Contacts of the helix formed by residues 267 - 282 (chain A) in PDB entry 1R6W
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 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A TRP* 3.8 6.3 - - - -
11A ILE* 3.5 23.1 - - - -
31A TYR* 2.6 30.0 + - - -
44A GLU* 2.6 28.5 + - - -
265A ILE 3.8 0.4 + - - -
266A GLU* 1.3 75.9 - - - +
268A SER* 1.3 66.8 + - - +
269A LEU 3.1 5.9 + - - -
270A GLY 3.2 1.7 + - - -
271A LEU* 2.9 19.9 + - - +
295A MET* 4.0 12.1 - - - +
299A GLN* 5.2 0.7 - - - -
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Residues in contact with SER 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 5.4 0.4 - - - +
267A SER* 1.3 73.4 - - - +
269A LEU* 1.3 58.6 + - - +
271A LEU* 3.7 7.4 - - - +
272A THR* 2.9 36.4 + - - +
292A LEU* 4.1 21.7 - - - +
298A GLN* 3.4 25.2 - - - +
299A GLN 3.0 23.5 + - - +
301A ARG 2.7 24.7 + - - -
303A TRP* 4.5 4.7 - - - -
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Residues in contact with LEU 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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31A TYR* 3.7 19.5 - - + +
42A TRP* 4.0 23.3 - - + -
43A GLY* 4.0 23.3 - - - +
44A GLU 4.2 1.3 - - - +
267A SER* 3.1 11.8 + - - +
268A SER* 1.3 79.1 + - - +
270A GLY* 1.3 64.2 + - - +
272A THR* 2.7 23.5 + - - -
273A GLN* 3.2 34.0 + - - +
299A GLN 4.0 4.0 - - - +
300A VAL* 3.8 32.1 - - + -
301A ARG* 3.8 22.0 - - + +
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Residues in contact with GLY 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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44A GLU* 2.9 31.4 + - - -
85A PHE* 5.2 5.1 - - - -
266A GLU* 4.1 12.6 - - - -
267A SER 3.2 0.6 + - - -
269A LEU* 1.3 74.5 - - - +
271A LEU* 1.3 56.5 + - - +
273A GLN* 3.1 15.7 + - - +
274A LEU* 2.9 32.3 + - - +
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Residues in contact with LEU 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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263A SER* 3.6 30.1 - - - +
266A GLU* 3.5 27.1 - - - +
267A SER 2.9 17.4 + - - +
268A SER* 3.7 4.9 - - - +
270A GLY* 1.3 77.5 - - - +
272A THR* 1.3 57.3 + - - +
274A LEU* 3.2 11.2 + - + +
275A ALA 2.9 23.0 + - - -
289A LEU* 3.9 16.8 - - + +
291A THR* 3.8 4.7 - - - +
292A LEU* 3.7 46.4 - - + +
303A TRP* 3.6 20.8 - - + -
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Residues in contact with THR 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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104A TYR* 3.6 20.7 - - + -
268A SER 2.9 19.7 + - - +
269A LEU* 2.7 22.5 + - - -
271A LEU* 1.3 75.1 - - - +
273A GLN* 1.3 63.3 + - - +
275A ALA* 3.2 5.6 + - - +
276A ARG* 3.1 28.4 + - - +
301A ARG* 4.2 17.7 + - + +
302A ARG 3.4 32.3 - - - +
303A TRP* 3.9 15.7 - - + -
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Residues in contact with GLN 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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42A TRP 2.8 28.7 + - - -
43A GLY* 3.8 9.0 - - - -
44A GLU* 4.1 2.9 + - - +
85A PHE* 5.1 4.3 - - + -
89A CYS* 3.8 26.4 - - - +
93A GLU* 2.9 26.8 + - - +
98A LEU* 4.3 8.8 - - + +
269A LEU* 3.2 27.5 + - - +
270A GLY* 3.1 13.8 + - - +
272A THR* 1.3 76.4 + - - +
274A LEU* 1.3 60.2 + - - +
276A ARG* 3.1 15.5 + - - +
277A ILE* 2.9 34.3 + - + +
301A ARG* 4.0 8.8 - - - +
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Residues in contact with LEU 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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85A PHE* 3.7 19.3 - - + -
236A PRO* 3.4 35.4 - - + -
261A ILE* 3.9 8.6 - - + +
262A SER 3.9 11.9 - - - +
263A SER* 4.1 1.1 - - - -
266A GLU* 3.4 34.1 - - - +
270A GLY 2.9 15.8 + - - +
271A LEU* 3.4 11.7 - - + +
273A GLN* 1.3 75.6 - - - +
275A ALA* 1.3 59.4 + - - +
277A ILE* 3.2 7.3 + - + +
278A ALA* 2.9 29.8 + - - +
289A LEU* 3.7 28.3 - - + -
