Contacts of the helix formed by residues 419 - 432 (chain A) in PDB entry 4XHS
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 GLY 419 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A LEU* 4.6 3.6 - - - -
417A LYS 3.5 3.2 + - - -
418A ALA* 1.3 74.6 - - - +
420A PRO* 1.3 72.6 - - - +
421A LEU 3.3 2.9 - - - -
422A GLU* 3.3 2.4 + - - +
423A MET* 2.9 28.8 + - - +
503A FMT 3.3 19.0 + - - -
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Residues in contact with PRO 420 (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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381A SER* 3.8 3.0 + - - +
384A LEU* 3.5 24.2 - - + +
385A GLU* 3.5 51.6 - - + +
392A LEU* 4.5 13.0 - - + -
419A GLY* 1.3 82.7 - - - +
421A LEU* 1.3 58.0 + - - +
423A MET* 3.4 4.4 + - + -
424A ALA* 3.0 24.8 + - - +
503A FMT 3.4 9.2 - - - +
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Residues in contact with LEU 421 (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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377A LEU* 3.9 26.9 - - + -
381A SER* 3.3 27.3 + - - +
385A GLU* 5.4 2.0 - - - +
420A PRO* 1.3 75.6 - - - +
422A GLU* 1.3 62.3 + - - +
424A ALA* 3.2 2.4 + - - +
425A GLN* 2.9 27.0 + - + +
503A FMT 2.9 18.0 + - - +
371B ARG* 3.6 23.3 - - + -
374B ALA* 4.1 4.0 - - + -
375B ALA* 3.5 40.2 - - + +
378B CYS* 4.6 9.9 - - + -
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Residues in contact with GLU 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A SER 3.7 15.1 - - - +
417A LYS* 4.7 2.3 - - - +
418A ALA* 3.3 31.3 + - + -
419A GLY 3.8 0.9 + - - +
421A LEU* 1.3 76.5 - - - +
423A MET* 1.3 57.8 + - - +
425A GLN* 3.2 12.2 + - - +
426A LEU* 2.9 39.0 + - + +
503A FMT 2.9 16.8 + - - +
364B ALA* 6.2 0.2 - - - +
367B THR* 4.7 2.9 - - + +
368B ASN* 3.1 24.0 + - - +
371B ARG* 3.2 28.1 + - - +
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Residues in contact with MET 423 (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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384A LEU* 3.8 14.4 - - + -
392A LEU* 4.3 9.6 - - + -
395A PHE* 4.2 9.2 - - + -
396A LYS* 4.1 24.0 - - + -
399A LEU* 3.6 31.6 - - + -
410A ILE* 5.8 0.7 - - + -
415A MET* 3.9 31.0 - - + -
418A ALA* 3.8 20.4 - - + +
419A GLY 2.9 19.4 + - - +
420A PRO* 3.6 6.5 - - + +
422A GLU* 1.3 78.3 - - - +
424A ALA* 1.3 61.6 + - - +
426A LEU* 3.3 8.9 + - + +
427A LEU* 3.0 30.4 + - + +
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Residues in contact with ALA 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU* 3.6 16.6 - - + -
380A LEU* 3.8 21.1 - - + -
381A SER* 3.6 28.9 - - - +
384A LEU* 3.7 2.4 - - + +
420A PRO 3.0 12.8 + - - +
421A LEU 3.2 8.3 + - - +
423A MET* 1.3 77.1 - - - +
425A GLN* 1.3 61.9 + - - +
427A LEU* 3.8 0.5 - - - +
428A ILE* 3.1 29.5 + - - +
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Residues in contact with GLN 425 (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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180A LYS* 5.7 3.2 - - - +
373A PHE* 5.7 4.0 - - + -
377A LEU* 3.6 23.5 - - + +
421A LEU* 2.9 16.9 + - + +
422A GLU* 3.4 8.0 - - - +
424A ALA* 1.3 77.4 - - - +
426A LEU* 1.3 57.4 + - - +
428A ILE* 4.0 1.9 - - - +
429A THR* 2.9 40.6 + - + +
367B THR* 3.1 38.0 + - + +
370B ALA* 4.3 5.9 + - - +
371B ARG* 2.9 56.1 + - - +
374B ALA* 4.5 6.3 - - - +
