Contacts of the helix formed by residues 254 - 268 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A PRO* 4.1 2.2 + - + -
253A ALA* 1.3 73.9 - - - +
255A TYR* 1.3 65.5 + - - +
256A ASP* 4.2 7.4 - - + +
257A ASP* 2.9 36.4 + - - +
258A ILE* 3.0 10.4 + - - +
305A ASP* 3.3 34.7 + - - +
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Residues in contact with TYR 255 (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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253A ALA 3.6 1.8 + - - -
254A LYS* 1.3 73.1 - - - +
256A ASP* 1.3 59.1 + - - +
258A ILE* 3.2 18.4 + - + +
259A LYS* 2.9 49.5 + - + +
295A PHE* 3.8 13.5 - + - -
296A ASP 3.9 0.3 + - - -
297A ALA* 2.6 35.7 + - - -
300A GLY* 3.4 31.9 + - - -
301A ILE* 4.1 2.9 - - - -
302A ALA* 4.4 28.0 - - + +
308A VAL* 5.2 0.7 - - + -
309A LYS 4.6 0.2 - - - -
310A LEU* 3.9 22.3 - - + +
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Residues in contact with ASP 256 (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 LYS* 3.1 6.1 - - + +
255A TYR* 1.3 81.4 - - - +
257A ASP* 1.3 58.4 + - - +
259A LYS* 3.5 29.9 + - - +
260A LYS* 3.1 26.7 + - - +
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Residues in contact with ASP 257 (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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168A PHE* 4.1 16.6 - - + -
252A PRO 5.7 0.2 - - - +
253A ALA* 5.1 0.6 - - - -
254A LYS* 2.9 36.7 + - - +
256A ASP* 1.3 77.9 - - - +
258A ILE* 1.3 65.0 + - - +
260A LYS* 3.3 16.4 + - + +
261A VAL* 3.1 28.9 + - + +
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Residues in contact with ILE 258 (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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164A ILE* 3.9 21.3 - - + -
168A PHE* 3.9 24.2 - - + -
249A LEU* 4.4 3.1 - - + -
253A ALA* 3.9 24.7 - - + +
254A LYS 3.0 10.1 + - - +
255A TYR* 3.5 15.3 - - + +
257A ASP* 1.3 73.4 - - - +
259A LYS* 1.3 67.0 + - + +
261A VAL* 3.4 1.5 + - - +
262A VAL* 3.1 24.5 + - + +
295A PHE* 4.0 23.1 - - + -
308A VAL* 4.1 30.7 - - + -
310A LEU* 4.1 12.6 - - + -
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Residues in contact with LYS 259 (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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255A TYR* 2.9 48.0 + - + +
256A ASP* 3.5 26.1 + - - +
257A ASP 3.3 0.2 - - - -
258A ILE* 1.3 77.0 - - - +
260A LYS* 1.3 56.7 + - - +
262A VAL 3.8 0.2 - - - -
263A LYS* 2.9 33.4 + - - +
276A TYR* 3.3 31.4 - - - +
278A GLU* 3.8 15.1 + - - +
295A PHE* 4.3 6.7 - - + -
297A ALA* 4.1 17.0 - - + +
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Residues in contact with LYS 260 (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 ASP 3.1 18.6 + - - +
257A ASP* 3.5 18.4 + - - +
258A ILE 3.2 0.2 - - - -
259A LYS* 1.3 76.6 - - - +
261A VAL* 1.3 64.2 + - + +
263A LYS* 3.8 5.3 - - - +
264A GLN* 3.0 35.9 + - + +
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Residues in contact with VAL 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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163A VAL* 3.8 17.5 - - + +
164A ILE* 5.2 1.3 - - + -
167A ASN* 3.7 29.6 - - - +
168A PHE* 3.8 25.4 - - + -
257A ASP* 3.1 13.2 + - + +
258A ILE* 3.5 10.8 - - - +
260A LYS* 1.3 82.3 - - + +
262A VAL* 1.3 65.9 + - + +
264A GLN* 3.7 15.7 - - - +
265A ALA* 3.0 27.7 + - - +
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Residues in contact with VAL 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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160A LEU* 4.2 18.2 - - + -
163A VAL* 4.1 19.3 - - + -
164A ILE* 4.3 10.5 - - + -
258A ILE* 3.1 23.9 + - + +
259A LYS 3.9 2.2 - - - +
261A VAL* 1.3 74.4 - - + +
263A LYS* 1.3 64.5 + - - +
265A ALA* 3.3 4.1 + - - +
266A SER* 3.0 22.0 + - - -
274A LEU* 4.1 16.7 - - + +
275A GLY 4.5 3.4 - - - +
276A TYR* 3.9 8.5 - - + -
295A PHE* 3.6 36.3 - - + -
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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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259A LYS 2.9 18.6 + - - +
260A LYS* 3.8 4.5 - - - +
262A VAL* 1.3 75.7 - - - +
264A GLN* 1.3 64.3 + - - +
266A SER* 2.8 24.6 + - - +
267A GLU* 3.2 35.7 + - - +
276A TYR* 3.8 38.5 - - + -
278A GLU* 5.2 6.2 + - - +
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Residues in contact with GLN 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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260A LYS* 3.0 26.6 + - + +
261A VAL* 3.7 17.7 - - - +
263A LYS* 1.3 77.6 - - - +
265A ALA* 1.3 62.4 + - - +
267A GLU* 3.2 10.4 + - - +
268A GLY* 3.1 19.4 + - - -
269A PRO* 4.3 3.6 - - + +
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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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163A VAL* 3.7 28.0 - - + -
261A VAL 3.0 18.0 + - - +
262A VAL 3.3 4.7 + - - +
264A GLN* 1.3 76.6 - - - +
266A SER* 1.3 61.6 + - - +
268A GLY 3.3 5.2 + - - -
269A PRO* 4.3 13.9 - - + -
270A LEU* 2.9 41.0 + - + +
274A LEU* 4.3 2.5 - - + -
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Residues in contact with SER 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 VAL 3.0 13.8 + - - -
263A LYS* 2.8 17.2 + - - +
265A ALA* 1.3 75.2 - - - +
267A GLU* 1.3 62.9 + - - +
270A LEU 4.5 1.3 - - - -
271A LYS* 3.3 27.3 + - - +
272A GLY 4.6 0.5 + - - -
274A LEU* 3.0 32.3 - - - +
275A GLY* 4.0 14.8 - - - -
276A TYR* 3.6 11.6 + - - +
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Residues in contact with GLU 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 45.9 + - - +
264A GLN* 3.2 8.7 + - - +
265A ALA 3.2 0.8 - - - -
266A SER* 1.3 85.0 + - - +
268A GLY* 1.3 59.2 + - - +
271A LYS* 4.0 22.9 + - - +
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Residues in contact with GLY 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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264A GLN 3.1 8.9 + - - -
265A ALA 3.3 1.2 + - - -
266A SER 3.4 0.2 - - - -
267A GLU* 1.3 80.2 - - - +
269A PRO* 1.3 74.8 - - - +
270A LEU 3.1 2.8 + - - -
271A LYS* 3.1 17.0 + - - +
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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