Contacts of the helix formed by residues 351 - 365 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A ASP* 3.5 35.6 - - + +
93A LEU* 5.1 0.2 - - + -
94A ILE* 4.2 8.5 - - + +
102A LYS* 4.0 5.2 - - - -
110A ILE* 3.7 18.6 - - + -
111A LEU* 4.1 6.1 - - - -
114A SER* 3.6 3.6 - - - +
349A ILE* 3.6 4.4 - - - +
350A GLY* 1.3 84.0 - - - +
352A LEU* 1.3 62.7 + - - +
353A SER 3.9 0.2 + - - -
354A GLU* 2.7 42.0 + - - +
355A SER* 3.0 27.4 + - - -
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Residues in contact with LEU 352 (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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86A GLN* 3.7 16.4 - - + +
111A LEU* 4.4 2.6 - - - +
114A SER* 3.0 19.3 + - - +
115A LEU* 4.2 11.2 - - + -
118A SER* 3.5 33.9 - - - +
133A LEU* 3.8 13.2 - - + -
136A LEU* 3.9 7.2 - - + -
346A VAL* 4.7 8.1 - - + -
351A THR* 1.3 71.4 - - - +
353A SER* 1.3 58.0 + - - +
355A SER* 3.1 7.1 + - - -
356A ILE* 2.8 43.7 + - + +
382A PHE* 3.8 25.8 - - + -
386A LEU* 3.9 18.8 - - + -
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Residues in contact with SER 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLN* 3.2 27.5 + - - +
87A LYS* 3.5 17.7 + - - +
90A ASP* 2.7 37.4 + - - -
351A THR* 3.4 0.6 - - - -
352A LEU* 1.3 72.4 - - - +
354A GLU* 1.3 58.6 + - - +
356A ILE* 3.3 8.8 + - - +
357A LYS* 2.9 29.1 + - - +
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Residues in contact with GLU 354 (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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94A ILE* 3.8 18.3 - - + +
102A LYS* 2.7 36.0 + - - -
327A PRO* 3.9 11.5 - - + +
349A ILE* 3.6 32.4 - - + +
351A THR* 2.7 24.5 + - - +
353A SER* 1.3 77.8 - - - +
355A SER* 1.3 56.9 + - - +
357A LYS* 3.4 7.8 + - - +
358A ALA* 2.9 28.2 + - - +
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Residues in contact with SER 355 (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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325A THR* 4.0 7.5 - - - +
344A LEU* 3.6 20.4 - - - +
346A VAL* 3.3 35.1 - - - +
349A ILE* 3.3 16.4 - - - +
351A THR 3.0 15.2 + - - -
352A LEU* 3.1 12.5 + - - -
354A GLU* 1.3 75.3 - - - +
356A ILE* 1.3 63.8 + - - +
358A ALA* 3.3 4.0 + - - +
359A ALA 3.1 17.5 + - - -
386A LEU* 5.6 0.9 - - - -
390A LEU* 6.0 0.2 - - - -
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Residues in contact with ILE 356 (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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86A GLN* 5.3 1.3 - - + -
133A LEU* 4.9 4.3 - - + +
136A LEU* 3.8 34.3 - - + +
137A SER* 3.9 18.6 - - - +
352A LEU* 2.8 45.9 + - + +
353A SER* 3.7 7.9 - - - +
355A SER* 1.3 71.4 - - - +
357A LYS* 1.3 61.5 + - - +
359A ALA* 3.2 8.2 + - - +
360A GLN* 2.9 52.5 + - + +
386A LEU* 4.9 4.3 - - + -
390A LEU* 4.3 14.1 - - + -
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Residues in contact with LYS 357 (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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327A PRO* 4.0 16.4 - - + +
353A SER 2.9 17.6 + - - +
354A GLU* 3.5 9.4 - - - +
356A ILE* 1.3 77.2 - - - +
358A ALA* 1.3 56.6 + - - +
360A GLN* 3.2 16.6 + - + +
361A ASP* 2.8 65.7 + - - +
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Residues in contact with ALA 358 (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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325A THR* 3.7 19.1 - - + +
