Contacts of the helix formed by residues 355 - 367 (chain A) in PDB entry 2XUG
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 SER 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A ILE* 1.3 79.3 - - - +
356A ARG* 1.3 58.9 + - - +
357A ALA* 3.3 10.7 + - - +
358A GLN* 3.0 36.5 + - - +
359A PHE* 2.9 27.2 + - - +
389A GLU 5.8 0.9 - - - -
394A LEU* 3.9 3.1 - - - -
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Residues in contact with ARG 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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355A SER* 1.3 74.2 - - - +
357A ALA* 1.3 56.3 + - - +
359A PHE* 3.2 8.2 + - + +
360A LEU* 3.0 29.4 + - + +
376A GLU* 5.5 0.2 + - - -
379A VAL* 3.4 21.8 - - - +
380A LEU* 4.9 1.4 - - - +
383A THR* 2.9 42.6 + - - +
385A TRP* 4.0 15.0 - - - -
388A PRO* 3.2 29.4 + - - +
389A GLU* 3.8 22.6 - - - +
394A LEU* 3.7 28.2 - - + +
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Residues in contact with ALA 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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355A SER* 3.3 8.4 + - - +
356A ARG* 1.3 77.8 - - - +
358A GLN* 1.3 60.0 + - + +
360A LEU* 3.4 7.4 + - - +
361A ALA* 3.0 29.0 + - - +
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Residues in contact with GLN 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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343A VAL* 4.7 5.5 - - - +
344A PRO* 4.4 14.3 + - + +
345A GLY* 4.0 18.7 - - - +
353A LEU 4.4 2.1 - - - +
354A ILE* 3.4 28.4 - - + +
355A SER* 3.0 37.7 + - - +
357A ALA* 1.3 78.0 - - + +
359A PHE* 1.3 57.4 + - - +
361A ALA* 3.8 6.3 - - - +
362A GLY* 2.9 25.5 + - - -
398A MET* 5.1 0.2 - - - +
1542A NAG 5.2 5.5 + - - -
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Residues in contact with PHE 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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354A ILE* 4.0 9.6 - - + +
355A SER 2.9 13.6 + - - +
356A ARG* 3.2 13.0 + - + +
358A GLN* 1.3 74.3 - - - +
360A LEU* 1.3 66.7 + - - +
362A GLY* 3.2 1.6 + - - -
363A VAL* 3.0 46.0 + - + +
379A VAL* 4.1 37.2 - - + -
382A TYR* 4.0 15.5 - - + -
383A THR* 4.5 5.2 - - - -
394A LEU* 3.7 39.9 - - + -
397A ALA* 3.9 17.3 - - + -
398A MET* 3.7 34.3 - - + -
401A VAL* 4.3 2.9 - - + -
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Residues in contact with LEU 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ARG* 3.0 15.5 + - + +
357A ALA* 3.9 5.6 - - - +
359A PHE* 1.3 76.6 - - - +
361A ALA* 1.3 62.8 + - - +
363A VAL* 3.3 10.0 + - + +
364A ARG* 3.4 31.1 + - + +
375A ALA* 4.8 7.4 - - + -
376A GLU* 4.5 16.2 - - - +
379A VAL* 4.4 26.2 - - + -
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Residues in contact with ALA 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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344A PRO* 5.7 7.9 - - + -
357A ALA 3.0 17.3 + - - +
358A GLN* 3.8 7.0 - - - +
360A LEU* 1.3 77.4 - - - +
362A GLY* 1.3 63.1 + - - +
363A VAL 3.5 0.2 + - - -
364A ARG* 3.5 10.0 + - - +
365A ILE* 3.5 29.4 + - + +
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Residues in contact with GLY 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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343A VAL* 3.6 30.1 - - - +
344A PRO* 5.7 0.2 - - - +
358A GLN 2.9 13.1 + - - -
359A PHE 3.2 0.4 + - - -
361A ALA* 1.3 76.3 - - - +
363A VAL* 1.3 58.3 + - - +
365A ILE* 3.1 6.0 + - - +
366A GLY 2.8 25.5 + - - -
398A MET* 3.4 20.9 - - - +
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Residues in contact with VAL 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 PHE* 3.0 44.9 + - + +
360A LEU 3.7 6.3 - - - +
361A ALA 3.3 0.4 - - - -
362A GLY* 1.3 75.9 - - - +
364A ARG* 1.3 57.7 + - - +
367A VAL* 2.8 37.2 + - + +
375A ALA* 3.9 28.0 - - + +
378A VAL* 3.7 29.8 - - + -
379A VAL* 3.8 15.0 - - + -
398A MET* 4.1 9.6 - - + -
401A VAL* 4.7 2.5 - - + -
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Residues in contact with ARG 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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292A GLU 4.4 2.1 - - - +
360A LEU* 3.4 24.6 + - + +
361A ALA* 3.7 10.3 - - - +
362A GLY 3.3 0.2 - - - -
363A VAL* 1.3 79.0 - - - +
365A ILE* 1.3 59.0 + - + +
367A VAL 3.7 4.4 + - - +
368A PRO* 3.3 25.9 + - - +
370A ALA 2.9 27.5 + - - -
371A SER 3.7 6.1 + - - -
372A ASP* 2.9 46.8 + - - +
375A ALA* 3.5 22.2 - - - +
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Residues in contact with ILE 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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292A GLU* 3.8 41.7 - - + +
293A SER* 3.4 27.8 - - - +
294A ILE* 3.3 25.6 + - + +
342A GLY* 3.9 8.7 - - - +
343A VAL* 4.5 5.8 - - + -
344A PRO* 3.8 25.8 - - + -
361A ALA* 3.6 17.7 - - + +
362A GLY* 3.1 7.9 + - - +
364A ARG* 1.3 78.8 - - + +
366A GLY* 1.3 64.1 + - - +
367A VAL 3.3 0.4 - - - -
368A PRO* 3.3 12.6 - - - +
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Residues in contact with GLY 366 (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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294A ILE* 4.0 21.1 - - - +
296A ARG* 4.5 0.9 + - - -
362A GLY 2.8 15.3 + - - -
363A VAL 3.9 0.9 - - - -
365A ILE* 1.3 77.3 - - - +
367A VAL* 1.3 63.2 + - - +
368A PRO* 3.3 6.8 - - - +
398A MET* 4.6 2.0 - - - -
401A VAL* 5.3 0.9 - - - -
402A VAL* 4.2 15.2 - - - +
405A HIS* 3.6 17.2 - - - +
406A ASN* 4.4 8.1 + - - -
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Residues in contact with VAL 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ARG* 5.6 0.2 - - - +
363A VAL* 2.8 27.5 + - + +
364A ARG* 3.7 8.2 + - - +
366A GLY* 1.3 82.2 - - - +
368A PRO* 1.3 64.7 - - - +
369A GLN* 3.2 3.6 - - + +
370A ALA* 3.1 35.9 + - + +
375A ALA* 6.1 0.2 - - - -
378A VAL* 4.4 5.6 - - + -
401A VAL* 4.0 14.8 - - + -
405A HIS* 3.9 21.8 - - + +
532A TRP* 4.0 32.1 - - + -
536A LEU* 4.9 5.2 - - + -
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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