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Residues in contact with ALA 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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101A ALA* 5.0 0.7 - - - -
103A ASN 4.4 4.4 - - - +
104A TYR* 3.5 31.6 - - + -
105A ARG 4.7 1.6 - - - +
271A LEU 2.9 12.4 + - - +
272A THR 3.4 9.6 - - - +
273A GLN 3.2 0.2 - - - -
274A LEU* 1.3 77.7 - - - +
276A ARG* 1.3 56.5 + - - +
278A ALA* 3.4 4.8 + - - +
279A ALA* 3.0 28.8 + - - +
287A PRO* 5.1 1.1 - - - -
289A LEU* 3.5 11.4 - - + +
303A TRP* 3.8 15.0 - - + -
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Residues in contact with ARG 276 (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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93A GLU* 2.9 32.7 + - - +
98A LEU* 2.9 51.7 + - + +
99A PRO* 3.0 23.3 + - - +
100A GLN* 3.4 27.2 + - - +
101A ALA* 4.1 14.5 - - + +
104A TYR* 3.4 28.7 - - + +
272A THR* 3.1 17.6 + - - +
273A GLN* 3.1 11.4 + - - +
275A ALA* 1.3 73.6 - - - +
277A ILE* 1.3 66.4 + - - +
279A ALA* 3.4 1.6 + - - +
280A TRP* 3.0 26.0 + - - +
301A ARG* 3.6 11.9 - - - +
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Residues in contact with ILE 277 (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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85A PHE* 3.8 30.7 - - + -
89A CYS* 4.4 5.8 - - - -
98A LEU* 3.9 12.8 - - + -
236A PRO* 5.0 2.5 - - + -
242A LEU* 3.8 26.9 - - + -
245A VAL* 4.3 7.2 - - + -
261A ILE* 4.0 23.3 - - + -
273A GLN* 2.9 21.1 + - + +
274A LEU* 3.5 13.2 - - + +
276A ARG* 1.3 75.5 - - - +
278A ALA* 1.3 58.9 + - - +
280A TRP* 3.6 4.7 - - - +
281A LEU* 2.9 50.9 + - + +
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Residues in contact with ALA 278 (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 ILE* 4.1 8.7 - - + -
274A LEU 2.9 17.0 + - - +
275A ALA 3.7 3.1 - - - +
277A ILE* 1.3 75.6 - - - +
279A ALA* 1.3 64.9 + - - +
282A THR* 2.9 46.8 + - - +
285A THR 4.8 0.7 - - - +
287A PRO* 3.6 39.0 - - + -
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Residues in contact with ALA 279 (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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101A ALA* 3.8 25.6 - - + -
102A ALA 5.6 0.2 - - - +
103A ASN* 4.3 11.9 - - + +
105A ARG* 6.2 1.6 - - - +
275A ALA 3.0 17.9 + - - +
276A ARG 3.4 2.2 + - - +
278A ALA* 1.3 77.1 - - - +
280A TRP* 1.3 60.8 - - - +
283A PRO* 3.4 24.0 - - - +
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Residues in contact with TRP 280 (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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97A THR 4.0 15.9 - - - -
98A LEU* 4.1 16.4 - - + -
99A PRO* 3.5 42.0 - - + +
242A LEU* 4.4 22.0 - - + -
246A ARG* 3.7 45.3 - - - +
276A ARG 3.0 19.0 + - - +
277A ILE* 3.6 4.3 - - - +
279A ALA* 1.3 81.0 - - - +
281A LEU* 1.3 84.1 - - + +
283A PRO* 3.8 9.0 - - - +
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Residues in contact with LEU 281 (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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242A LEU* 5.0 2.5 - - + -
245A VAL* 4.7 1.8 - - + -
246A ARG* 3.8 52.7 - - + +
249A VAL* 3.5 20.5 - - + +
253A HIS* 3.5 15.8 + - - -
277A ILE* 2.9 36.3 + - + +
280A TRP* 1.3 112.9 - - + +
282A THR* 1.3 66.5 + - + +
283A PRO* 3.3 9.3 - - - +
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Residues in contact with THR 282 (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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105A ARG* 4.7 1.0 + - - -
249A VAL* 3.8 27.6 - - + -
253A HIS* 4.3 6.7 - - - +
259A ALA* 3.4 28.5 + - + +
261A ILE* 4.0 13.0 + - + +
278A ALA* 2.9 31.9 + - - +
281A LEU* 1.3 85.9 - - + +
283A PRO* 1.3 66.9 - - - +
284A ASP 3.2 2.7 - - - -
285A THR* 3.1 28.7 + - - +
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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