Contacts of the helix formed by residues 351 - 365 (chain D) in PDB entry 2XH2
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 THR 351 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90D ASP* 3.6 33.4 - - + +
93D LEU* 5.1 0.7 - - + -
94D ILE* 4.2 9.4 - - + +
102D LYS* 3.9 5.4 - - - -
110D ILE* 3.8 17.9 - - + -
111D LEU* 4.2 7.0 - - - -
114D SER* 3.7 4.3 - - - +
349D ILE* 3.6 4.0 + - - +
350D GLY* 1.3 81.8 - - - +
352D LEU* 1.3 63.0 + - - +
354D GLU* 2.7 40.5 + - - +
355D SER* 2.9 28.8 + - - -
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Residues in contact with LEU 352 (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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86D GLN* 3.8 17.3 - - + +
111D LEU* 4.5 2.0 - - - +
114D SER* 3.0 19.3 + - - +
115D LEU* 4.1 11.2 - - + -
118D SER* 3.6 33.0 - - - +
133D LEU* 3.7 16.2 - - + -
136D LEU* 4.0 3.8 - - + -
346D VAL* 5.4 1.8 - - + -
351D THR* 1.3 69.8 - - - +
353D SER* 1.3 60.4 + - - +
355D SER* 3.1 9.4 + - - -
356D ILE* 2.8 44.4 + - + +
382D PHE* 3.9 25.1 - - + -
386D LEU* 4.0 19.1 - - + -
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Residues in contact with SER 353 (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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86D GLN* 3.2 26.6 + - - +
87D LYS* 3.5 17.2 + - - +
90D ASP* 2.6 34.7 + - - -
94D ILE* 6.3 0.2 - - - -
351D THR* 3.3 0.8 - - - -
352D LEU* 1.3 75.8 - - - +
354D GLU* 1.3 59.9 + - - +
356D ILE* 3.3 8.9 + - - +
357D LYS* 2.9 29.2 + - - +
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Residues in contact with GLU 354 (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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94D ILE* 3.6 20.2 - - + +
102D LYS* 2.8 34.1 + - - -
327D PRO* 5.6 3.0 - - + +
349D ILE* 3.4 35.0 - - + +
351D THR* 2.7 24.8 + - - +
353D SER* 1.3 80.4 - - - +
355D SER* 1.3 57.3 + - - +
357D LYS* 3.4 8.2 + - + +
358D ALA* 3.0 28.6 + - - +
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Residues in contact with SER 355 (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 THR* 5.4 0.2 - - - -
344D LEU* 3.6 19.7 - - - +
346D VAL* 3.5 34.1 - - - +
349D ILE* 3.3 18.3 - - - +
351D THR 2.9 19.6 + - - -
352D LEU* 3.1 13.4 + - - -
354D GLU* 1.3 75.2 - - - +
356D ILE* 1.3 64.6 + - - +
358D ALA* 3.3 7.1 + - - +
359D ALA* 3.1 17.8 + - - +
386D LEU* 5.4 2.5 - - - -
390D LEU* 5.7 0.9 - - - -
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Residues in contact with ILE 356 (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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86D GLN* 5.5 1.6 - - + -
133D LEU* 4.9 4.7 - - + +
136D LEU* 3.8 35.2 - - + +
137D SER* 3.8 17.9 - - - +
352D LEU* 2.8 45.0 + - + +
353D SER* 3.7 8.1 - - - +
355D SER* 1.3 77.7 - - - +
357D LYS* 1.3 62.3 + - - +
359D ALA* 3.2 4.2 + - - +
360D GLN* 3.0 46.9 + - + +
386D LEU* 4.9 4.5 - - + -
390D LEU* 4.3 18.2 - - + -
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Residues in contact with LYS 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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327D PRO* 6.4 2.2 - - + +
353D SER 2.9 16.5 + - - +
354D GLU* 3.7 9.0 - - + +
355D SER 3.3 0.2 - - - -
356D ILE* 1.3 78.2 - - - +
358D ALA* 1.3 56.6 + - - +
360D GLN* 3.2 14.5 + - + +
361D ASP* 2.9 56.5 + - - +
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Residues in contact with ALA 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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325D THR* 4.7 10.8 - - + -
