Contacts of the helix formed by residues 356 - 368 (chain D) in PDB entry 2IB8
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 PHE 356 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192D HIS* 4.9 4.5 - + - -
193D MET* 3.8 19.1 - - + -
194D GLY* 3.4 34.3 - - - -
197D ALA* 4.3 9.9 - - + -
271D PHE* 4.6 6.3 - + - -
278D VAL* 3.8 14.8 - - + -
282D ASN 4.0 4.5 - - - +
283D ALA* 3.4 30.1 - - + +
284D SER* 5.1 2.9 - - - -
325D PHE* 4.0 22.7 - + - -
354D GLU 4.0 5.6 - - - -
355D ALA* 1.3 89.3 - - + +
357D SER* 1.3 67.0 + - - +
358D LEU* 4.1 12.3 - - + +
359D VAL* 3.0 31.6 + - + +
360D VAL* 3.7 4.9 + - - +
381D VAL* 4.1 4.7 - - - -
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Residues in contact with SER 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D GLN* 3.4 30.9 + - - -
214D TYR* 3.6 27.7 - - - -
215D ALA* 3.6 8.5 + - - +
282D ASN* 2.8 34.8 + - - +
356D PHE* 1.3 71.6 - - - +
358D LEU* 1.3 63.2 + - - +
360D VAL* 3.1 14.9 + - - +
361D LEU* 3.2 18.2 + - - +
381D VAL* 3.7 7.7 - - - +
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Residues in contact with LEU 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D ALA* 3.8 28.3 - - + +
200D THR* 3.9 8.7 - - + -
201D ALA* 3.6 33.7 - - + +
206D ILE* 3.8 25.1 - - + -
211D GLN* 3.7 21.1 + - - +
278D VAL* 5.3 3.4 - - + -
326D PRO* 3.9 28.0 - - + -
356D PHE* 4.3 9.9 - - + -
357D SER* 1.3 77.4 - - - +
359D VAL* 1.3 66.7 + - + +
361D LEU* 3.3 6.4 + - - +
362D ALA* 2.9 25.5 + - - +
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Residues in contact with VAL 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D PHE* 4.5 0.7 - - + -
326D PRO* 3.8 38.4 - - + +
329D PRO* 4.8 4.0 - - + -
352D VAL* 4.8 4.5 - - + -
353D ASN 4.1 15.9 - - - +
355D ALA* 4.3 4.9 - - + -
356D PHE* 3.0 41.0 + - + +
358D LEU* 1.3 82.0 - - + +
360D VAL* 1.3 63.2 + - - +
362D ALA* 3.3 1.4 + - - +
363D ASN* 3.0 35.0 + - - +
413D CYS* 4.1 17.0 - - - -
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Residues in contact with VAL 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D TYR* 3.3 41.5 - - + +
352D VAL* 3.6 21.1 - - + +
353D ASN 4.3 2.0 - - - +
354D GLU* 3.7 21.1 - - + -
356D PHE 3.7 3.3 + - - +
357D SER 3.1 4.5 + - - +
359D VAL* 1.3 74.2 - - - +
361D LEU* 1.3 53.7 + - - +
363D ASN* 3.2 3.8 + - - +
364D ILE* 2.8 44.9 + - + +
374D VAL* 3.9 9.9 - - + -
375D ASN* 3.5 24.7 - - - +
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Residues in contact with LEU 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D ILE* 3.7 32.5 - - + +
210D GLU* 3.5 47.1 - - + +
211D GLN* 3.8 13.9 - - + +
214D TYR* 4.0 26.7 - - + -
357D SER 3.2 14.0 + - - +
358D LEU 3.8 4.5 - - - +
360D VAL* 1.3 73.7 - - - +
362D ALA* 1.3 60.9 + - - +
364D ILE* 3.9 13.3 - - + +
365D LYS* 2.9 31.2 + - - +
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Residues in contact with ALA 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D THR* 4.1 13.0 - - + -
204D LEU* 3.7 23.1 - - + -
206D ILE* 3.8 13.6 - - + +
326D PRO 4.9 4.9 - - - +
327D ILE* 4.9 3.8 - - + -
358D LEU* 2.9 18.5 + - + +
359D VAL* 3.6 7.0 - - - +
361D LEU* 1.3 75.6 - - - +
363D ASN* 1.3 62.2 + - - +
365D LYS* 3.5 2.3 + - - +
366D MET* 3.0 35.9 + - - +
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Residues in contact with ASN 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326D PRO 3.1 24.2 + - - -
329D PRO* 3.4 12.5 - - - +
330D VAL* 3.3 36.5 + - - +
352D VAL* 4.0 23.7 - - + +
359D VAL* 3.0 31.6 + - - +
360D VAL 3.6 7.2 - - - +
362D ALA* 1.3 75.6 - - - +
364D ILE* 1.3 65.0 + - + +
367D LEU* 3.1 40.1 + - + +
369D ILE* 4.2 2.5 - - + -
411D SER* 4.6 1.6 + - - -
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Residues in contact with ILE 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D TYR* 4.6 9.9 - - + -
352D VAL* 6.3 0.9 - - + -
360D VAL* 2.8 43.6 + - + +
361D LEU* 3.9 15.5 - - + +
363D ASN* 1.3 72.0 - - + +
365D LYS* 1.3 58.8 + - - +
368D GLU* 3.0 27.4 + - - -
369D ILE* 3.5 19.2 + - + +
371D PRO* 3.9 35.7 - - + -
374D VAL* 4.2 27.1 - - + -
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Residues in contact with LYS 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D LEU* 3.7 42.0 - - + +
205D ASN 5.0 3.4 + - - -
206D ILE* 3.8 20.0 - - + -
210D GLU* 4.9 13.4 + - - -
361D LEU 2.9 16.0 + - - +
362D ALA* 3.5 5.8 - - - +
364D ILE* 1.3 80.4 - - - +
366D MET* 1.3 65.5 - - + +
368D GLU* 3.4 17.2 + - - +
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Residues in contact with MET 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D LEU* 4.3 21.3 - - + -
327D ILE* 3.7 35.4 - - + -
330D VAL* 3.9 33.7 - - + +
331D TYR* 4.1 20.9 - - + +
344D LYS* 4.6 2.4 + - - -
362D ALA 3.0 18.3 + - - +
365D LYS* 1.3 79.5 - - + +
367D LEU* 1.3 61.9 + - - +
368D GLU* 4.2 8.8 - - - +
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Residues in contact with LEU 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330D VAL* 3.9 31.0 - - + +
333D ALA* 4.6 9.6 - - + -
334D SER* 4.0 16.8 - - - +
337D LEU* 5.7 3.4 - - + -
344D LYS* 2.8 43.3 + - - +
350D TRP* 4.3 22.0 - - + -
352D VAL* 5.8 1.8 - - + -
363D ASN* 3.1 38.5 + - + +
366D MET* 1.3 75.6 - - - +
368D GLU* 1.3 69.7 + - - +
369D ILE* 3.5 22.2 - - + -
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Residues in contact with GLU 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D LYS* 4.3 14.6 + - + +
345D GLU* 5.5 0.7 - - - +
364D ILE 3.0 13.7 + - - -
365D LYS 3.5 14.1 - - - +
366D MET 3.4 7.9 - - - +
367D LEU* 1.3 82.7 - - - +
369D ILE* 1.3 62.0 + - - +
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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