Contacts of the helix formed by residues 266 - 278 (chain A) in PDB entry 4Z1H
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 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A THR* 4.2 2.7 - - - -
263A GLU* 3.0 17.9 + - - +
265A SER* 1.3 81.2 + - - +
267A GLU* 1.3 65.1 + - - +
268A ALA* 4.0 5.3 + - - +
269A ARG* 3.2 19.9 + - - +
270A VAL* 3.2 21.8 + - - +
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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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147A THR* 3.8 14.1 + - - +
266A SER* 1.3 72.2 - - - +
268A ALA* 1.3 57.4 + - - +
270A VAL* 4.8 0.7 - - - -
271A ARG* 2.9 60.2 + - - +
287A LEU* 3.9 12.2 - - + +
288A ASN* 3.0 36.9 + - - +
290A ARG* 3.7 20.6 + - - -
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Residues in contact with ALA 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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266A SER* 3.2 5.5 - - - +
267A GLU* 1.3 78.8 - - - +
269A ARG* 1.3 65.2 + - - +
271A ARG* 3.0 15.6 + - - +
272A ASP* 2.9 30.2 + - - +
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Residues in contact with ARG 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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108A GLU* 5.7 1.2 + - - -
109A LYS* 5.5 1.8 - - - +
110A GLU* 2.5 33.9 + - - +
263A GLU* 2.7 43.2 + - + +
264A PHE* 3.6 34.9 - - + -
266A SER* 3.2 17.9 + - - +
268A ALA* 1.3 77.4 - - - +
270A VAL* 1.3 58.4 + - - +
272A ASP* 3.1 16.0 + - - +
273A VAL* 2.9 47.8 + - - +
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Residues in contact with VAL 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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113A ILE* 4.1 13.2 - - + -
145A LEU* 4.1 19.1 - - + -
147A THR* 3.7 11.4 - - + -
154A ILE* 4.0 10.3 - - + -
264A PHE* 3.5 32.3 - - + +
266A SER 3.2 18.2 + - - +
267A GLU 4.1 2.7 - - - +
269A ARG* 1.3 75.0 - - - +
271A ARG* 1.3 57.4 + - - +
273A VAL* 3.2 8.0 + - - +
274A VAL* 2.9 29.4 + - + +
287A LEU* 3.8 24.7 - - + -
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Residues in contact with ARG 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 GLU* 2.9 62.8 + - - +
268A ALA* 3.0 9.5 + - - +
270A VAL* 1.3 75.1 - - - +
272A ASP* 1.3 66.3 + - - +
274A VAL* 3.7 2.9 - - - +
275A THR* 2.8 41.2 + - + +
287A LEU* 3.5 15.2 + - + +
290A ARG* 4.0 21.0 - - - +
292A MET* 3.8 29.5 - - + +
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Residues in contact with ASP 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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268A ALA* 2.9 23.7 + - - +
269A ARG* 3.4 15.8 + - - +
271A ARG* 1.3 85.7 - - - +
273A VAL* 1.3 57.0 - - + +
275A THR* 2.9 17.9 + - - -
276A LYS* 2.9 21.5 + - - +
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Residues in contact with VAL 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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110A GLU* 3.2 38.1 - - + +
113A ILE* 3.9 22.0 - - + -
114A ARG 5.3 0.7 - - - +
264A PHE* 4.1 7.4 - - + -
269A ARG* 2.9 44.7 + - - +
270A VAL 3.7 5.4 - - - +
272A ASP* 1.3 77.5 - - - +
274A VAL* 1.3 56.8 + - - +
276A LYS* 3.2 4.6 + - - -
277A TYR* 2.9 46.2 + - + +
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Residues in contact with VAL 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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113A ILE* 4.1 12.3 - - + -
117A ILE* 4.3 4.5 - - + -
145A LEU* 4.0 27.6 - - + -
270A VAL* 2.9 23.7 + - + +
271A ARG* 3.7 5.4 - - - +
273A VAL* 1.3 76.8 - - - +
275A THR* 1.3 59.3 + - - +
278A SER* 2.8 47.5 + - - +
279A ASN* 5.7 0.9 - - - +
285A LEU* 3.7 27.1 - - + -
287A LEU* 4.7 4.7 - - + -
292A MET* 4.0 18.6 - - + -
293A ASN 5.6 0.2 - - - +
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Residues in contact with THR 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 ARG* 2.8 38.0 + - + +
272A ASP* 2.9 18.5 + - - -
274A VAL* 1.3 73.9 - - + +
276A LYS* 1.3 60.3 + - - +
279A ASN* 2.4 46.0 + - - +
292A MET* 4.9 17.3 - - + +
317A TYR* 4.8 2.1 + - - -
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Residues in contact with LYS 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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108A GLU* 4.6 7.9 + - - -
110A GLU* 3.7 11.5 + - - +
272A ASP 2.9 18.5 + - - +
273A VAL* 3.6 6.1 - - - +
274A VAL 3.1 0.2 - - - -
275A THR* 1.3 81.9 + - - +
277A TYR* 1.3 96.6 + - + +
279A ASN* 5.2 1.4 + - - +
317A TYR* 5.6 1.4 + - - -
366A TYR* 4.8 4.7 + - - -
371A LEU* 3.1 36.8 - - + +
374A THR* 4.7 9.9 - - + -
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Residues in contact with TYR 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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108A GLU* 4.5 8.3 + - - +
110A GLU* 3.2 34.8 + - + +
111A VAL* 4.1 22.4 - - + +
114A ARG* 3.8 25.8 - - + -
273A VAL* 2.9 34.4 + - + +
276A LYS* 1.3 109.6 + - + +
278A SER* 1.3 65.8 + - - +
279A ASN 3.7 2.7 + - - -
366A TYR* 4.7 2.6 - - - -
369A LYS 4.6 0.7 - - - +
370A VAL* 3.2 9.8 - - + +
371A LEU* 3.1 62.1 + - + +
372A ILE 4.9 6.5 - - - -
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Residues in contact with SER 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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114A ARG* 4.4 4.2 - - - -
117A ILE* 3.6 43.4 - - - +
274A VAL* 2.8 28.3 + - - +
277A TYR* 1.3 83.4 + - - +
279A ASN* 1.3 55.3 + - - +
280A PHE 3.1 6.1 - - - +
281A VAL* 3.2 29.1 - - - +
285A LEU* 4.9 0.2 - - - -
293A ASN* 3.8 5.0 - - - +
369A LYS 5.3 1.8 - - - -
370A VAL* 4.3 8.6 - - - +
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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