2.8 12.7 + - - +
266A VAL* 3.6 12.3 - - - +
268A MET* 1.3 76.6 - - - +
270A LEU* 1.3 61.9 + - - +
272A SER* 3.2 16.3 + - - -
275A LEU* 3.8 5.7 - - - +
333A VAL* 4.0 10.3 - - + +
335A LEU* 3.7 19.1 - - + -
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Residues in contact with LEU 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 VAL* 2.8 28.4 + - + +
267A SER* 3.8 5.8 - - - +
269A ALA* 1.3 73.4 - - - +
271A ASN* 1.3 62.2 + - - +
272A SER 3.8 0.9 + - - +
275A LEU* 4.1 15.7 - - + +
279A ILE* 3.9 30.3 - - + +
306A THR* 3.7 31.6 - - + +
307A VAL* 4.2 11.7 - - + -
310A ARG* 3.7 39.9 + - + +
335A LEU* 3.6 22.0 - - + -
337A ILE* 5.8 1.3 - - + -
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Residues in contact with ASN 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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267A SER* 3.0 29.8 + - - +
268A MET* 3.1 5.4 + - - +
270A LEU* 1.3 80.3 - - - +
272A SER* 1.3 67.1 + - - +
273A PRO* 3.4 5.9 - - - +
310A ARG* 5.0 8.8 + - - -
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Residues in contact with SER 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ILE* 4.4 3.8 - - - +
252A GLY* 3.7 13.0 - - - -
253A ILE* 3.8 15.3 + - - +
268A MET* 2.7 12.7 + - - -
269A ALA 3.2 16.8 + - - -
270A LEU 3.4 0.5 - - - +
271A ASN* 1.3 79.1 - - - +
273A PRO* 1.3 68.2 - - - +
274A LEU* 3.1 25.2 + - - +
275A LEU* 3.1 25.8 + - - +
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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