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Residues in contact with LEU 426 (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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410A ILE* 4.1 17.0 - - + -
414A SER* 3.5 31.2 - - - +
415A MET* 4.1 10.3 - - + -
418A ALA* 4.4 0.4 - - + -
422A GLU* 2.9 33.0 + - + +
423A MET* 3.3 24.9 + - + +
425A GLN* 1.3 73.7 - - - +
427A LEU* 1.3 67.4 + - + +
429A THR* 3.6 5.6 - - - +
430A HIS* 3.0 46.7 + - + +
364B ALA* 5.7 9.9 - - + -
367B THR* 4.8 15.3 - - + +
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Residues in contact with LEU 427 (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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380A LEU* 3.9 17.5 - - + -
384A LEU* 4.4 7.0 - - + -
395A PHE* 3.9 29.2 - - + -
399A LEU* 3.6 29.8 - - + -
410A ILE* 4.2 4.3 - - + -
423A MET* 3.0 22.4 + - + +
424A ALA 3.8 3.6 - - - +
426A LEU* 1.3 77.2 - - - +
428A ILE* 1.3 59.3 + - - +
431A PHE* 2.9 58.3 + - + +
436A ALA* 3.6 24.1 - - + +
439A LEU* 5.1 4.9 - - + -
440A ALA* 4.6 2.2 - - + -
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Residues in contact with ILE 428 (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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176A LYS* 4.5 1.4 + - - -
179A ILE* 5.4 0.9 - - + -
373A PHE* 3.6 29.4 - - + -
376A ALA* 3.7 15.3 - - + +
377A LEU* 3.6 40.4 - - + +
380A LEU* 3.9 10.1 - - + -
424A ALA 3.1 17.2 + - - +
425A GLN* 4.1 1.8 - - - +
427A LEU* 1.3 73.7 - - - +
429A THR* 1.3 62.2 + - - +
432A GLY* 2.8 26.3 + - - -
433A PRO* 4.1 24.5 - - + +
436A ALA* 3.9 19.5 - - + -
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Residues in contact with THR 429 (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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176A LYS* 2.8 23.2 + - - +
180A LYS* 5.8 5.6 - - + +
373A PHE* 4.8 17.3 - - + -
425A GLN* 2.9 28.5 + - + +
426A LEU* 3.2 11.3 + - - +
428A ILE* 1.3 76.9 - - - +
430A HIS* 1.3 68.0 + - - +
367B THR* 4.3 17.3 + - - +
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Residues in contact with HIS 430 (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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174A ALA* 6.0 0.3 - - - +
176A LYS* 3.2 13.8 - - - -
410A ILE* 3.6 46.9 - - + +
411A PRO* 4.8 6.0 - - + +
414A SER* 6.3 0.4 - - - -
426A LEU* 3.0 37.3 + - + +
429A THR* 1.3 87.9 + - - +
431A PHE* 1.3 73.9 + + + +
363B ALA* 6.3 3.1 - - + -
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Residues in contact with PHE 431 (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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176A LYS* 3.8 11.1 - - - +
399A LEU* 5.3 5.6 - - + -
403A THR* 4.0 28.7 - - + -
410A ILE* 3.6 35.7 - - + -
427A LEU* 2.9 36.0 + - + +
430A HIS* 1.3 86.5 - + + +
432A GLY* 1.3 62.9 + - - +
435A GLU* 3.3 33.9 - - + +
436A ALA* 4.1 3.6 - - - +
439A LEU* 3.7 27.8 - - + -
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Residues in contact with GLY 432 (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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176A LYS* 3.7 13.9 - - - +
177A TYR 5.4 2.0 - - - -
428A ILE* 2.8 20.1 + - - -
431A PHE* 1.3 79.5 - - - +
433A PRO* 1.3 70.3 - - - +
434A GLU* 3.5 2.0 - - - -
436A ALA* 3.0 30.1 + - - +
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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