Contacts of the helix formed by residues 381 - 399 (chain A) in PDB entry 2H5G
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 GLU 381 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A THR 3.9 3.3 + - - +
380A LEU* 1.3 76.0 - - - +
382A PRO* 1.4 81.7 - - - +
383A GLU* 3.4 16.7 - - + +
384A GLN* 2.9 40.0 + - + +
385A ARG* 3.3 8.4 + - - +
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Residues in contact with PRO 382 (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 3.8 3.1 - - - +
381A GLU* 1.4 88.1 - - + +
383A GLU* 1.3 68.7 + - - +
385A ARG* 3.1 29.5 + - - +
386A ALA* 2.9 26.9 + - - +
447A SER* 5.1 1.9 + - - +
448A GLN* 3.2 48.3 - - + +
451A VAL 5.6 2.9 - - - +
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Residues in contact with GLU 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A GLU* 3.4 24.7 - - + +
382A PRO* 1.3 81.4 - - - +
384A GLN* 1.3 59.0 + - + +
386A ALA* 3.6 3.2 + - - +
387A GLU* 2.9 26.6 + - - +
448A GLN* 3.1 34.7 - - - +
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Residues in contact with GLN 384 (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* 3.8 18.7 - - + +
381A GLU* 2.9 46.2 + - + +
383A GLU* 1.3 77.0 - - + +
385A ARG* 1.3 64.0 + - - +
387A GLU* 3.2 7.2 + - - +
388A ILE* 3.1 28.2 + - - +
527A HIS* 3.5 42.7 + - + +
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Residues in contact with ARG 385 (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* 2.9 43.1 + - + +
378A ALA* 3.3 13.5 + - - -
380A LEU* 2.9 29.7 + - + -
381A GLU 3.3 0.6 + - - -
382A PRO* 3.1 38.0 + - - +
384A GLN* 1.3 75.5 - - - +
386A ALA* 1.3 64.1 + - - +
388A ILE* 3.3 11.9 + - - +
389A ILE* 3.2 27.5 + - - +
447A SER* 5.6 3.9 + - - +
448A GLN 5.2 0.8 + - - -
451A VAL* 3.8 31.4 + - - +
495A ILE* 3.2 31.5 + - + +
496A ALA* 4.2 13.7 + - - -
498A GLY 4.5 4.5 - - - +
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Residues in contact with ALA 386 (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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382A PRO 2.9 9.4 + - - +
383A GLU 3.6 9.2 - - - +
385A ARG* 1.3 74.9 - - - +
387A GLU* 1.3 57.1 + - - +
389A ILE* 3.0 6.8 + - - +
390A HIS* 2.8 28.6 + - - +
444A ALA* 3.5 38.0 - - + +
447A SER* 5.0 3.9 + - - +
448A GLN* 3.7 21.1 - - + +
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Residues in contact with GLU 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A GLU 2.9 17.7 + - - +
384A GLN* 3.4 10.6 - - - +
385A ARG 3.2 0.4 - - - -
386A ALA* 1.3 74.2 - - - +
388A ILE* 1.3 65.1 + - - +
390A HIS* 3.5 6.6 + - + +
391A HIS* 3.0 24.2 + - + +
526A ILE* 3.9 15.8 - - + +
527A HIS* 2.9 26.9 + - - +
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Residues in contact with ILE 388 (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* 4.2 10.8 - - + -
380A LEU* 4.0 14.8 - - + -
384A GLN 3.1 16.8 + - - +
385A ARG* 3.3 9.2 + - - +
387A GLU* 1.3 75.8 - - - +
389A ILE* 1.3 58.4 + - - +
391A HIS* 3.3 1.2 + - - +
392A LEU* 2.9 24.7 + - + +
495A ILE* 3.9 16.4 - - + -
523A ALA* 3.4 35.8 - - + +
524A LEU* 3.8 16.6 - - + +
526A ILE* 4.0 8.1 - - + -
527A HIS* 3.8 14.1 - - + -
529A VAL* 3.9 28.7 - - + -
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Residues in contact with ILE 389 (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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385A ARG 3.4 15.5 - - - +
386A ALA* 3.0 7.9 + - - +
388A ILE* 1.3 76.0 - - - +
390A HIS* 1.3 60.8 + - - +
392A LEU* 3.2 8.1 + - + +
393A ALA* 2.9 26.9 + - - +
440A LEU* 3.1 38.3 - - + +
443A ILE* 3.9 7.6 - - + -
444A ALA* 3.9 11.7 - - + +
447A SER* 4.9 1.1 - - - +
492A ALA* 3.4 37.5 - - + +
495A ILE* 3.8 13.9 - - + -
496A ALA* 3.6 26.5 - - + +
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Residues in contact with HIS 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ALA 2.8 16.4 + - - +
387A GLU* 3.9 7.2 - - - +
389A ILE* 1.3 74.1 - - - +
391A HIS* 1.3 64.6 + - - +
393A ALA* 3.2 6.3 + - - +
394A ASP* 3.0 45.5 + - - -
441A ARG* 3.8 37.3 - - + -
444A ALA* 4.2 8.8 - - + +
