Contacts of the helix formed by residues 259 - 268 (chain A) in PDB entry 2HVY
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 LYS 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ASP* 3.4 30.3 + - - +
28A ALA* 4.9 5.4 - - + -
29A GLU 5.9 0.7 - - - +
258A ILE* 1.3 75.7 - - - +
260A ASP* 1.3 66.0 + - - +
261A SER* 3.9 11.0 - - - +
262A ALA* 3.0 14.2 + - - +
263A VAL* 3.5 9.1 + - - +
275A PRO 3.1 23.8 + - - +
276A GLY 2.9 15.0 + - - +
277A ILE 3.9 15.0 - - - -
278A ALA* 4.2 11.4 - - + -
295A LEU* 4.5 7.2 - - - -
60E A 4.1 6.1 - - - +
61E G 2.9 32.6 + - - +
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Residues in contact with ASP 260 (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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29A GLU 4.0 7.5 + - - +
30A THR* 2.9 25.8 + - - -
31A ASN* 2.7 39.2 + - - +
34A TRP* 3.7 19.2 - - + -
258A ILE 4.9 2.3 - - - +
259A LYS* 1.3 72.1 - - - +
261A SER* 1.3 57.8 + - - +
262A ALA 3.1 5.1 + - - -
263A VAL* 3.2 23.8 + - - +
264A ALA 4.5 1.7 + - - -
294A THR* 5.4 0.7 - - - -
295A LEU* 4.9 6.0 + - - +
333A TYR* 3.7 22.9 + - + +
334A PRO 5.1 1.2 - - - +
336A LEU* 4.3 7.2 - - + +
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Residues in contact with SER 261 (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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259A LYS* 3.9 4.9 - - - +
260A ASP* 1.3 76.6 - - - +
262A ALA* 1.3 57.1 + - - +
263A VAL 3.6 0.2 - - - -
264A ALA* 5.2 1.4 + - - +
265A ALA* 5.0 2.6 + - - +
336A LEU* 3.8 42.3 + - - +
337A TRP* 4.2 1.4 + - - +
60E A 2.7 56.0 + - - -
61E G 3.0 12.2 + - - -
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Residues in contact with ALA 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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258A ILE* 4.0 11.7 - - + -
259A LYS 3.0 10.1 + - - +
261A SER* 1.3 77.5 + - - +
263A VAL* 1.3 65.3 + - - +
264A ALA 3.5 1.3 - - - -
265A ALA* 3.4 5.6 + - - +
266A VAL* 3.3 24.4 + - - +
272A LEU* 4.6 2.9 - - + -
276A GLY* 4.1 10.1 - - - +
60E A 3.5 45.0 - - + +
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Residues in contact with VAL 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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258A ILE* 3.8 18.8 - - + +
259A LYS 3.5 17.0 - - - +
260A ASP* 3.2 18.7 + - - +
262A ALA* 1.3 77.7 - - - +
264A ALA* 1.3 63.7 + - - +
266A VAL* 3.3 6.1 + - - +
267A THR* 3.1 23.2 + - + +
294A THR* 3.9 20.6 - - + -
300A VAL* 4.3 7.0 - - + -
328A MET* 3.6 31.4 - - - -
333A TYR* 3.6 22.4 - - + -
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Residues in contact with ALA 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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260A ASP 4.5 1.4 + - - -
261A SER 5.2 1.7 - - - +
262A ALA 3.5 0.2 - - - -
263A VAL* 1.3 78.1 - - - +
265A ALA* 1.3 64.1 + - - +
267A THR* 3.0 14.0 + - - +
268A HIS* 2.8 31.5 + - + -
330A ARG 4.7 0.9 - - - +
333A TYR* 3.5 18.0 - - - +
334A PRO 3.2 30.7 - - - +
335A LYS* 3.9 10.3 - - + +
336A LEU 4.8 0.7 - - - +
337A TRP* 3.6 5.2 - - + -
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Residues in contact with ALA 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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261A SER 5.0 1.5 + - - +
262A ALA 3.4 6.0 + - - +
263A VAL 3.3 0.4 - - - -
264A ALA* 1.3 77.9 - - - +
266A VAL* 1.3 60.0 + - - +
268A HIS* 3.1 10.4 + - - +
269A GLY 3.3 0.5 + - - -
270A ALA* 2.9 25.5 + - + +
337A TRP* 3.6 22.1 - - + -
58E A 3.6 10.6 - - + +
60E A 3.3 42.2 - - + +
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Residues in contact with VAL 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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258A ILE* 4.4 11.0 - - + -
262A ALA 3.3 13.2 + - - +
263A VAL* 3.3 8.8 + - - +
265A ALA* 1.3 76.0 - - - +
267A THR* 1.3 61.8 + - - +
268A HIS 3.1 0.2 - - - -
269A GLY* 3.2 12.6 + - - -
270A ALA 3.4 16.1 - - - +
271A ASP 4.7 0.9 - - - -
272A LEU* 4.4 26.7 - - + -
292A ILE* 4.6 4.9 - - + -
300A VAL* 3.8 22.0 - - + -
301A ALA* 4.0 14.1 - - + -
323A VAL* 3.8 21.3 - - + +
326A VAL* 3.6 13.0 - - + +
60E A 4.8 3.4 - - - +
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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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263A VAL* 3.1 13.4 + - + +
264A ALA* 3.0 21.7 + - - -
266A VAL* 1.3 75.8 - - - +
268A HIS* 1.3 59.7 + - - +
269A GLY 3.4 0.4 - - - -
300A VAL* 3.9 20.2 - - + -
326A VAL* 3.8 11.3 - - + +
328A MET* 3.4 36.3 - - + +
329A PRO 4.1 4.0 + - - +
330A ARG* 3.3 41.7 + - - +
4E U 3.7 7.7 + - - -
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Residues in contact with HIS 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 ALA* 2.8 32.4 + - + +
265A ALA 3.1 6.2 + - - +
267A THR* 1.3 85.6 - - - +
269A GLY* 1.3 53.4 + - - +
270A ALA 3.7 0.7 - - - -
330A ARG* 3.6 33.9 + - + +
335A LYS* 3.5 33.9 - - - +
337A TRP* 3.7 9.4 - + + -
3E G 2.7 29.8 + - - -
4E U 4.6 1.1 - - - -
55E C 3.2 28.0 + - - -
56E C 3.7 25.6 + - - +
58E A 2.9 11.4 + - - +
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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