Contacts of the helix formed by residues 381 - 399 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379B THR 3.9 5.9 + - - +
380B LEU* 1.3 78.0 - - - +
382B PRO* 1.3 80.5 - - - +
383B GLU* 3.4 14.8 - - + +
384B GLN* 2.9 38.0 + - + +
385B ARG* 3.4 8.8 + - - +
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Residues in contact with PRO 382 (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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380B LEU 4.3 1.8 - - - +
381B GLU* 1.3 92.0 - - + +
383B GLU* 1.3 67.8 + - - +
385B ARG* 3.1 30.4 + - - +
386B ALA* 3.0 26.9 + - - +
447B SER* 5.0 2.0 + - - +
448B GLN* 3.2 47.2 - - + +
451B VAL 5.5 3.1 - - - +
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Residues in contact with GLU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B GLU* 3.4 22.8 - - + +
382B PRO* 1.3 80.3 - - - +
384B GLN* 1.3 58.3 + - + +
386B ALA* 3.6 2.9 - - - +
387B GLU* 3.0 27.3 + - - +
448B GLN* 3.2 35.3 - - - +
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Residues in contact with GLN 384 (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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380B LEU* 3.8 22.3 - - + +
381B GLU* 2.9 45.7 + - + +
383B GLU* 1.3 76.7 - - + +
385B ARG* 1.3 63.7 + - - +
387B GLU* 3.3 7.2 - - - +
388B ILE* 3.1 20.3 + - - +
527B HIS* 3.3 52.2 + - + +
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Residues in contact with ARG 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B LEU* 3.0 39.5 + - + +
378B ALA* 3.3 13.5 + - - +
380B LEU* 2.9 30.2 + - + -
381B GLU 3.4 2.4 + - - +
382B PRO* 3.1 38.4 + - - +
384B GLN* 1.3 76.4 - - - +
386B ALA* 1.3 64.0 + - - +
388B ILE* 3.2 11.6 + - - +
389B ILE* 3.2 27.7 + - - +
447B SER* 5.5 4.6 + - - +
448B GLN 5.1 0.8 + - - -
451B VAL* 3.7 31.5 + - - +
495B ILE* 3.1 32.1 - - + +
496B ALA* 4.1 14.3 + - - -
498B GLY 4.4 4.5 - - - +
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Residues in contact with ALA 386 (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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382B PRO 3.0 13.1 + - - +
383B GLU 3.6 9.0 - - - +
385B ARG* 1.3 74.3 - - - +
387B GLU* 1.3 57.2 + - - +
389B ILE* 3.0 7.5 + - - +
390B HIS* 2.8 31.8 + - - +
444B ALA* 3.5 37.1 - - + +
447B SER* 4.9 3.5 + - - +
448B GLN* 3.8 17.0 - - + +
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Residues in contact with GLU 387 (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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383B GLU 3.0 18.2 + - - +
384B GLN* 3.3 10.5 - - - +
386B ALA* 1.3 77.5 - - - +
388B ILE* 1.3 61.7 + - - +
390B HIS* 3.3 6.3 + - + +
391B HIS* 3.0 24.7 + - + +
526B ILE* 3.8 17.3 - - + +
527B HIS* 2.9 28.8 + - - +
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Residues in contact with ILE 388 (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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377B LEU* 4.0 15.0 - - + -
380B LEU* 4.0 5.2 - - + -
384B GLN 3.1 15.5 + - - +
385B ARG* 3.2 9.8 + - - +
387B GLU* 1.3 74.3 - - - +
389B ILE* 1.3 60.2 + - - +
391B HIS* 3.3 1.2 + - - +
392B LEU* 3.0 24.8 + - + +
495B ILE* 4.0 17.7 - - + -
523B ALA* 3.4 19.8 - - + +
524B LEU* 3.8 34.1 - - + +
526B ILE* 3.9 8.1 - - + -
527B HIS* 3.8 19.1 - - + -
529B VAL* 3.8 28.7 - - + -
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Residues in contact with ILE 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B ARG 3.4 16.4 - - - +
386B ALA* 3.0 7.5 + - - +
388B ILE* 1.3 79.8 - - - +
390B HIS* 1.3 55.8 + - - +
392B LEU* 3.3 8.0 + - - +
393B ALA* 2.9 27.2 + - - +
440B LEU* 3.2 37.8 - - + +
443B ILE* 3.8 8.5 - - + -
444B ALA* 3.9 11.0 - - + +
447B SER* 4.8 1.3 - - - +
492B ALA* 3.5 37.0 - - + +
495B ILE* 3.7 14.8 - - + -
496B ALA* 3.6 27.1 - - + +
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Residues in contact with HIS 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B ALA 2.8 20.0 + - - +
387B GLU* 3.7 8.3 - - + +
389B ILE* 1.3 75.3 - - - +
391B HIS* 1.3 56.5 + - - +
393B ALA* 3.3 7.1 + - - +
