Contacts of the helix formed by residues 429 - 447 (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 SER 429 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A LEU* 4.2 4.5 - - - -
427A SER* 4.1 1.7 - - - -
428A LEU* 1.3 75.0 - - - +
430A THR* 1.3 66.1 + - - +
431A SER* 3.2 11.2 + - - -
432A LYS* 2.9 29.5 + - - +
433A LEU* 3.0 24.9 + - - +
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Residues in contact with THR 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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400A ARG* 4.2 20.1 - - - +
404A LEU* 4.3 21.1 - - - +
429A SER* 1.3 74.0 - - - +
431A SER* 1.3 62.0 + - - +
433A LEU* 3.6 8.7 + - - +
434A ASN* 3.1 27.3 + - - +
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Residues in contact with SER 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A SER* 3.6 9.6 - - - -
430A THR* 1.3 83.1 - - - +
432A LYS* 1.3 65.4 + - - +
434A ASN* 3.0 17.0 + - - +
435A SER* 3.0 19.9 + - - -
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Residues in contact with LYS 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A SER 5.6 1.8 - - - +
428A LEU* 4.6 7.0 - - + -
429A SER* 2.9 30.8 + - - +
431A SER* 1.3 73.9 + - - +
433A LEU* 1.3 62.6 + - - +
435A SER* 3.2 7.7 + - - -
436A LEU* 2.9 37.4 + - + +
485A ASP* 4.2 30.3 - - + +
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Residues in contact with LEU 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A LEU* 4.3 22.9 - - + +
397A THR* 5.2 1.2 + - - -
400A ARG* 4.1 22.7 - - + -
403A ILE* 3.8 47.6 - - + -
404A LEU* 4.0 22.4 - - + -
428A LEU* 4.7 12.1 - - + -
429A SER 3.0 14.5 + - - +
430A THR* 3.8 6.5 - - - +
432A LYS* 1.3 76.2 - - - +
434A ASN* 1.3 57.1 + - - +
436A LEU* 3.5 19.6 + - + +
437A ALA* 3.1 28.6 + - - +
516A LEU* 4.9 2.5 - - + -
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Residues in contact with ASN 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A THR* 5.3 4.4 + - - -
430A THR 3.1 14.0 + - - +
431A SER* 3.0 13.6 + - - +
433A LEU* 1.3 77.8 - - - +
435A SER* 1.3 57.9 + - - +
437A ALA* 3.5 6.2 + - - +
438A ILE* 3.0 45.9 + - - +
441A ARG* 5.1 5.2 + - - -
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Residues in contact with SER 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A SER* 3.0 15.7 + - - -
432A LYS* 3.7 8.9 - - - -
434A ASN* 1.3 77.2 + - - +
436A LEU* 1.3 54.5 + - - +
438A ILE* 3.3 12.0 + - - +
439A GLY* 2.7 32.6 + - - -
731A TYR* 3.9 30.8 + - - -
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Residues in contact with LEU 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A LEU* 3.9 13.0 - - + -
428A LEU* 5.0 2.0 - - + -
432A LYS* 2.9 24.5 + - + +
433A LEU* 3.6 26.2 - - + +
435A SER* 1.3 75.0 - - - +
437A ALA* 1.3 53.0 + - - +
439A GLY* 3.1 1.9 + - - +
440A LEU* 2.7 45.7 + - + +
485A ASP* 3.7 31.0 - - + +
488A PRO* 4.1 17.0 - - + -
489A GLN* 3.5 38.4 - - + +
516A LEU* 6.3 0.2 - - + -
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Residues in contact with ALA 437 (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* 3.7 30.0 - - - +
396A LEU* 4.1 6.9 - - + +
397A THR* 3.8 13.0 - - - +
433A LEU 3.1 15.0 + - - +
434A ASN* 3.7 6.5 - - - +
436A LEU* 1.3 78.0 - - - +
438A ILE* 1.3 63.4 + - - +
440A LEU 3.4 0.2 + - - -
441A ARG* 3.1 45.8 + - - +
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Residues in contact with ILE 438 (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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434A ASN* 3.0 44.8 + - - +
435A SER* 3.7 9.0 - - - +
437A ALA* 1.3 75.0 - - - +
439A GLY* 1.3 61.9 + - - +
441A ARG* 3.3 19.8 + - - +
442A GLN* 3.1 32.1 + - + +
731A TYR* 3.7 25.6 - - + +
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Residues in contact with GLY 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A SER 2.7 18.7 + - - -
436A LEU* 3.6 2.2 - - - -
