Contacts of the helix formed by residues 399 - 415 (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 GLN 399 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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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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Residues in contact with ARG 400 (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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396A LEU 3.5 12.9 + - - +
397A THR* 3.1 28.3 + - - +
398A ASP 3.3 2.3 - - - +
399A GLN* 1.3 75.4 - - - +
401A ASP* 1.3 70.8 + - - +
403A ILE* 3.2 6.9 + - - +
404A LEU* 2.9 39.1 + - + +
430A THR* 4.2 18.8 - - - +
433A LEU* 4.1 14.8 - - + -
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Residues in contact with ASP 401 (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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398A ASP 5.0 1.0 + - - -
399A GLN 3.2 1.0 + - - -
400A ARG* 1.3 87.2 - - - +
402A GLU* 1.3 60.8 + - + +
404A LEU* 3.4 11.0 + - - +
405A LEU* 3.0 27.5 + - - +
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Residues in contact with GLU 402 (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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399A GLN* 3.2 34.5 + - - +
401A ASP* 1.3 75.6 - - + +
403A ILE* 1.3 68.3 + - - +
405A LEU* 3.2 7.6 + - - +
406A ALA* 3.0 23.2 + - - +
515A ILE* 3.6 20.2 - - + +
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Residues in contact with ILE 403 (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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396A LEU* 3.5 40.6 - - + +
399A GLN 3.1 15.8 + - - +
400A ARG* 3.5 7.0 - - - +
402A GLU* 1.3 77.5 - - - +
404A LEU* 1.3 58.0 + - + +
406A ALA* 3.3 2.8 + - - +
407A ASN* 2.9 26.3 + - - +
428A LEU* 3.9 23.3 - - + -
433A LEU* 3.8 21.8 - - + -
512A SER* 5.0 1.5 + - - -
515A ILE* 3.8 18.9 - - + +
516A LEU* 4.2 9.4 - - + -
519A LEU* 3.8 29.6 - - + -
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Residues in contact with LEU 404 (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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400A ARG* 2.9 26.4 + - + +
401A ASP* 3.9 10.1 - - - +
403A ILE* 1.3 72.4 - - - +
405A LEU* 1.3 55.8 + - - +
407A ASN* 3.7 3.7 - - + +
408A LYS* 2.8 34.1 + - - +
428A LEU* 3.1 36.6 - - + +
429A SER* 4.2 4.3 - - - -
430A THR* 4.3 23.3 - - - +
433A LEU* 4.0 17.9 - - + -
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Residues in contact with LEU 405 (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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401A ASP 3.0 17.7 + - - +
402A GLU* 3.6 8.1 - - - +
404A LEU* 1.3 77.1 - - - +
406A ALA* 1.3 57.2 + - - +
408A LYS* 3.3 11.9 + - - +
409A LYS* 3.1 29.4 + - - +
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Residues in contact with ALA 406 (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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402A GLU 3.0 16.1 + - - +
403A ILE 3.7 3.8 - - - +
405A LEU* 1.3 73.4 - - - +
407A ASN* 1.3 65.4 + - - +
409A LYS* 3.3 5.3 + - - +
410A ASP* 3.2 16.6 + - - -
511A HIS* 3.2 45.6 - - + +
512A SER* 4.1 1.3 - - - +
515A ILE* 4.0 14.1 - - + -
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Residues in contact with ASN 407 (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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403A ILE 2.9 16.3 + - - +
404A LEU* 3.8 6.5 - - + +
406A ALA* 1.3 74.7 - - - +
408A LYS* 1.3 63.6 + - - +
410A ASP* 3.1 7.8 + - - +
411A LEU* 2.9 40.9 + - - +
426A LEU* 2.8 24.6 + - - +
428A LEU* 2.7 43.2 + - + +
484A PRO* 3.9 6.5 - - - +
512A SER* 2.8 26.7 + - - +
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Residues in contact with LYS 408 (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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404A LEU 2.8 21.7 + - - +
405A LEU* 3.4 11.0 - - - +
407A ASN* 1.3 73.8 + - - +
409A LYS* 1.3 61.9 + - + +
411A LEU* 3.3 11.5 + - + +
412A GLU* 2.9 55.8 + - + +
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Residues in contact with LYS 409 (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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405A LEU 3.1 16.7 + - - +
406A ALA* 3.5 11.2 - - - +
407A ASN 3.2 0.2 - - - -
408A LYS* 1.3 77.2 - - + +
410A ASP* 1.3 56.2 + - - +
412A GLU* 3.3 12.4 + - - +
413A GLU* 3.0 37.7 + - - +
511A HIS* 3.8 24.9 - - + +
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Residues in contact with ASP 410 (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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406A ALA 3.2 2.4 + - - -
407A ASN* 3.1 9.3 + - - +
409A LYS* 1.3 79.1 - - - +
411A LEU* 1.3 57.4 + - - +
413A GLU* 3.4 6.7 + - - +
414A ALA* 2.9 29.1 + - - +
426A LEU* 3.9 12.3 - - + +
507A LYS 4.8 0.7 - - - +
508A GLU 3.4 23.3 - - - +
509A ALA* 3.3 7.0 - - - -
510A ALA* 3.7 2.6 + - - +
511A HIS* 3.0 37.5 + - - -
512A SER* 2.6 38.6 + - - +
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Residues in contact with LEU 411 (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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407A ASN* 2.9 40.0 + - - +
408A LYS* 3.7 9.9 - - + +
410A ASP* 1.3 76.7 - - - +
412A GLU* 1.3 57.1 + - + +
414A ALA* 3.2 4.1 + - - +
415A GLU* 2.8 30.7 + - - +
423A LEU* 4.2 15.2 - - + +
426A LEU* 4.0 24.0 - - + -
427A SER* 4.0 26.0 - - - +
428A LEU 5.7 0.7 - - - +
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Residues in contact with GLU 412 (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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408A LYS* 2.9 53.2 + - + +
409A LYS* 3.8 12.1 - - - +
411A LEU* 1.3 77.4 - - + +
413A GLU* 1.3 62.2 + - + +
414A ALA 3.4 0.5 + - - -
415A GLU* 3.5 20.2 + - - +
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Residues in contact with GLU 413 (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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409A LYS* 3.0 22.1 + - - +
410A ASP* 3.8 6.2 - - - +
412A GLU* 1.3 76.8 - - + +
414A ALA* 1.3 58.2 + - - +
417A ARG* 2.8 33.5 + - - +
511A HIS* 3.3 29.8 + - - -
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Residues in contact with ALA 414 (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 ASP 2.9 17.3 + - - +
411A LEU 3.6 4.5 - - - +
412A GLU 3.2 0.2 - - - -
413A GLU* 1.3 78.3 - - - +
415A GLU* 1.3 65.8 + - - +
416A GLY 3.2 0.3 + - - -
417A ARG* 2.9 19.1 + - - +
418A LEU* 2.9 33.6 + - + +
423A LEU* 3.9 10.0 - - + +
426A LEU* 3.7 22.0 - - + -
508A GLU* 5.3 3.1 - - + +
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Residues in contact with GLU 415 (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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411A LEU 2.8 16.6 + - - +
412A GLU* 3.7 16.0 - - - +
413A GLU 3.5 0.8 - - - -
414A ALA* 1.3 75.7 - - - +
416A GLY* 1.3 61.6 + - - +
417A ARG* 3.2 14.4 + - - +
423A LEU* 5.2 7.9 - - - -
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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