Contacts of the helix formed by residues 263 - 275 (chain A) in PDB entry 1I4A
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 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A ARG* 5.4 2.1 + - - -
255A LYS 5.3 0.7 - - - +
256A SER* 2.8 27.9 + - - +
262A THR* 1.3 70.5 - - - +
264A ASP* 1.3 60.4 + - - +
265A ASP* 3.5 9.4 + - - +
266A THR* 2.9 34.1 + - - +
267A LEU* 3.0 20.3 + - - +
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Residues in contact with ASP 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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74A ASN* 3.7 32.1 + - - +
77A GLN* 5.5 0.7 - - - +
262A THR* 3.1 29.8 + - - +
263A ASP* 1.3 73.3 - - - +
265A ASP* 1.3 57.8 - - - +
267A LEU* 4.2 3.1 - - - -
268A ILE* 2.8 39.7 + - + +
302A THR* 4.9 0.7 - - - +
306A TYR* 2.8 31.1 + - - +
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Residues in contact with ASP 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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77A GLN* 3.0 31.5 + - - +
93A GLU* 4.7 1.2 - - - +
96A LYS* 3.6 19.5 + - - +
104A ASP* 5.0 10.6 - - - +
263A ASP* 3.3 8.2 + - - +
264A ASP* 1.3 77.5 - - - +
266A THR* 1.3 57.6 + - - +
268A ILE* 4.0 0.9 - - - +
269A ARG* 3.1 42.3 + - - +
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Residues in contact with THR 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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104A ASP* 5.1 3.8 + - - -
110A GLU* 3.9 3.4 - - - +
252A ARG* 3.5 50.9 + - + +
253A LEU* 5.7 0.2 - - - -
256A SER* 4.1 13.0 - - - -
263A ASP* 2.9 32.0 + - - +
265A ASP* 1.3 76.1 - - - +
267A LEU* 1.3 69.0 + - - +
269A ARG* 3.4 16.8 + - - +
270A VAL* 2.9 26.1 + - + +
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Residues in contact with LEU 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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253A LEU* 3.9 22.2 - - + +
256A SER* 3.8 12.5 - - - +
257A MET* 4.1 26.2 - - + -
262A THR* 3.9 19.5 - - + -
263A ASP 3.0 16.9 + - - +
264A ASP* 3.7 3.8 - - - +
266A THR* 1.3 77.0 - - - +
268A ILE* 1.3 62.2 + - - +
270A VAL* 4.1 0.3 - - - -
271A MET* 3.1 41.4 + - + +
298A ILE* 4.6 4.5 - - + -
302A THR* 3.9 11.2 - - + -
306A TYR* 3.7 10.8 - - - +
310A LEU* 3.7 28.3 - - + -
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Residues in contact with ILE 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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74A ASN* 4.0 9.0 - - - +
77A GLN* 3.5 43.5 - - + +
78A VAL* 3.4 46.0 - - + -
89A TYR* 4.0 8.5 - - - +
264A ASP 2.8 24.6 + - - +
265A ASP 4.0 2.5 - - - +
267A LEU* 1.3 73.2 - - - +
269A ARG* 1.3 58.7 + - - +
271A MET* 3.3 3.7 + - - +
272A VAL* 2.9 42.2 + - + +
306A TYR* 3.5 22.2 - - + +
310A LEU* 4.8 2.9 - - + -
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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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89A TYR* 3.4 19.7 - - + +
90A ASP* 5.9 0.7 - - - +
93A GLU* 2.9 48.2 + - + +
96A LYS* 5.6 0.4 - - - +
104A ASP* 4.8 4.0 + - - -
107A CYS* 3.7 28.9 - - - +
110A GLU* 2.7 40.4 + - - +
111A ILE* 4.3 9.6 - - - +
115A ARG* 5.5 2.5 - - - +
252A ARG* 3.4 9.3 - - - +
265A ASP* 3.1 34.2 + - - +
266A THR* 3.4 23.0 + - - +
268A ILE* 1.3 77.2 - - - +
270A VAL* 1.3 51.8 + - - +
272A VAL* 4.0 0.2 - - - +
273A SER* 2.7 45.6 + - - +
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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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110A GLU* 3.6 28.7 - - - +
249A PHE* 3.8 25.4 - - + +
252A ARG* 3.7 18.6 - - + -
253A LEU* 3.5 35.4 - - + -
266A THR* 2.9 22.5 + - + +
269A ARG* 1.3 76.1 - - - +
271A MET* 1.3 62.2 + - - +
273A SER* 3.7 5.4 - - - -
274A ARG* 3.0 30.5 + - + +
279A MET* 4.5 0.4 - - + +
282A ILE* 5.0 1.1 - - + -
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Residues in contact with MET 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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253A LEU* 3.7 26.5 - - - -
267A LEU* 3.1 34.5 + - + +
268A ILE 3.9 2.5 - - - +
270A VAL* 1.3 75.2 - - - +
272A VAL* 1.3 57.3 + - - +
275A ALA* 3.1 32.4 + - - +
279A MET* 3.7 25.6 - - + +
294A LEU* 4.1 2.0 - - + -
298A ILE* 3.8 21.5 - - + -
310A LEU* 3.9 17.7 - - + +
313A LEU* 3.9 17.7 - - + +
314A CYS* 3.6 37.9 - - + +
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Residues in contact with VAL 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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48A ARG* 5.9 0.9 - - - +
78A VAL* 4.1 9.4 - - + +
81A GLY* 3.6 28.5 - - - +
82A MET* 3.9 26.2 - - + +
89A TYR* 3.7 19.7 - - + +
268A ILE* 2.9 36.5 + - + +
271A MET* 1.3 79.4 - - + +
273A SER* 1.3 64.2 + - - +
274A ARG 3.4 0.5 + - - -
275A ALA* 3.6 11.3 + - - +
276A GLU 4.9 0.7 + - - -
313A LEU* 4.1 12.8 - - + -
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Residues in contact with SER 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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86A THR* 6.1 0.7 - - - +
89A TYR* 4.4 14.8 - - - -
90A ASP* 4.9 0.2 - - - -
110A GLU* 4.9 2.1 + - - -
115A ARG* 3.7 27.7 + - - -
249A PHE* 5.2 0.9 - - - -
269A ARG* 2.7 31.6 + - - +
270A VAL* 3.5 5.4 + - - -
272A VAL* 1.3 76.3 - - - +
274A ARG* 1.3 69.8 + - - +
276A GLU* 5.0 0.9 + - - +
277A ILE* 3.2 23.7 - - - +
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Residues in contact with ARG 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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114A SER* 5.0 4.4 + - - -
115A ARG* 4.6 12.4 - - - +
245A LYS* 3.2 27.3 - - - +
249A PHE* 3.3 44.0 - - + -
270A VAL* 3.0 18.7 + - + +
273A SER* 1.3 88.8 - - - +
275A ALA* 1.3 66.7 + - - +
276A GLU 3.2 3.4 - - - -
277A ILE* 2.9 43.1 + - - +
278A ASP* 2.9 50.9 + - - +
279A MET* 3.6 8.6 + - + -
282A ILE* 3.6 18.8 - - + -
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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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48A ARG* 6.2 0.7 - - - +
271A MET 3.1 22.7 + - - +
272A VAL 3.6 9.2 + - - +
274A ARG* 1.3 77.1 - - - +
276A GLU* 1.3 65.0 + - + +
279A MET* 3.7 23.9 + - - +
280A LEU* 5.8 1.6 - - - +
313A LEU* 3.9 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