438A ILE* 1.3 71.0 - - - +
440A LEU* 1.3 66.1 + - - +
442A GLN* 3.1 17.4 + - - +
443A ILE* 3.0 20.0 + - - +
731A TYR* 4.0 2.9 - - - -
736A GLY* 3.2 30.8 - - - -
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Residues in contact with LEU 440 (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* 3.1 15.6 - - + +
392A LEU* 3.5 40.2 - - + -
393A ALA* 3.8 16.2 - - + +
396A LEU* 4.0 18.2 - - + -
436A LEU* 2.7 37.2 + - + +
439A GLY* 1.3 74.9 - - - +
441A ARG* 1.3 56.7 + - - +
443A ILE* 3.3 9.6 + - + +
444A ALA 2.9 23.7 + - - -
488A PRO* 4.0 22.4 - - + +
489A GLN* 4.6 7.9 - - + +
492A ALA* 3.5 18.6 - - + -
736A GLY 5.4 0.2 - - - +
737A ALA* 5.2 2.2 - - + -
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Residues in contact with ARG 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A HIS* 3.8 28.7 + - + +
393A ALA* 3.8 24.3 + - + +
394A ASP* 3.6 22.6 + - - +
397A THR* 4.7 5.9 + - - -
434A ASN* 5.1 4.4 + - - -
437A ALA* 3.1 35.8 + - - +
438A ILE* 3.7 18.0 - - - +
439A GLY 3.2 0.2 - - - -
440A LEU* 1.3 76.0 - - - +
442A GLN* 1.3 58.0 + - - +
444A ALA* 3.3 7.6 + - - +
445A ALA* 2.9 31.9 + - - +
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Residues in contact with GLN 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ILE* 3.1 24.7 + - + +
439A GLY* 3.1 12.7 + - - +
441A ARG* 1.3 76.4 - - - +
443A ILE* 1.3 62.5 + - - +
445A ALA* 3.3 5.1 + - - +
446A SER* 3.1 28.7 + - - -
731A TYR* 3.5 27.4 + - - +
734A GLY* 4.9 16.8 + - - +
735A LEU 5.3 1.1 - - - -
736A GLY* 3.6 17.1 + - - +
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Residues in contact with ILE 443 (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* 3.9 10.3 - - + -
439A GLY 3.0 15.4 + - - +
440A LEU* 3.5 9.9 - - + +
441A ARG 3.3 0.2 - - - -
442A GLN* 1.3 72.7 - - - +
444A ALA* 1.3 67.4 + - - +
446A SER* 3.1 16.6 + - - -
447A SER* 3.1 20.8 + - - -
492A ALA* 4.1 22.2 - - + +
493A LEU* 3.8 22.9 - - + -
496A ALA* 3.6 29.8 - - + -
735A LEU 3.8 18.8 - - - +
737A ALA* 3.8 20.4 - - + -
754A LEU* 4.5 6.5 - - + -
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Residues in contact with ALA 444 (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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386A ALA* 3.5 47.7 - - + +
389A ILE* 3.9 11.2 - - + +
390A HIS* 4.2 12.1 - - + +
440A LEU 2.9 17.1 + - - +
441A ARG* 3.7 7.2 - - - +
443A ILE* 1.3 77.9 - - - +
445A ALA* 1.3 61.9 + - - +
446A SER 3.4 0.3 + - - -
447A SER* 3.7 9.8 + - - -
448A GLN* 4.3 6.8 + - - +
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Residues in contact with ALA 445 (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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441A ARG 2.9 17.4 + - - +
442A GLN* 4.0 5.6 - - - +
444A ALA* 1.3 76.5 - - - +
446A SER* 1.3 57.8 + - - +
447A SER 3.7 0.2 - - - -
448A GLN* 5.2 5.6 + - - +
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Residues in contact with SER 446 (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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442A GLN 3.1 18.6 + - - -
443A ILE* 3.6 7.1 + - - -
445A ALA* 1.3 78.4 - - - +
447A SER* 1.3 63.0 + - - +
448A GLN 3.5 3.2 + - - -
449A ASP* 4.9 5.2 - - - +
450A SER* 4.4 2.6 + - - -
735A LEU 5.8 0.3 + - - -
754A LEU* 5.0 5.2 - - - +
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Residues in contact with SER 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A PRO* 5.1 2.3 + - - +
385A ARG* 5.6 4.2 + - - +
386A ALA* 5.0 5.2 + - - +
389A ILE* 4.9 2.1 - - - +
443A ILE 3.1 18.2 + - - -
444A ALA* 3.7 9.1 + - - -
445A ALA 3.7 0.8 - - - -
446A SER* 1.3 76.5 - - - +
448A GLN* 1.3 66.3 + - - +
449A ASP 3.4 2.5 - - - -
450A SER* 3.1 24.7 + - - -
451A VAL* 4.9 0.3 + - - +
496A ALA* 3.9 21.9 + - - +
754A LEU* 3.5 25.4 - - - -
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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