Contacts of the helix formed by residues 257 - 270 (chain A) in PDB entry 4CNT
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 SER 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A GLU* 3.5 34.9 - - - +
232A GLU* 2.8 24.2 + - - +
255A VAL* 4.2 0.9 - - - +
256A MET* 1.3 80.2 - - - +
258A LYS* 1.3 62.5 + - - +
259A SER* 3.7 4.0 + - - -
260A ALA* 3.2 21.3 + - - +
261A ALA* 3.2 22.2 + - - +
308A SER* 5.0 4.9 - - - -
313A THR* 4.6 1.6 - - - -
317A ILE* 3.8 7.0 - - - +
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Residues in contact with LYS 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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229A GLU* 4.0 7.8 + - - +
256A MET 4.3 0.2 + - - -
257A SER* 1.3 72.1 - - - +
259A SER* 1.3 58.1 + - - +
261A ALA* 3.1 5.4 + - - +
262A ASP* 2.8 35.8 + - - +
310A ASP* 3.4 14.8 + - - -
312A THR* 2.8 30.6 + - - +
313A THR* 3.9 23.7 - - + +
316A TYR* 3.5 52.1 - - + +
317A ILE* 4.8 1.1 - - + -
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Residues in contact with SER 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A GLU* 2.5 35.1 + - - +
230A GLU* 5.2 0.5 - - - -
233A ALA* 3.7 19.7 - - - +
257A SER* 3.7 2.9 + - - -
258A LYS* 1.3 75.7 - - - +
260A ALA* 1.3 63.0 + - - +
262A ASP* 3.4 9.8 + - - +
263A LEU* 3.2 28.6 + - - +
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Residues in contact with ALA 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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232A GLU* 3.5 28.3 - - + +
233A ALA* 4.7 3.4 - - - +
236A VAL* 4.3 13.8 - - + +
252A VAL* 5.9 0.4 - - + -
255A VAL* 4.5 7.2 - - + -
257A SER* 3.2 24.5 + - - +
259A SER* 1.3 75.9 + - - +
261A ALA* 1.3 62.7 + - - +
263A LEU* 3.2 20.9 + - - +
264A ILE* 3.3 21.1 + - + +
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Residues in contact with ALA 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A VAL* 4.1 16.5 - - + +
257A SER 3.2 10.1 + - - +
258A LYS* 3.1 9.7 + - - +
260A ALA* 1.3 78.0 - - - +
262A ASP* 1.3 64.7 + - - +
264A ILE* 3.3 4.4 + - - +
265A SER* 3.1 22.5 + - - -
316A TYR* 4.8 0.9 - - + -
317A ILE* 4.4 7.4 - - + -
320A LEU* 3.7 22.9 - - + +
326A LEU* 4.2 19.2 - - + +
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Residues in contact with ASP 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LYS* 2.8 25.9 + - - +
259A SER* 3.8 8.3 - - - +
260A ALA 3.3 0.4 - - - -
261A ALA* 1.3 73.2 - - - +
263A LEU* 1.3 59.4 + - + +
265A SER* 3.3 6.3 + - - -
266A GLN* 2.8 31.9 + - - +
316A TYR* 2.2 35.6 + - - -
320A LEU* 4.1 4.2 - - - +
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Residues in contact with LEU 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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233A ALA* 3.2 44.4 - - + +
236A VAL* 4.1 18.2 - - + -
237A PHE* 3.9 30.5 - - + +
240A ILE* 4.1 5.6 - - + +
259A SER* 3.2 13.1 + - - +
260A ALA* 3.6 6.3 - - - +
261A ALA 3.2 0.6 - - - -
262A ASP* 1.3 79.1 - - + +
264A ILE* 1.3 58.1 + - - +
266A GLN* 3.4 21.0 + - - +
267A ALA* 2.9 28.4 + - - +
237B PHE* 4.6 12.8 - - + -
266B GLN* 5.9 3.6 - - - +
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Residues in contact with ILE 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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236A VAL* 4.5 8.1 - - + -
240A ILE* 4.5 2.0 - - + -
252A VAL* 3.8 33.2 - - + -
255A VAL* 4.0 13.0 - - + -
260A ALA 3.3 17.0 + - - +
261A ALA* 3.7 6.7 - - - +
262A ASP 3.1 0.4 - - - -
263A LEU* 1.3 76.0 - - - +
265A SER* 1.3 59.1 + - - +
267A ALA* 3.2 5.7 + - - +
268A ARG* 2.9 36.8 + - - +
274A VAL* 3.9 23.8 - - + -
276A GLY* 3.9 21.5 - - - +
325A ASP 3.6 19.3 - - - +
326A LEU* 4.2 6.3 - - + -
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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 3.1 15.3 + - - -
262A ASP* 3.4 8.5 - - - -
264A ILE* 1.3 79.5 - - - +
266A GLN* 1.3 64.6 + - - +
268A ARG* 3.4 3.1 + - - +
269A LYS* 3.2 21.7 + - - +
320A LEU* 4.4 5.7 - - - +
325A ASP* 3.1 45.5 + - - +
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Residues in contact with GLN 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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237A PHE* 4.3 18.6 - - - -
262A ASP 2.8 18.4 + - - +
263A LEU* 3.5 21.2 - - - +
265A SER* 1.3 78.1 - - - +
267A ALA* 1.3 61.9 + - - +
269A LYS* 3.4 13.8 + - - +
270A LYS* 3.5 16.6 + - + +
263B LEU* 6.2 2.0 - - - +
266B GLN* 5.4 8.1 - - - +
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Residues in contact with ALA 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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240A ILE* 4.0 31.9 - - + -
263A LEU 2.9 18.3 + - - +
264A ILE 3.2 4.2 + - - +
266A GLN* 1.3 77.0 - - - +
268A ARG* 1.3 63.0 + - - +
269A LYS 3.3 0.2 + - - -
270A LYS* 3.3 16.3 + - + +
271A GLY 3.4 0.2 + - - -
272A ASN* 3.0 36.5 + - + +
274A VAL* 4.1 6.5 - - + -
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Residues in contact with ARG 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 ILE* 2.9 23.5 + - - +
265A SER* 3.8 4.7 - - - +
266A GLN 3.4 0.2 - - - -
267A ALA* 1.3 76.9 - - - +
269A LYS* 1.3 64.3 + - - +
271A GLY* 3.1 13.0 + - - -
272A ASN 3.7 13.6 + - - +
273A VAL* 6.0 0.2 - - - +
274A VAL* 2.9 35.2 + - + +
275A PHE* 3.9 14.1 - - - -
324A GLY 3.5 12.3 + - - -
325A ASP* 3.7 15.1 + - - +
327A GLN* 3.0 41.7 - - - +
477A TYR* 5.2 4.0 + - - -
481A ARG* 6.1 1.0 - - - +
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Residues in contact with LYS 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 3.2 14.5 + - - +
266A GLN* 3.7 8.1 - - - +
267A ALA 3.2 0.8 - - - -
268A ARG* 1.3 80.3 - - - +
270A LYS* 1.3 58.4 + - - +
271A GLY* 3.0 5.1 + - - -
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Residues in contact with LYS 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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244A SER* 4.8 4.4 + - - -
266A GLN* 3.5 11.8 + - + +
267A ALA* 3.5 13.5 - - + +
269A LYS* 1.3 79.5 - - - +
271A GLY* 1.3 55.6 + - - +
272A ASN* 3.3 29.5 + - - +
230B GLU* 3.5 33.4 + - - +
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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