Contacts of the helix formed by residues 351 - 365 (chain B) in PDB entry 2XGZ
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B ASP* 3.5 35.6 - - + +
93B LEU* 5.1 0.2 - - + -
94B ILE* 4.2 8.5 - - + -
102B LYS* 3.9 4.7 - - - -
110B ILE* 3.7 18.2 - - + -
111B LEU* 4.0 6.5 - - - +
114B SER* 3.7 4.7 - - - +
349B ILE* 3.6 3.3 - - - +
350B GLY* 1.3 84.4 - - - +
352B LEU* 1.3 65.3 + - - +
353B SER 3.9 0.2 + - - -
354B GLU* 2.8 40.2 + - - +
355B SER* 3.1 26.1 + - - -
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Residues in contact with LEU 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B GLN* 3.8 10.1 - - + +
111B LEU* 4.4 2.2 - - - +
114B SER* 3.0 19.3 + - - +
115B LEU* 4.1 11.2 - - + -
118B SER* 3.6 33.2 - - - +
133B LEU* 3.7 14.6 - - + -
136B LEU* 3.8 13.7 - - + -
346B VAL* 5.4 1.8 - - + -
351B THR* 1.3 69.8 - - - +
353B SER* 1.3 61.1 + - - +
355B SER* 3.0 9.4 + - - -
356B ILE* 2.9 45.5 + - + +
382B PHE* 3.7 24.0 - - + -
386B LEU* 3.9 24.0 - - + -
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Residues in contact with SER 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLN* 3.2 26.9 + - - +
87B LYS* 3.5 9.5 - - - -
90B ASP* 2.6 33.9 + - - +
91B ASP* 6.2 0.2 - - - -
351B THR 3.4 0.2 - - - -
352B LEU* 1.3 75.8 - - - +
354B GLU* 1.3 60.1 + - - +
356B ILE* 3.4 8.3 + - - +
357B LYS* 2.9 30.4 + - - +
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Residues in contact with GLU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ILE* 3.7 18.7 - - + +
102B LYS* 2.8 35.2 + - - -
327B PRO* 5.5 8.4 - - + +
349B ILE* 3.6 31.6 - - + +
351B THR* 2.8 25.1 + - - +
353B SER* 1.3 81.5 - - - +
355B SER* 1.3 55.9 + - - +
357B LYS* 3.7 7.2 - - - +
358B ALA* 2.9 29.1 + - - +
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Residues in contact with SER 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B THR* 5.3 0.2 - - - -
344B LEU* 3.3 23.5 - - - +
346B VAL* 3.3 35.5 - - - +
349B ILE* 3.3 18.7 - - - +
351B THR 3.1 16.6 + - - -
352B LEU* 3.0 14.9 + - - -
354B GLU* 1.3 73.1 - - - +
356B ILE* 1.3 66.8 + - - +
358B ALA* 3.3 4.2 + - - +
359B ALA* 3.1 18.4 + - - +
386B LEU* 5.3 1.3 - - - -
390B LEU* 5.5 0.9 - - - -
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Residues in contact with ILE 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLN* 5.7 0.7 - - + -
133B LEU* 4.6 7.0 - - + +
136B LEU* 3.7 35.2 - - + +
137B SER* 3.9 16.4 - - - +
352B LEU* 2.9 45.4 + - + +
353B SER* 3.6 7.2 - - - +
355B SER* 1.3 75.9 - - - +
357B LYS* 1.3 57.1 + - - +
359B ALA* 3.3 4.0 + - - +
360B GLN* 2.9 51.8 + - + +
386B LEU* 4.6 7.2 - - + -
390B LEU* 4.4 17.2 - - + +
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Residues in contact with LYS 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B SER 2.9 18.7 + - - +
354B GLU* 3.7 8.3 - - - +
356B ILE* 1.3 76.9 - - - +
358B ALA* 1.3 56.6 + - - +
360B GLN* 3.3 16.9 + - + +
361B ASP* 2.9 61.4 + - - +
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Residues in contact with ALA 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B THR* 4.6 13.5 - - + +