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Residues in contact with HIS 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A GLU* 3.0 17.9 + - + +
388A ILE 3.5 4.7 - - - +
390A HIS* 1.3 76.8 + - - +
392A LEU* 1.3 64.3 + - - +
394A ASP* 3.1 12.8 + - + +
395A LEU* 2.9 59.5 + - + +
522A GLU* 4.4 12.7 + - - +
523A ALA* 3.6 18.4 - - + -
526A ILE* 4.1 26.1 - - + +
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Residues in contact with LEU 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ILE* 2.9 14.6 + - + +
389A ILE* 3.2 10.3 + - - +
391A HIS* 1.3 75.4 - - - +
393A ALA* 1.3 65.8 + - - +
395A LEU* 3.1 4.7 + - + +
396A LEU* 3.0 36.2 + - + +
440A LEU* 3.5 21.5 - - + -
488A PRO* 4.3 18.4 - - + +
491A ALA* 4.9 0.2 - - + -
492A ALA* 4.8 8.7 - - + +
495A ILE* 5.3 4.3 - - + -
516A LEU 4.9 0.9 - - - +
519A LEU* 4.2 14.1 - - + +
520A THR* 4.0 47.8 - - + +
523A ALA* 3.8 9.4 - - + +
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Residues in contact with ALA 393 (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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389A ILE 2.9 13.2 + - - +
390A HIS* 3.5 8.5 - - - +
392A LEU* 1.3 76.7 - - - +
394A ASP* 1.3 62.2 + - - +
396A LEU* 3.3 17.2 + - - +
397A THR* 3.5 9.5 + - - -
437A ALA* 3.7 32.4 - - - +
440A LEU* 3.8 15.8 - - + +
441A ARG* 3.8 23.1 + - + +
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Residues in contact with ASP 394 (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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390A HIS* 3.0 38.8 + - - +
391A HIS* 3.5 14.3 + - + +
393A ALA* 1.3 75.7 - - - +
395A LEU* 1.3 54.1 + - + +
397A THR* 3.2 6.2 + - - -
398A ASP* 2.7 51.2 + - - +
441A ARG* 3.6 18.1 + - - +
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Residues in contact with LEU 395 (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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391A HIS* 2.9 44.3 + - + +
392A LEU* 3.1 9.8 + - + +
394A ASP* 1.3 76.0 - - + +
396A LEU* 1.3 58.5 + - - +
398A ASP* 4.4 9.2 - - + +
399A GLN* 2.9 49.7 + - + +
519A LEU* 3.3 44.5 - - + +
522A GLU* 3.7 30.5 - - + +
523A ALA 4.3 0.2 - - - +
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Residues in contact with LEU 396 (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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392A LEU* 3.0 29.0 + - + +
393A ALA* 3.5 9.2 - - - +
394A ASP 3.3 0.4 - - - -
395A LEU* 1.3 77.7 - - - +
397A THR* 1.3 60.0 + - - +
400A ARG* 3.5 11.8 + - - +
403A ILE* 3.5 23.8 - - + +
433A LEU* 4.3 26.2 - - + +
436A LEU* 3.9 26.9 - - + -
437A ALA* 4.1 7.9 - - + +
440A LEU* 4.0 25.1 - - + -
488A PRO* 4.2 11.9 - - + -
516A LEU* 3.8 28.0 - - + -
519A LEU* 4.7 3.4 - - + -
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Residues in contact with THR 397 (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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393A ALA 3.5 3.3 + - - -
394A ASP* 3.2 9.6 + - - -
396A LEU* 1.3 76.0 - - - +
398A ASP* 1.3 74.7 + - - +
400A ARG* 3.1 33.8 + - - +
433A LEU* 5.2 1.7 + - - -
434A ASN* 5.3 4.5 + - - -
437A ALA* 3.8 21.8 - - - +
441A ARG* 4.7 6.7 + - - -
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Residues in contact with ASP 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A ASP* 2.7 35.8 + - - +
395A LEU* 4.3 9.7 + - + +
397A THR* 1.3 80.7 - - - +
399A GLN* 1.3 72.4 + - - +
400A ARG* 3.5 2.9 + - - +
401A ASP* 5.0 1.2 + - - +
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Residues in contact with GLN 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A LEU* 2.9 29.8 + - + +
398A ASP* 1.3 89.3 + - - +
400A ARG* 1.3 65.1 + - - +
401A ASP 3.2 3.4 + - - -
402A GLU* 3.2 26.9 + - + +
403A ILE* 3.1 23.7 + - + +
515A ILE* 5.5 1.9 - - + +
519A LEU* 3.9 33.2 - - + +
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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
------------------------------------------------------------
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