Contacts of the helix formed by residues 304 - 315 (chain A) in PDB entry 4I6H
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 LEU 304 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A GLU* 3.6 38.3 + - - +
302A SER 3.7 6.8 + - - +
303A LEU* 1.3 78.1 - - - +
305A ALA* 1.3 68.5 + - - +
306A PRO* 3.5 9.4 - - + -
307A ALA* 3.4 3.7 + - - +
308A LYS* 3.2 20.1 + - - +
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Residues in contact with ALA 305 (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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303A LEU 4.0 0.4 + - - -
304A LEU* 1.3 70.4 - - - +
306A PRO* 1.4 74.0 - - + +
308A LYS* 3.2 14.5 - - - +
309A HIS* 3.0 41.5 + - + +
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Residues in contact with PRO 306 (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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179A GLU* 5.7 0.9 - - - +
304A LEU* 3.7 11.2 - - + -
305A ALA* 1.4 94.4 - - + +
307A ALA* 1.3 61.0 + - - +
309A HIS* 3.4 11.2 + - + -
310A LEU* 3.3 9.7 + - - +
331A HIS* 3.3 23.1 - - + -
332A ASP* 4.3 14.6 - - + +
333A PHE* 3.9 30.0 - - + +
336A GLN* 6.0 2.9 - - + -
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Residues in contact with ALA 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLU* 3.5 22.8 + - - +
270A MET* 3.3 11.6 - - - +
274A LEU* 3.8 19.5 - - + -
303A LEU* 4.6 5.8 - - + -
304A LEU 3.4 7.8 + - - +
305A ALA 3.3 0.4 - - - -
306A PRO* 1.3 79.0 - - - +
308A LYS* 1.3 63.4 + - - +
310A LEU 3.3 1.7 + - - -
311A ILE* 3.1 24.3 + - - +
333A PHE* 3.7 24.0 - - + -
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Residues in contact with LYS 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A MET* 3.7 33.1 - - + +
300A PRO 3.7 21.9 + - - -
301A SER* 4.3 8.7 + - - +
303A LEU* 3.2 39.6 + - + +
304A LEU 3.2 8.9 + - - +
305A ALA* 3.2 15.0 - - - +
307A ALA* 1.3 79.0 - - - +
309A HIS* 1.3 68.6 + - + +
311A ILE* 3.6 0.6 + - - +
312A ALA* 3.1 24.5 + - + +
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Residues in contact with HIS 309 (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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305A ALA* 3.0 40.4 + - + +
306A PRO* 3.7 10.8 - - + +
307A ALA 3.3 0.4 - - - -
308A LYS* 1.3 82.8 - - + +
310A LEU* 1.3 58.1 + - - +
312A ALA* 3.4 7.0 + - - +
313A SER* 2.9 27.2 + - - -
331A HIS* 4.0 13.9 - + - +
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Residues in contact with LEU 310 (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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270A MET* 3.9 10.3 - - + -
306A PRO 3.3 10.6 + - - +
307A ALA 3.9 3.1 - - - +
309A HIS* 1.3 75.3 - - - +
311A ILE* 1.3 60.3 + - - +
313A SER* 3.1 9.4 + - - -
314A MET* 2.9 47.9 + - + +
323A PRO* 4.8 2.7 - - + -
328A ILE* 4.3 22.4 - - + +
331A HIS* 3.6 36.1 + - + +
333A PHE* 3.6 35.0 - - + -
334A PHE* 4.1 16.2 - - + -
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Residues in contact with ILE 311 (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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267A GLY* 4.5 7.0 - - - +
270A MET* 3.6 29.6 - - + -
271A TYR* 3.8 41.1 - - + +
274A LEU* 4.3 7.4 - - + -
297A TYR* 3.9 6.3 - - - +
299A MET* 4.1 4.9 - - + -
303A LEU* 4.0 23.8 - - + -
307A ALA 3.1 13.7 + - - +
308A LYS 3.9 3.8 - - - +
310A LEU* 1.3 75.7 - - - +
312A ALA* 1.3 56.7 + - - +
314A MET* 3.3 7.9 + - - +
315A LEU* 2.9 51.3 + - + +
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Residues in contact with ALA 312 (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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297A TYR* 3.4 17.5 + - - +
299A MET* 5.0 4.5 - - + -
308A LYS 3.1 16.4 + - - +
309A HIS* 3.6 7.0 - - - +
311A ILE* 1.3 78.9 - - - +
313A SER* 1.3 61.7 + - - +
315A LEU* 3.8 2.5 - - - +
316A SER* 3.6 17.0 + - - -
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Residues in contact with SER 313 (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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309A HIS 2.9 14.4 + - - -
310A LEU* 3.1 16.8 + - - -
312A ALA* 1.3 77.2 - - - +
314A MET* 1.3 60.5 + - - +
316A SER* 2.7 26.0 + - - -
321A ASP 4.4 2.4 + - - +
322A ARG* 3.8 0.3 - - - -
323A PRO* 3.4 31.7 - - - +
331A HIS* 5.5 4.5 - - - -
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Residues in contact with MET 314 (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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186A LEU* 5.6 3.6 - - + -
263A ILE* 3.8 21.6 - - + +
264A TRP* 3.7 12.5 - - - -
266A LEU* 3.9 35.4 - - + +
267A GLY* 4.1 11.0 - - - -
270A MET* 3.7 30.3 - - + -
310A LEU* 2.9 30.5 + - + +
311A ILE 4.1 2.7 - - - +
313A SER* 1.3 75.2 - - - +
315A LEU* 1.3 59.1 + - - +
316A SER 3.3 0.9 - - - -
322A ARG* 3.3 22.6 - - - +
323A PRO* 3.9 19.7 - - + -
328A ILE* 3.8 25.8 - - + -
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Residues in contact with LEU 315 (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 TRP* 3.4 58.0 - - + +
267A GLY* 3.6 17.9 - - - -
268A CYS* 3.7 9.6 - - - +
279A PRO* 4.0 23.8 - - + -
280A PHE* 4.3 2.5 - - + -
295A ALA* 3.9 11.1 - - - +
297A TYR* 3.6 36.4 - - + +
311A ILE* 2.9 26.1 + - + +
312A ALA 3.8 4.5 - - - +
313A SER 3.3 0.2 - - - -
314A MET* 1.3 76.0 - - - +
316A SER* 1.3 64.1 + - - +
317A LYS 3.5 1.4 + - - -
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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