Contacts of the helix formed by residues 254 - 268 (chain O) in PDB entry 4WNC
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 254 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253O ALA* 1.3 75.7 - - - +
255O TYR* 1.3 67.0 + - - +
256O ASP* 4.2 9.2 - - + +
257O ASP* 2.9 33.7 + - - +
258O ILE* 3.1 11.0 + - - +
305O ASP* 3.1 36.6 + - - +
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Residues in contact with TYR 255 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253O ALA 3.9 1.0 + - - -
254O LYS* 1.3 73.4 - - - +
256O ASP* 1.3 59.8 + - - +
258O ILE* 3.2 17.3 + - + +
259O LYS* 2.9 47.5 + - + +
295O PHE* 3.7 17.8 - + - -
296O ASP 3.9 0.5 + - - -
297O ALA* 2.7 32.0 + - - -
300O GLY* 3.3 32.6 + - - -
301O ILE* 4.2 2.9 - - - -
302O ALA* 4.3 29.8 - - + +
308O VAL* 5.1 0.4 - - + -
309O LYS 4.6 0.2 - - - -
310O LEU* 3.9 22.1 - - + +
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Residues in contact with ASP 256 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254O LYS* 3.1 7.0 - - + +
255O TYR* 1.3 81.3 - - - +
257O ASP* 1.3 59.0 + - - +
259O LYS* 3.5 29.7 + - - +
260O LYS* 3.0 27.2 + - - +
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Residues in contact with ASP 257 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168O PHE* 4.1 17.7 - - + -
252O PRO 5.0 1.0 - - - +
253O ALA* 3.9 4.9 - - + -
254O LYS* 2.9 40.6 + - - +
256O ASP* 1.3 76.8 - - - +
258O ILE* 1.3 65.9 + - - +
260O LYS* 3.3 11.5 + - - +
261O VAL* 3.2 28.1 + - + +
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Residues in contact with ILE 258 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164O ILE* 3.7 23.1 - - + -
168O PHE* 3.9 24.0 - - + -
249O LEU* 4.3 13.5 - - + -
253O ALA* 3.9 7.9 - - + +
254O LYS 3.1 11.6 + - - +
255O TYR* 3.2 15.9 + - + +
257O ASP* 1.3 75.1 - - - +
259O LYS* 1.3 68.3 + - - +
260O LYS 3.2 0.2 + - - -
261O VAL* 3.3 2.4 + - - +
262O VAL* 3.0 24.2 + - + +
295O PHE* 4.2 11.9 - - + -
308O VAL* 4.0 33.2 - - + -
310O LEU* 4.2 22.4 - - + -
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Residues in contact with LYS 259 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255O TYR* 2.9 46.3 + - + +
256O ASP* 3.6 25.9 + - - +
258O ILE* 1.3 78.0 - - - +
260O LYS* 1.3 62.2 + - - +
263O LYS* 2.9 26.5 + - - +
276O TYR* 3.4 31.3 - - - +
278O GLU* 3.8 14.7 + - - +
295O PHE* 4.1 8.3 - - + -
297O ALA* 4.0 17.8 - - + +
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Residues in contact with LYS 260 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256O ASP 3.0 17.5 + - - +
257O ASP* 3.5 11.9 - - - +
258O ILE 3.2 0.4 - - - -
259O LYS* 1.3 76.5 - - - +
261O VAL* 1.3 61.8 + - + +
263O LYS* 3.8 5.1 - - - +
264O GLN* 3.0 38.4 + - + +
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Residues in contact with VAL 261 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163O VAL* 3.9 17.3 - - + +
164O ILE* 5.1 1.3 - - + -
167O ASN* 3.6 30.1 - - - +
168O PHE* 3.8 26.7 - - + -
257O ASP* 3.2 13.2 + - + +
258O ILE* 3.4 9.9 - - - +
260O LYS* 1.3 78.9 - - + +
262O VAL* 1.3 69.4 + - + +
264O GLN* 3.8 12.4 - - - +
265O ALA* 3.0 23.6 + - - +
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Residues in contact with VAL 262 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160O LEU* 4.0 21.8 - - + -
163O VAL* 4.2 16.6 - - + -
164O ILE* 4.3 9.6 - - + -
258O ILE* 3.0 21.9 + - + +
259O LYS 4.0 2.5 - - - +
261O VAL* 1.3 77.3 - - + +
263O LYS* 1.3 63.4 + - - +
265O ALA* 3.2 4.4 + - - +
266O SER* 3.0 21.5 + - - -
274O LEU* 4.0 18.5 - - + +
275O GLY 4.5 2.2 - - - +
276O TYR* 3.9 8.1 - - + -
295O PHE* 3.6 36.3 - - + -
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Residues in contact with LYS 263 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259O LYS 2.9 18.3 + - - +
260O LYS* 3.8 5.8 - - - +
262O VAL* 1.3 77.6 - - - +
264O GLN* 1.3 61.4 + - - +
266O SER* 2.8 24.2 + - - +
267O GLU* 3.1 35.3 + - - +
276O TYR* 3.8 38.6 - - + +
278O GLU* 5.3 4.6 + - - +
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Residues in contact with GLN 264 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260O LYS* 3.0 29.4 + - + +
261O VAL* 3.8 13.4 - - - +
263O LYS* 1.3 76.4 - - - +
265O ALA* 1.3 61.7 + - - +
267O GLU* 3.3 10.0 + - - +
268O GLY* 3.1 20.3 + - - -
269O PRO* 4.3 3.1 - - + +
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Residues in contact with ALA 265 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163O VAL* 3.7 28.9 - - + -
261O VAL 3.0 18.6 + - - +
262O VAL 3.5 5.2 - - - +
264O GLN* 1.3 78.4 - - - +
266O SER* 1.3 59.4 + - - +
268O GLY 3.3 5.0 + - - -
269O PRO* 4.4 11.9 - - + -
270O LEU* 2.9 40.1 + - + +
274O LEU* 4.2 2.2 - - + -
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Residues in contact with SER 266 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262O VAL 3.0 12.8 + - - -
263O LYS* 2.8 15.6 + - - +
265O ALA* 1.3 77.9 - - - +
267O GLU* 1.3 63.2 + - - +
268O GLY 3.4 0.2 - - - -
270O LEU 4.5 1.3 - - - -
271O LYS* 3.2 25.4 + - - +
272O GLY 4.6 0.5 + - - -
274O LEU* 3.0 32.6 - - - +
275O GLY* 4.0 3.8 - - - -
276O TYR* 3.6 24.0 + - - +
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Residues in contact with GLU 267 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263O LYS* 3.1 47.9 + - + +
264O GLN* 3.9 6.5 - - - +
265O ALA 3.2 0.2 - - - -
266O SER* 1.3 82.3 + - - +
268O GLY* 1.3 59.6 + - - +
271O LYS* 4.1 21.2 + - - +
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Residues in contact with GLY 268 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264O GLN 3.1 9.8 + - - -
265O ALA 3.3 1.0 + - - -
267O GLU* 1.3 78.3 - - - +
269O PRO* 1.3 74.0 - - - +
270O LEU 3.3 2.0 - - - -
271O LYS* 3.1 20.3 + - - +
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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