327D PRO* 5.7 4.5 - - + -
330D ILE* 4.0 25.5 - - + +
342D LEU* 3.9 9.6 - - + +
344D LEU* 4.8 0.7 - - + -
349D ILE* 4.9 5.4 - - + -
354D GLU 3.0 17.2 + - - +
355D SER* 3.3 8.5 + - - +
357D LYS* 1.3 76.9 - - - +
359D ALA* 1.3 61.3 - - - +
361D ASP* 3.7 7.1 + - - +
362D SER* 2.8 28.6 + - - -
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Residues in contact with ALA 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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344D LEU* 3.7 22.8 - - + +
355D SER 3.1 7.7 + - - +
356D ILE 3.6 7.9 - - - +
358D ALA* 1.3 74.2 - - - +
360D GLN* 1.3 59.3 + - - +
362D SER* 3.2 3.3 + - - -
363D PHE* 2.8 43.5 + - + -
369D VAL* 4.0 17.7 - - + -
390D LEU* 4.0 24.5 - - + -
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Residues in contact with GLN 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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136D LEU 4.4 3.0 + - - -
137D SER* 2.9 40.2 + - - +
138D LYS* 4.6 7.3 - - - +
356D ILE* 3.0 29.0 + - + +
357D LYS* 3.6 16.2 - - + +
359D ALA* 1.3 76.0 - - + +
361D ASP* 1.3 61.1 + - - +
363D PHE* 3.3 11.7 + - + +
364D ALA* 2.9 30.0 + - - +
390D LEU* 5.8 1.3 - - + -
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Residues in contact with ASP 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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327D PRO* 5.7 4.9 - - - +
330D ILE* 5.3 5.2 - - + -
334D ILE* 3.9 12.2 - - + +
357D LYS* 2.9 53.3 + - - +
358D ALA* 4.0 6.7 - - - +
360D GLN* 1.3 79.4 - - - +
362D SER* 1.3 63.2 + - - +
364D ALA* 3.5 8.9 + - - +
365D ALA* 3.3 19.2 + - - +
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Residues in contact with SER 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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330D ILE* 4.0 9.5 - - - +
334D ILE* 4.5 8.0 - - - +
342D LEU* 3.6 19.1 - - - +
358D ALA 2.8 19.6 + - - -
359D ALA 3.2 8.0 + - - -
361D ASP* 1.3 72.7 - - - +
363D PHE* 1.3 64.6 - - - +
365D ALA* 2.9 12.6 + - - -
367D TRP* 3.0 38.2 + - - +
368D GLY 4.3 1.6 - - - -
369D VAL* 3.7 17.7 - - - -
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Residues in contact with PHE 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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359D ALA* 2.8 36.4 + - + +
360D GLN* 3.7 11.2 - - + +
362D SER* 1.3 71.2 - - - +
364D ALA* 1.3 57.4 + - - +
366D GLY 3.0 11.4 + - - -
367D TRP 3.5 15.0 - - - -
368D GLY* 4.4 1.6 - - - -
369D VAL* 3.6 28.0 - - + -
390D LEU* 3.5 29.6 - - + -
392D THR* 3.8 25.8 - - + -
431D HIS 5.7 0.2 - - - -
434D ASP* 3.4 43.1 - - + +
435D LYS* 2.8 25.5 + - - +
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Residues in contact with ALA 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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360D GLN 2.9 17.2 + - - +
361D ASP* 3.5 11.7 - - - +
362D SER 3.2 0.2 - - - -
363D PHE* 1.3 75.9 - - - +
365D ALA* 1.3 58.6 + - - +
366D GLY 3.2 2.8 + - - -
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Residues in contact with ALA 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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334D ILE* 3.7 45.5 - - + -
361D ASP 3.3 2.4 + - - +
362D SER 2.9 10.3 + - - +
364D ALA* 1.3 76.5 - - - +
366D GLY* 1.3 58.2 + - - +
367D TRP* 3.2 14.3 + - + -
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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