327B PRO* 5.5 7.6 - - + -
330B ILE* 3.8 27.7 - - + +
342B LEU* 3.9 7.9 - - + +
344B LEU* 4.7 0.2 - - + -
349B ILE* 6.0 0.2 - - + -
354B GLU 2.9 18.0 + - - +
355B SER* 3.6 7.9 - - - +
357B LYS* 1.3 75.1 - - - +
359B ALA* 1.3 61.5 + - - +
361B ASP* 3.5 8.2 + - - +
362B SER* 2.9 28.6 + - - -
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Residues in contact with ALA 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B LEU* 3.7 16.0 - - + +
355B SER 3.1 12.9 + - - +
356B ILE 3.4 8.7 - - - +
358B ALA* 1.3 76.6 - - - +
360B GLN* 1.3 57.2 + - - +
362B SER* 3.2 3.4 + - - -
363B PHE* 2.9 39.9 + - + -
369B VAL* 3.9 17.8 - - + +
390B LEU* 3.9 26.2 - - + -
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Residues in contact with GLN 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B LEU 4.1 3.8 + - - -
137B SER* 2.9 42.1 + - - +
138B LYS* 4.3 14.4 - - - +
356B ILE* 2.9 27.8 + - + +
357B LYS* 3.3 26.5 + - + +
359B ALA* 1.3 72.7 - - + +
361B ASP* 1.3 60.7 + - - +
363B PHE* 3.4 12.0 + - + +
364B ALA* 2.9 30.8 + - - +
390B LEU* 5.7 1.3 - - + -
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Residues in contact with ASP 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B PRO* 5.6 6.1 - - - +
330B ILE* 5.1 6.3 - - + -
334B ILE* 3.7 12.3 - - + +
357B LYS* 2.9 55.3 + - - +
358B ALA* 3.8 7.3 - - - +
360B GLN* 1.3 78.3 - - - +
362B SER* 1.3 59.7 + - - +
364B ALA* 3.5 7.8 + - - +
365B ALA* 3.3 21.5 + - - +
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Residues in contact with SER 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B ILE* 4.1 8.7 - - - +
334B ILE* 4.5 7.4 - - - +
342B LEU* 3.3 22.5 - - - +
358B ALA 2.9 15.3 + - - -
359B ALA 3.2 8.3 + - - -
361B ASP* 1.3 72.6 - - - +
363B PHE* 1.3 64.0 + - - +
365B ALA* 3.0 9.5 + - - -
367B TRP* 3.0 42.0 + - - +
368B GLY 4.2 1.6 - - - -
369B VAL* 3.7 17.3 - - - -
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Residues in contact with PHE 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B ALA* 2.9 34.9 + - + +
360B GLN* 3.7 11.2 - - + +
362B SER* 1.3 72.4 - - - +
364B ALA* 1.3 58.7 + - - +
366B GLY* 3.0 19.1 + - - -
367B TRP 3.5 13.9 - - - -
368B GLY* 4.4 0.9 - - - -
369B VAL* 3.4 33.2 - - + -
390B LEU* 3.4 29.8 - - + -
392B THR* 3.8 20.9 - - + -
434B ASP* 3.3 46.5 - - + +
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Residues in contact with ALA 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B GLN 2.9 22.9 + - - +
361B ASP* 3.7 9.4 - - - +
362B SER 3.2 0.2 - - - -
363B PHE* 1.3 72.8 - - - +
365B ALA* 1.3 58.3 + - - +
366B GLY 3.2 1.5 + - - -
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Residues in contact with ALA 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334B ILE* 3.6 47.1 - - + -
361B ASP 3.3 4.1 + - - +
362B SER 3.0 9.9 + - - +
364B ALA* 1.3 76.4 - - - +
366B GLY* 1.3 61.7 + - - +
367B TRP* 3.5 10.9 + - + -
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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