327A PRO* 4.1 8.0 - - + +
330A ILE* 3.5 27.1 - - + +
342A LEU* 3.7 10.4 - - + +
354A GLU 2.9 15.3 + - - +
355A SER 3.4 9.9 - - - +
357A LYS* 1.3 74.7 - - - +
359A ALA* 1.3 56.6 + - - +
361A ASP* 3.6 4.1 + - - +
362A SER* 2.8 33.1 + - - -
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Residues in contact with ALA 359 (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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342A LEU* 4.1 2.8 - - - +
344A LEU* 3.7 22.2 - - + -
355A SER 3.1 7.1 + - - +
356A ILE 3.5 7.9 - - - +
358A ALA* 1.3 73.6 - - - +
360A GLN* 1.3 61.1 + - + +
362A SER* 3.2 2.9 + - - -
363A PHE* 2.9 42.0 + - + -
369A VAL* 4.0 17.4 - - + +
390A LEU* 4.2 21.1 - - + -
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Residues in contact with GLN 360 (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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87A LYS* 5.8 2.6 + - - +
136A LEU 4.2 3.4 + - - -
137A SER* 3.0 40.4 + - - +
138A LYS* 4.5 13.7 - - - +
356A ILE* 2.9 29.4 + - + +
357A LYS* 3.7 18.9 - - + +
359A ALA* 1.3 77.6 - - + +
361A ASP* 1.3 60.1 + - - +
363A PHE* 3.5 9.5 + - + +
364A ALA* 3.0 30.2 + - - +
390A LEU* 6.2 0.2 - - + -
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Residues in contact with ASP 361 (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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327A PRO* 3.8 17.8 - - - +
330A ILE* 4.6 11.9 - - + -
334A ILE* 3.8 8.6 - - + +
357A LYS* 2.8 53.2 + - - +
358A ALA* 3.9 4.5 - - - +
360A GLN* 1.3 78.6 - - - +
362A SER* 1.3 61.4 + - - +
364A ALA* 3.4 7.9 + - - +
365A ALA* 3.3 21.7 + - - +
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Residues in contact with SER 362 (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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330A ILE* 3.8 14.1 - - - +
334A ILE* 4.7 1.3 - - - -
342A LEU* 3.5 19.2 - - - +
358A ALA 2.8 19.3 + - - -
359A ALA 3.4 7.6 - - - -
361A ASP* 1.3 73.4 - - - +
363A PHE* 1.3 66.2 + - - +
365A ALA* 3.0 9.5 + - - +
367A TRP* 2.9 47.1 + - - +
369A VAL* 3.9 15.3 - - - -
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Residues in contact with PHE 363 (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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359A ALA* 2.9 36.3 + - + +
360A GLN* 3.9 9.6 - - + +
362A SER* 1.3 72.7 - - - +
364A ALA* 1.3 61.9 + - - +
366A GLY 3.1 7.8 + - - -
367A TRP 3.4 14.4 - - - -
368A GLY* 4.4 0.9 - - - -
369A VAL* 3.5 39.3 - - + -
390A LEU* 3.6 25.1 - - + -
392A THR* 3.9 14.8 - - + -
434A ASP* 3.3 47.6 - - + +
435A LYS* 3.1 24.9 + - - +
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Residues in contact with ALA 364 (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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360A GLN 3.0 17.9 + - - +
361A ASP* 3.6 8.7 - - - +
362A SER 3.2 0.2 - - - -
363A PHE* 1.3 76.4 - - - +
365A ALA* 1.3 58.7 + - - +
366A GLY 3.2 0.8 + - - -
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Residues in contact with ALA 365 (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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334A ILE* 3.5 48.7 - - + -
361A ASP 3.3 3.5 + - - +
362A SER 3.0 8.6 + - - +
364A ALA* 1.3 75.6 - - - +
366A GLY* 1.3 61.1 + - - +
367A TRP* 3.3 11.3 + - + -
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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