Contacts of the helix formed by residues 258 - 275 (chain A) in PDB entry 4NLG
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 ASP 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A THR* 3.1 15.6 + - - +
257A ARG* 1.3 75.5 - - - +
259A VAL* 1.3 59.6 + - - +
260A LYS* 2.9 42.3 + - - +
261A VAL* 2.9 41.2 + - + +
262A ILE* 2.9 16.3 + - - +
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Residues in contact with VAL 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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257A ARG 3.4 2.5 + - - +
258A ASP* 1.3 73.4 + - - +
260A LYS* 1.3 55.1 + - + +
262A ILE* 4.3 7.4 - - - +
263A LEU* 2.7 39.3 + - + +
316A GLU* 4.5 13.5 - - + +
319A LEU* 4.0 20.6 - - + -
320A ARG* 3.2 51.4 - - + +
323A LEU* 3.5 28.3 - - + -
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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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258A ASP* 2.9 35.5 + - - +
259A VAL* 1.3 75.8 - - + +
261A VAL* 1.3 62.2 + - + +
263A LEU* 4.3 5.9 - - - +
264A PRO* 3.5 17.3 - - - +
320A ARG* 4.9 11.4 - - - +
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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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252A LEU* 6.3 1.8 - - + -
253A PRO* 5.5 4.3 - - + -
254A TYR* 3.5 35.2 - - + +
256A THR* 3.9 18.6 - - + +
258A ASP* 2.9 35.9 + - + +
260A LYS* 1.3 78.1 - - + +
262A ILE* 1.3 64.3 + - - +
264A PRO* 3.4 10.6 - - - +
265A TYR* 3.4 21.8 - - + -
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Residues in contact with ILE 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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252A LEU* 4.0 13.0 - - + -
256A THR* 3.5 34.5 - - + +
257A ARG 4.4 2.9 - - - -
258A ASP 2.9 26.2 + - - +
259A VAL* 3.1 4.9 + - - +
261A VAL* 1.3 77.1 - - - +
263A LEU* 1.3 65.1 + - - +
265A TYR* 2.9 20.3 + - - +
266A LEU* 3.1 7.2 + - + -
319A LEU* 3.6 13.5 - - + -
323A LEU* 4.4 10.8 - - + -
331A VAL* 3.9 18.6 - - + -
334A ILE* 3.1 40.2 - - + -
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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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259A VAL* 2.7 25.6 + - + +
260A LYS* 4.3 5.6 - - - +
262A ILE* 1.3 71.9 - - - +
264A PRO* 1.3 62.5 - - + +
265A TYR 2.9 0.7 + - - -
266A LEU* 3.0 22.0 + - + +
267A LYS* 2.7 63.7 + - + +
270A ILE* 6.4 0.2 - - + -
312A TYR 5.0 0.9 - - - +
316A GLU* 3.2 52.3 - - + +
319A LEU* 5.2 1.1 - - - -
320A ARG* 5.5 0.4 - - - +
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Residues in contact with PRO 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 3.5 11.9 - - - +
261A VAL* 3.4 15.0 - - - +
263A LEU* 1.3 95.9 - - + +
265A TYR* 1.3 65.9 + - + +
267A LYS* 3.8 10.7 - - + +
268A LYS* 3.1 24.8 + - - +
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Residues in contact with TYR 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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250A LEU* 3.2 29.4 - - + +
251A THR 4.9 7.2 - - - -
252A LEU* 4.1 22.4 - - + -
253A PRO* 3.1 43.7 - - + +
261A VAL* 3.4 28.7 - - + -
262A ILE 2.9 7.2 + - - +
264A PRO* 1.3 82.8 - - + +
266A LEU* 1.3 57.4 + - - +
267A LYS 3.2 0.2 - - - -
268A LYS* 3.1 8.7 + - + -
269A ALA* 2.8 31.2 + - - +
334A ILE* 4.3 4.9 - - + -
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Residues in contact with LEU 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 ILE* 3.1 10.7 + - + +
263A LEU* 3.4 18.8 - - + +
265A TYR* 1.3 76.1 - - - +
267A LYS* 1.3 56.7 + - - +
269A ALA* 3.3 6.2 + - + +
270A ILE* 2.9 46.7 + - + +
286A VAL* 4.2 18.4 - - + -
315A ALA* 3.8 31.4 - - + +
316A GLU 4.0 2.9 - - - +
319A LEU* 3.9 24.7 - - + -
334A ILE* 4.3 27.4 - - + +
335A GLY 4.4 1.8 - - - +
336A VAL* 4.4 13.9 - - + -
