Contacts of the helix formed by residues 261 - 271 (chain A) in PDB entry 1JV1
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 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A HIS* 4.2 3.3 + - + -
258A LYS* 3.2 42.1 + - + +
259A VAL 3.2 0.6 - - - -
260A ALA* 1.3 72.9 - - - +
262A PRO* 1.3 76.1 - - - +
263A ARG* 3.1 16.6 + - - +
264A PHE* 3.2 24.9 + - + +
265A ILE* 3.0 25.0 + - - +
278A LYS* 2.9 27.8 + - - +
395A TYR* 4.6 2.3 - - - -
402A GLU* 4.4 2.8 - - - +
472A TYR* 3.3 6.0 - - - -
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Residues in contact with PRO 262 (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 TRP 3.2 10.2 - - - +
91A GLU* 3.8 24.5 - - + +
94A GLY* 3.4 8.9 - - - -
95A LEU* 3.8 32.5 - - + +
98A ILE* 4.4 4.0 - - + -
146A LEU* 3.8 25.1 - - + -
260A ALA 3.0 9.4 - - - +
261A ASP* 1.3 90.4 - - - +
263A ARG* 1.3 58.3 + - + +
265A ILE* 4.4 2.2 - - + -
266A GLY 2.8 22.9 + - - -
472A TYR* 4.0 9.6 - - + -
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Residues in contact with ARG 263 (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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80A ALA* 6.2 1.1 - - - -
87A LEU* 3.9 34.5 - - + +
90A TRP* 3.7 5.1 - - + +
91A GLU* 2.7 49.5 + - + +
258A LYS* 3.7 24.9 - - - +
261A ASP* 3.1 12.5 + - - +
262A PRO* 1.3 76.5 - - + +
264A PHE* 1.3 61.5 + - - +
267A PHE* 3.0 30.5 + - - +
395A TYR* 3.8 16.6 + - + +
473A ALA* 4.8 15.6 + - - +
475A GLU* 5.8 3.6 + - - +
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Residues in contact with PHE 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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248A HIS* 4.3 17.0 - + - -
261A ASP* 3.2 24.7 + - + +
263A ARG* 1.3 78.6 - - - +
265A ILE* 1.3 67.0 + - + +
267A PHE* 3.4 2.3 + - - +
268A CYS* 3.1 37.1 + - - -
276A GLY* 3.7 23.3 - - - -
277A ALA 4.1 3.4 - - - -
278A LYS* 3.6 37.9 - - + +
330A ASN 3.8 9.4 - - - -
331A HIS 3.7 21.1 - - - -
332A PHE* 3.7 11.4 - - + -
393A VAL* 5.8 0.2 - - + -
395A TYR* 3.6 38.3 - + + -
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Residues in contact with ILE 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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94A GLY* 4.2 13.7 - - - -
97A GLN* 4.7 2.9 - - + -
98A ILE* 5.1 2.7 - - + -
103A VAL* 3.7 41.7 - - + -
246A SER* 4.5 4.9 - - - +
248A HIS* 4.7 13.0 - - + +
260A ALA* 3.6 33.7 - - - +
261A ASP 3.0 13.6 + - - +
262A PRO* 4.1 4.5 - - + +
264A PHE* 1.3 81.7 - - + +
266A GLY* 1.3 62.9 + - - +
268A CYS* 3.4 2.6 + - - +
269A ILE* 3.0 40.9 + - + +
332A PHE* 4.2 24.6 - - + -
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Residues in contact with GLY 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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90A TRP* 3.2 25.4 - - - -
93A GLU* 3.9 8.1 - - - -
94A GLY* 3.7 9.9 - - - -
262A PRO 2.8 15.5 + - - -
264A PHE 3.3 0.2 - - - -
265A ILE* 1.3 72.2 - - - +
267A PHE* 1.3 57.6 + - - +
269A ILE* 3.7 1.0 - - - +
270A GLN* 2.7 43.5 + - - +
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Residues in contact with PHE 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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76A VAL 4.4 3.1 - - - -
77A LEU 4.5 0.7 - - - -
78A GLY* 3.6 24.2 - - - -
90A TRP* 3.6 41.8 - + + +
263A ARG 3.0 19.0 + - - +
264A PHE 3.6 2.7 - - - +
266A GLY* 1.3 76.2 - - - +
268A CYS* 1.3 74.2 + - - +
270A GLN* 3.8 0.9 - - - +
271A LYS* 3.0 56.6 + - + +
393A VAL* 3.6 26.7 - - + -
394A VAL 3.5 26.2 - - - -
395A TYR* 3.6 28.5 - + + -
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Residues in contact with CYS 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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264A PHE* 3.1 43.7 + - - +
265A ILE 3.8 0.7 - - - +
266A GLY 3.3 0.2 - - - -
267A PHE* 1.3 80.5 - - - +
269A ILE* 1.3 62.6 + - - +
271A LYS* 3.3 1.4 + - - -
272A GLY 3.2 3.3 + - - -
273A ALA* 3.0 33.1 + - + +
276A GLY* 4.2 2.0 - - - -
332A PHE* 3.6 47.3 - - + -
393A VAL* 3.8 20.6 - - - -
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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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93A GLU* 3.8 27.6 - - + +
97A GLN* 4.2 20.2 - - + +
245A TRP* 3.8 22.4 - - + +
246A SER* 3.5 22.7 - - - +
265A ILE* 3.0 32.5 + - + +
266A GLY* 3.7 4.7 - - - +
267A PHE 3.3 0.2 - - - -
268A CYS* 1.3 74.6 - - - +
270A GLN* 1.3 60.2 + - - +
272A GLY* 3.0 20.3 + - - -
273A ALA 5.2 1.1 - - - +
332A PHE* 4.0 7.2 - - + -
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Residues in contact with GLN 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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89A ALA* 3.7 23.6 - - - +
90A TRP* 3.5 25.9 - - + +
93A GLU* 3.6 30.2 + - + +
266A GLY 2.7 28.6 + - - +
267A PHE 3.8 3.4 - - - +
269A ILE* 1.3 76.9 - - - +
271A LYS* 1.3 63.2 + - + +
272A GLY 3.2 0.8 + - - -
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Residues in contact with LYS 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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75A GLU 5.7 5.1 + - - +
86A GLN* 4.8 9.5 + - - +
90A TRP* 4.4 14.4 - - - +
267A PHE* 3.0 55.8 + - + +
268A CYS* 3.9 4.5 - - - +
269A ILE 3.2 0.2 - - - -
270A GLN* 1.3 79.2 - - + +
272A GLY* 1.3 60.2 + - - +
273A ALA 4.4 0.2 - - - +
391A LYS* 2.9 30.0 + - - +
393A VAL* 4.0 21.3 - - + -
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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