Contacts of the helix formed by residues 264 - 275 (chain A) in PDB entry 6B3I
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 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A ARG* 4.9 2.1 + - - -
257A SER* 2.8 28.2 + - - +
263A THR* 1.3 68.3 - - - +
265A GLU* 1.3 58.9 + - - +
266A GLU* 3.5 17.5 + - - +
267A THR* 2.4 29.5 + - - -
268A LEU* 3.5 14.9 + - - +
401A EDO 3.3 20.0 + - - +
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Residues in contact with GLU 265 (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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75A ASN* 2.3 45.2 + - - +
262A GLY 5.0 1.8 - - - +
263A THR* 2.8 34.0 + - + +
264A ASP* 1.3 71.6 + - - +
266A GLU* 1.3 64.4 + - - +
268A LEU* 3.3 9.7 + - + +
269A ILE* 3.1 29.6 + - - +
302A ASP 4.5 3.1 - - - +
303A THR* 4.2 13.9 - - + +
307A PHE* 3.6 27.7 - - + -
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Residues in contact with GLU 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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75A ASN* 5.3 3.4 - - - +
78A LYS* 2.3 43.6 + - + +
90A TYR* 4.8 1.0 + - - -
94A GLN* 3.4 29.0 + - - +
97A LYS* 2.9 21.4 + - - +
264A ASP* 3.3 9.5 - - - +
265A GLU* 1.3 75.5 - - - +
267A THR* 1.3 66.4 + - - +
269A ILE* 3.3 8.6 + - - +
270A ARG* 3.0 31.2 + - - +
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Residues in contact with THR 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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108A VAL* 5.7 0.5 - - - +
253A ARG* 3.5 24.2 + - - +
257A SER* 4.2 14.6 - - - -
264A ASP* 2.4 33.2 + - - -
265A GLU 3.4 0.2 - - - -
266A GLU* 1.3 77.6 - - - +
268A LEU* 1.3 62.9 + - - +
270A ARG* 3.1 31.0 + - - +
271A ILE* 3.1 44.3 + - + +
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Residues in contact with LEU 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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254A LEU* 4.1 17.8 - - + +
257A SER* 4.5 2.9 + - - +
258A MET* 3.7 38.8 - - + -
263A THR* 4.6 8.7 - - + -
264A ASP 3.5 8.9 + - - +
265A GLU* 3.3 13.2 + - + +
266A GLU 3.2 0.4 - - - -
267A THR* 1.3 79.8 - - - +
269A ILE* 1.3 61.6 + - + +
272A ILE* 3.3 53.9 + - + +
295A LEU* 6.3 0.4 - - + -
299A VAL* 4.3 8.7 - - + -
303A THR* 4.3 20.4 - - + -
307A PHE* 5.4 0.7 - - + -
311A LEU* 3.6 21.3 - - + -
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Residues in contact with ILE 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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75A ASN* 4.0 19.7 - - - +
78A LYS* 4.3 11.9 - - + +
79A THR* 3.3 38.6 - - + +
82A ALA* 4.4 0.2 - - + -
90A TYR* 3.5 20.2 - - + +
265A GLU 3.1 18.4 + - - +
266A GLU* 3.8 7.4 - - - +
267A THR 3.3 0.2 - - - -
268A LEU* 1.3 73.8 - - - +
270A ARG* 1.3 66.9 + - - +
272A ILE* 3.4 3.2 + - - -
273A VAL* 3.0 40.7 + - + +
307A PHE* 3.5 24.0 - - + -
311A LEU* 4.9 5.2 - - + -
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Residues in contact with ARG 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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90A TYR* 3.8 11.0 + - + -
91A ALA* 5.9 0.9 - - + +
94A GLN* 3.4 49.1 + - + +
107A SER 5.8 0.2 - - - -
108A VAL* 3.9 31.5 - - - +
111A GLU* 2.9 40.4 + - - +
112A VAL* 4.5 9.9 - - + -
116A ARG* 5.8 1.3 - - - +
253A ARG* 4.2 3.0 - - - +
266A GLU* 3.0 21.6 + - - +
267A THR* 3.1 33.1 + - - +
269A ILE* 1.3 76.4 - - - +
271A ILE* 1.3 55.0 + - - +
274A THR* 2.5 47.5 + - + +
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Residues in contact with ILE 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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111A GLU* 3.8 18.2 - - - +
250A PHE* 3.8 31.6 - - + +
253A ARG* 3.9 23.8 - - + +
254A LEU* 3.8 42.0 - - + +
267A THR* 3.1 33.9 + - + +
270A ARG* 1.3 75.4 - - - +
272A ILE* 1.3 66.8 + - - +
274A THR* 4.0 2.9 - - - -
275A ARG* 3.1 35.7 + - + +
280A LEU* 5.8 0.7 - - + -
283A ILE* 4.6 4.5 - - + -
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Residues in contact with ILE 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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254A LEU* 4.4 13.0 - - + -
268A LEU* 3.3 40.6 + - + +
269A ILE* 4.2 2.9 - - - +
271A ILE* 1.3 75.7 - - - +
273A VAL* 1.3 62.1 + - + +
276A ALA* 3.3 24.9 + - + +
280A LEU* 4.0 27.6 - - + +
295A LEU* 4.7 5.4 - - + -
299A VAL* 5.1 0.4 - - + -
311A LEU* 4.3 12.8 - - + -
314A LEU* 4.1 31.0 - - + -
315A LEU* 4.0 28.5 - - + -
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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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79A THR* 4.6 6.3 - - + -
82A ALA* 3.7 29.8 - - + +
83A LEU* 3.8 27.5 - - + +
85A ASP 5.8 0.2 - - - +
87A PRO* 4.8 8.6 - - + +
90A TYR* 3.9 21.5 - - + -
269A ILE* 3.0 36.4 + - + +
272A ILE* 1.3 76.8 - - + +
274A THR* 1.3 67.6 + - + +
275A ARG 3.2 1.1 + - - -
276A ALA* 3.3 16.6 + - - +
277A GLU 5.0 0.2 + - - -
314A LEU* 4.9 3.8 - - + -
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Residues in contact with THR 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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87A PRO* 4.1 33.7 - - + +
90A TYR* 3.9 23.3 - - + -
91A ALA* 4.5 10.3 - - + +
116A ARG* 3.7 28.7 + - - +
270A ARG* 2.5 32.2 + - + +
271A ILE* 4.0 1.0 - - - -
273A VAL* 1.3 76.2 - - + +
275A ARG* 1.3 67.6 + - - +
276A ALA 3.5 0.2 - - - -
277A GLU 5.3 0.2 + - - -
278A VAL* 3.8 14.7 - - - +
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Residues in contact with ARG 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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115A THR 3.4 17.6 + - - -
116A ARG* 3.2 30.8 - - - +
120A GLU* 4.7 3.6 + - - -
246A CYS* 4.3 8.1 - - - +
250A PHE* 3.5 32.3 - - + -
271A ILE* 3.1 26.9 + - + +
272A ILE 4.1 0.9 - - - -
274A THR* 1.3 89.8 - - - +
276A ALA* 1.3 61.2 + - - +
277A GLU 3.4 2.0 - - - -
278A VAL* 3.7 23.1 - - - +
279A ASP* 3.0 46.4 + - - +
280A LEU* 2.9 26.5 + - + +
283A ILE* 4.0 16.8 - - + -
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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