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Residues in contact with LYS 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 LEU* 2.7 53.6 + - + +
264A PRO* 3.8 9.9 - - + +
266A LEU* 1.3 72.7 - - - +
268A LYS* 1.3 58.0 + - - +
270A ILE* 3.0 10.4 + - + +
271A ASN* 2.9 37.9 + - - +
312A TYR* 3.5 49.9 + - + +
316A GLU* 4.6 4.0 + - - -
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Residues in contact with LYS 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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248A ARG* 4.7 3.4 - - - +
250A LEU* 3.7 27.3 - - + +
264A PRO 3.1 16.7 + - - +
265A TYR* 3.1 14.1 + - + +
267A LYS* 1.3 76.5 - - - +
269A ALA* 1.3 62.7 + - - +
271A ASN* 3.4 10.0 + - - +
272A GLU* 2.4 66.6 + - + +
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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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248A ARG* 3.3 39.8 - - + +
250A LEU* 4.3 10.5 - - + -
265A TYR 2.8 19.5 + - - +
266A LEU* 3.6 10.1 - - + +
268A LYS* 1.3 74.0 - - - +
270A ILE* 1.3 59.3 + - - +
272A GLU 3.3 0.2 + - - -
273A ALA* 2.8 31.7 + - - +
334A ILE* 5.0 5.6 - - + +
335A GLY* 5.1 0.4 - - - -
336A VAL* 3.9 10.3 - - + +
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Residues in contact with ILE 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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263A LEU* 6.4 0.4 - - + -
266A LEU* 2.9 29.6 + - + +
267A LYS* 3.4 7.2 - - + +
269A ALA* 1.3 75.6 - - - +
271A ASN* 1.3 55.5 + - - +
273A ALA* 3.3 1.1 + - - +
274A TYR* 2.8 52.5 + - + +
284A ILE* 4.5 2.9 - - + -
308A ILE* 4.2 2.7 - - + -
311A ALA* 3.9 18.6 - - + +
312A TYR* 3.8 30.7 - - + +
315A ALA* 3.4 31.4 - - + -
336A VAL* 4.0 26.0 - - + -
338A LEU* 5.4 0.4 - - + -
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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 LYS* 2.9 21.3 + - - +
268A LYS* 3.6 9.9 - - - +
269A ALA 3.3 0.2 - - - -
270A ILE* 1.3 77.7 - - - +
272A GLU* 1.3 61.8 + - + +
274A TYR* 3.6 0.5 + - - +
275A ASN* 2.6 34.8 + - - +
308A ILE* 3.2 13.7 - - - +
312A TYR* 2.3 39.4 + - - -
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Residues in contact with GLU 272 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A ARG* 2.6 51.4 + - + -
268A LYS* 2.4 52.4 + - + +
270A ILE 3.2 0.2 - - - -
271A ASN* 1.3 77.8 - - + +
273A ALA* 1.3 68.6 + - - +
275A ASN* 3.4 10.7 + - - +
276A LYS* 3.3 19.4 + - - +
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Residues in contact with ALA 273 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A HIS* 3.9 11.1 - - - +
247A GLY 4.2 6.5 - - - -
248A ARG* 4.0 5.2 - - - +
269A ALA 2.8 17.7 + - - +
270A ILE 3.6 2.5 - - - +
272A GLU* 1.3 75.8 - - - +
274A TYR* 1.3 64.1 + - - +
276A LYS* 2.8 29.1 + - - +
277A VAL* 3.5 7.6 + - - +
336A VAL* 3.7 17.9 - - + -
338A LEU* 3.6 20.9 - - + -
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Residues in contact with TYR 274 (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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270A ILE* 2.8 32.4 + - + +
271A ASN 3.8 5.2 - - - +
272A GLU 3.3 0.2 - - - -
273A ALA* 1.3 72.3 - - - +
275A ASN* 1.3 60.7 + - - +
276A LYS 2.9 5.4 + - - -
277A VAL* 3.0 22.0 + - + +
279A GLY 5.1 6.6 - - - +
280A ILE* 5.5 0.4 - - - -
281A PRO* 3.3 26.1 - - + +
306A ILE* 2.4 42.9 + - - +
307A SER* 3.6 0.7 + - - -
308A ILE* 3.7 36.1 - - + -
311A ALA* 3.7 16.6 - - + +
338A LEU* 3.2 38.1 - - + +
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Residues in contact with ASN 275 (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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271A ASN* 2.6 29.9 + - - +
272A GLU* 3.9 7.6 - - - +
273A ALA 3.0 1.6 + - - -
274A TYR* 1.3 80.5 - - - +
276A LYS* 1.3 60.3 + - + +
277A VAL 3.6 1.6 - - - +
308A ILE* 5.1 4.4 - - - +
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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