Contacts of the helix formed by residues 258 - 267 (chain A) in PDB entry 5IVI
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 HIS 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A GLN 5.0 1.7 + - - +
256A CYS 3.2 0.8 - - - -
257A GLN* 1.3 75.9 - - - +
259A ARG* 1.3 65.9 + - + +
260A ALA 3.3 2.3 + - - -
261A PHE* 3.5 37.2 + + - +
262A THR* 3.5 15.1 + - - -
273A ASP* 3.4 28.7 + - - -
302A GLU* 6.0 2.2 - - - -
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Residues in contact with ARG 259 (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 THR* 2.8 29.6 + - - -
255A GLN 4.6 6.0 + - - +
256A CYS* 3.0 26.4 + - - +
258A HIS* 1.3 80.5 - - + +
260A ALA* 1.3 59.4 + - - +
261A PHE 3.3 0.2 - - - -
262A THR* 3.2 8.8 + - - -
263A LEU* 2.9 31.0 + - - +
297A VAL* 4.0 11.9 - - + +
298A LEU* 3.7 7.2 - - - -
302A GLU* 3.2 30.2 + - - +
307A VAL* 3.5 21.8 - - - +
309A PHE 3.6 3.2 + - - -
310A PRO* 2.7 49.3 + - - +
311A PHE* 3.6 19.7 - - + -
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Residues in contact with ALA 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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173A LEU* 3.7 31.4 - - + -
174A SER 4.7 2.5 - - - +
175A LEU* 3.6 31.6 - - + -
256A CYS 4.1 2.0 + - - -
257A GLN 4.2 3.6 + - - +
258A HIS 3.3 0.4 - - - -
259A ARG* 1.3 77.4 - - - +
261A PHE* 1.3 56.6 + - - +
263A LEU* 3.3 3.8 + - - +
264A ALA* 2.9 29.8 + - - +
278A VAL* 3.6 5.6 - - + +
282A LEU* 4.0 11.2 - - + +
311A PHE* 4.0 4.6 - - + -
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Residues in contact with PHE 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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257A GLN 5.1 0.2 + - - -
258A HIS* 3.5 35.3 + + - +
260A ALA* 1.3 79.7 - - - +
262A THR* 1.3 68.8 + - - +
264A ALA* 3.2 3.3 + - - +
265A LYS* 3.0 64.3 + - + +
269A TYR* 4.3 3.1 - + - -
271A GLY 4.4 1.1 - - - -
272A GLU 3.8 5.6 - - - -
273A ASP* 3.5 53.2 - - + +
278A VAL* 3.8 23.8 - - + +
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Residues in contact with THR 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 HIS* 3.5 23.8 + - - -
259A ARG* 3.2 13.6 + - - -
261A PHE* 1.3 84.5 - - - +
263A LEU* 1.3 61.8 + - - +
265A LYS* 3.3 7.6 + - + +
266A LEU* 3.1 28.2 + - + +
297A VAL* 3.8 31.6 - - + +
299A THR* 6.0 3.6 - - + -
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Residues in contact with LEU 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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73A PHE* 6.2 0.4 - - + -
169A ALA* 3.9 26.5 - - + -
173A LEU* 4.5 6.7 - - + -
259A ARG 2.9 16.4 + - - +
260A ALA 3.6 3.6 - - - +
262A THR* 1.3 75.3 - - - +
264A ALA* 1.3 63.6 + - - +
266A LEU* 3.1 6.4 + - - +
267A ALA* 3.1 20.8 + - - +
282A LEU* 4.0 20.2 - - + -
290A LEU* 3.7 36.8 - - + +
293A LEU* 4.3 12.7 - - + +
294A GLU* 4.4 5.4 - - + -
297A VAL* 3.7 25.7 - - + +
311A PHE* 3.9 13.7 - - + -
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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 ALA 2.9 14.5 + - - +
261A PHE 3.2 8.7 + - - +
263A LEU* 1.3 76.3 - - - +
265A LYS* 1.3 61.8 + - - +
267A ALA* 3.0 14.0 + - - +
268A GLY 3.1 0.7 + - - -
269A TYR* 3.0 32.0 + - + +
278A VAL* 3.9 16.4 - - + -
281A PHE* 3.5 28.2 - - + -
282A LEU* 4.1 5.6 - - + +
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Residues in contact with LYS 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 PHE* 3.0 49.2 + - + +
262A THR* 3.3 9.4 + - - +
264A ALA* 1.3 76.7 - - - +
266A LEU* 1.3 62.4 + - + +
268A GLY* 3.1 13.7 + - - -
269A TYR* 3.3 39.3 + - + +
270A LYS* 5.1 12.5 + - - +
271A GLY 4.3 11.8 + - - +
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Residues in contact with LEU 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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262A THR* 3.1 21.0 + - + +
263A LEU* 3.1 8.3 + - - +
265A LYS* 1.3 76.7 - - + +
267A ALA* 1.3 58.7 + - - +
268A GLY 3.2 1.2 + - - -
293A LEU* 3.8 28.2 - - + +
296A LYS* 3.8 42.0 - - + +
297A VAL* 3.8 31.9 - - + -
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Residues in contact with ALA 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 LEU 3.1 10.2 + - - +
264A ALA 3.0 9.5 + - - +
266A LEU* 1.3 76.0 - - - +
268A GLY* 1.3 58.8 + - - +
269A TYR 3.6 0.2 - - - -
281A PHE* 3.6 22.6 - - + -
289A ASP* 6.0 2.9 - - + -
290A LEU* 4.3 13.7 - - + -
293A LEU* 3.6 18.4 - - + -
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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