Contacts of the helix formed by residues 264 - 274 (chain A) in PDB entry 4NLK
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 GLN 264 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A SER* 3.9 18.1 - - - -
260A ILE* 3.6 6.1 - - + +
261A PRO* 3.0 30.2 + - - +
263A ASP* 1.3 91.8 - - - +
265A TYR* 1.3 64.6 + - - +
266A TYR 3.3 3.3 + - - +
267A CYS* 3.5 3.7 + - - +
268A GLY 3.1 16.6 + - - -
295A GLU 4.0 1.2 - - - +
296A TYR* 3.2 56.3 - - - +
297A THR* 3.5 16.1 - - + +
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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
----------------------------------------------------------
174A ILE* 5.9 2.9 - - + -
176A THR* 4.2 20.1 + - - +
182A ARG* 4.4 8.0 + - - -
194A LEU* 3.7 29.6 - - + -
196A THR* 4.4 13.0 - - + -
260A ILE* 4.4 6.1 - - - -
261A PRO 3.6 3.3 + - - -
262A LYS* 3.5 18.0 + - + +
263A ASP 3.4 2.4 - - - -
264A GLN* 1.3 78.8 - - - +
266A TYR* 1.3 90.6 + + + +
268A GLY* 3.0 1.4 + - - -
269A VAL* 2.7 64.5 + - + +
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Residues in contact with TYR 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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263A ASP 5.3 4.9 + - - -
264A GLN 3.3 1.2 - - - -
265A TYR* 1.3 105.6 - + + +
267A CYS* 1.3 56.5 + - - +
269A VAL* 3.5 5.7 - - + +
270A LEU* 3.1 27.0 + - - +
313A VAL* 3.8 27.6 - - + -
314A ASP* 3.1 35.1 + - - -
315A SER* 3.5 23.9 - - - -
316A GLU* 3.7 13.7 - - + +
319A ILE* 3.7 4.6 - - - +
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Residues in contact with CYS 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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264A GLN* 3.5 3.6 + - - +
265A TYR 3.3 0.2 - - - -
266A TYR* 1.3 74.8 - - - +
268A GLY* 1.3 66.6 + - - +
269A VAL 3.2 0.2 - - - -
270A LEU* 3.4 3.7 + - - +
271A TYR* 3.0 24.9 + - - +
293A ILE* 5.2 1.8 - - + -
294A ASN 3.9 6.4 - - - +
295A GLU* 3.2 8.0 - - - +
296A TYR 3.5 22.9 - - - +
297A THR* 3.4 36.3 - - - +
298A ILE* 3.8 3.6 - - - -
313A VAL* 4.5 14.1 - - - +
319A ILE* 3.9 24.5 - - - -
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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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194A LEU* 3.6 14.5 - - - +
260A ILE* 4.2 12.3 - - - -
264A GLN 3.1 6.7 + - - -
265A TYR 3.0 7.4 + - - -
267A CYS* 1.3 77.3 - - - +
269A VAL* 1.3 58.2 + - - +
271A TYR* 3.4 4.7 - - - +
272A PHE* 2.8 31.2 + - - +
295A GLU* 2.9 18.5 + - - -
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Residues in contact with VAL 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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176A THR* 4.6 3.4 - - + -
178A CYS* 3.8 23.3 - - - -
182A ARG* 4.1 15.0 - - - +
194A LEU* 3.8 6.2 - - + +
265A TYR* 2.7 59.6 + - + +
266A TYR* 3.5 11.0 - - + +
268A GLY* 1.3 71.1 - - - +
270A LEU* 1.3 61.8 + - - +
272A PHE* 4.4 0.9 - - - +
273A THR* 2.4 38.1 + - - -
316A GLU* 3.8 24.0 - - + +
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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 TYR 3.1 18.7 + - - +
267A CYS* 3.7 4.9 - - - +
269A VAL* 1.3 75.9 - - - +
271A TYR* 1.3 64.2 + - - +
273A THR* 3.2 11.4 + - - -
274A GLY* 3.4 9.2 + - - +
278A PHE* 4.3 7.1 - - + -
279A ASN* 3.8 8.3 - - - +
282A MET* 3.9 22.4 - - + -
293A ILE* 4.4 15.5 - - + -
316A GLU* 3.8 12.6 - - + +
319A ILE* 3.8 36.6 - - + -
320A PHE* 3.7 30.5 - - + -
333A ARG* 4.1 12.9 + - - +
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Residues in contact with TYR 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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258A ARG* 4.1 27.6 + - + -
260A ILE* 5.7 0.9 - - + -
267A CYS 3.0 17.5 + - - +
268A GLY* 3.4 6.1 - - - +
270A LEU* 1.3 79.0 - - - +
272A PHE* 1.3 93.2 + + + +
273A THR 3.2 1.2 + - - -
274A GLY 3.3 3.8 + - - -
279A ASN* 2.9 34.2 + - - +
283A ARG* 3.7 19.7 - - - +
294A ASN 5.0 0.4 - - - +
295A GLU* 3.7 30.5 - - + -
405A 0KX 3.4 31.3 - - - +
10P A 2.9 45.0 + + - +
6T BGM 4.3 2.0 - - - -
7T T 5.0 0.9 - - - -
8T C 5.3 0.2 + - - -
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Residues in contact with PHE 272 (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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178A CYS* 3.3 21.0 - - + +
179A GLY* 3.0 22.2 + - - -
192A ASP* 3.8 11.2 - - + -
193A VAL 3.4 31.9 - - - -
194A LEU* 3.8 24.7 - - + -
256A ASP* 4.1 17.5 - - + -
258A ARG* 3.6 21.8 - - + -
268A GLY 2.8 19.5 + - - +
271A TYR* 1.3 94.9 - + + +
273A THR* 1.3 58.7 + - - +
274A GLY 3.5 0.2 - - - -
405A 0KX 3.6 19.4 - - - +
10P A 4.1 20.2 - - + -
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Residues in contact with THR 273 (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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178A CYS* 4.3 1.2 - - - -
179A GLY 3.6 6.5 - - - +
182A ARG* 3.0 47.0 + - + +
183A ARG* 2.9 47.3 + - + +
269A VAL* 2.4 26.7 + - - +
270A LEU 3.7 3.8 - - - -
271A TYR 3.1 0.6 - - - -
272A PHE* 1.3 79.1 - - - +
274A GLY* 1.3 56.0 + - - +
330A PRO* 4.2 5.2 - - + -
333A ARG* 3.9 14.8 - - - +
405A 0KX 3.7 2.0 - - - -
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Residues in contact with GLY 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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183A ARG* 3.8 1.1 - - - -
270A LEU 3.4 3.9 + - - +
271A TYR 3.3 6.7 + - - -
272A PHE 3.5 0.4 - - - -
273A THR* 1.3 82.4 - - - +
275A SER* 1.3 71.2 + - - -
278A PHE* 3.6 10.8 - - - -
279A ASN* 3.6 7.2 - - - -
333A ARG* 3.3 26.9 - - - +
405A 0KX 3.4 13.5 - - - -
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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