394B ASP* 3.0 51.5 + - - +
440B LEU 5.7 0.2 - - - -
441B ARG* 4.0 32.6 - - + -
444B ALA* 4.2 11.6 - - + +
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Residues in contact with HIS 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B GLU 3.0 17.3 + - - +
388B ILE 3.6 4.3 - - - +
390B HIS* 1.3 73.6 - - - +
392B LEU* 1.3 60.4 + - - +
394B ASP* 3.2 12.7 + - + +
395B LEU* 2.9 75.5 + - + +
522B GLU* 4.1 11.7 + - - -
523B ALA* 3.8 18.6 - - + -
526B ILE* 4.3 20.9 - - + +
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ILE* 3.0 14.8 + - + +
389B ILE* 3.5 10.3 - - - +
391B HIS* 1.3 76.0 - - - +
393B ALA* 1.3 61.7 + - - +
395B LEU* 3.2 4.5 + - + +
396B LEU* 3.0 38.0 + - + +
440B LEU* 3.7 21.1 - - + -
488B PRO* 4.5 15.7 - - + +
491B ALA* 4.8 4.0 - - + -
492B ALA* 4.9 6.1 - - + +
495B ILE* 5.0 6.5 - - + -
516B LEU 4.9 0.9 - - - +
519B LEU* 3.7 31.4 - - + +
520B THR* 3.7 35.0 - - + +
523B ALA* 3.8 9.3 - - + +
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Residues in contact with ALA 393 (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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389B ILE 2.9 13.4 + - - +
390B HIS* 3.5 9.2 - - - +
392B LEU* 1.3 76.9 - - - +
394B ASP* 1.3 61.3 + - - +
396B LEU* 3.3 14.6 + - - +
397B THR* 3.5 14.7 + - - -
437B ALA* 3.6 23.2 - - - +
440B LEU* 3.7 26.4 - - + +
441B ARG* 3.8 18.2 - - + +
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Residues in contact with ASP 394 (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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390B HIS* 3.0 34.5 + - - +
391B HIS* 3.5 16.0 + - + +
393B ALA* 1.3 73.3 - - - +
395B LEU* 1.3 55.1 + - + +
397B THR* 3.1 6.2 + - - -
398B ASP* 2.8 48.6 + - - +
441B ARG* 3.8 22.2 + - - +
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Residues in contact with LEU 395 (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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391B HIS* 2.9 43.2 + - + +
392B LEU* 3.2 8.7 + - - +
394B ASP* 1.3 73.8 - - + +
396B LEU* 1.3 60.3 + - - +
398B ASP* 4.3 10.1 - - + +
399B GLN* 2.9 46.7 + - + +
519B LEU* 3.5 31.5 - - + +
522B GLU* 3.3 46.0 - - + +
523B ALA 4.3 0.4 - - - +
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Residues in contact with LEU 396 (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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392B LEU* 3.0 26.9 + - + +
393B ALA* 3.5 6.3 - - - +
394B ASP 3.2 0.4 - - - -
395B LEU* 1.3 76.1 - - - +
397B THR* 1.3 61.9 + - - +
400B ARG* 3.5 17.2 + - - +
403B ILE* 3.6 15.8 - - + +
433B LEU* 4.5 24.7 - - + +
436B LEU* 3.8 28.7 - - + -
437B ALA* 4.1 9.6 - - + +
440B LEU* 3.9 24.7 - - + -
488B PRO* 4.3 14.8 - - + -
516B LEU* 3.8 29.6 - - + -
519B LEU* 4.8 3.1 - - + -
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Residues in contact with THR 397 (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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393B ALA 3.5 10.1 + - - -
394B ASP* 3.1 9.3 + - - -
396B LEU* 1.3 74.9 - - - +
398B ASP* 1.3 71.7 + - - +
400B ARG* 3.0 26.3 + - - +
433B LEU* 6.0 0.9 - - - -
434B ASN* 5.9 1.0 - - - -
437B ALA* 3.8 8.8 - - - +
441B ARG* 3.7 15.7 + - - +
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Residues in contact with ASP 398 (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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394B ASP* 2.8 35.5 + - - +
395B LEU* 4.3 11.2 + - + +
397B THR* 1.3 79.7 - - - +
399B GLN* 1.3 68.5 + - + +
400B ARG* 3.4 2.8 + - - +
401B ASP* 4.9 1.2 + - - -
402B GLU* 3.9 5.5 - - - +
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Residues in contact with GLN 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B LEU* 2.9 28.0 + - + +
398B ASP* 1.3 81.4 - - + +
400B ARG* 1.3 64.2 + - - +
401B ASP 3.2 3.7 + - - -
402B GLU* 3.2 37.6 + - + +
403B ILE* 3.0 24.1 + - + +
515B ILE* 5.3 2.8 - - + +
519B LEU* 3.9 32.6 - - + +
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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