Contacts of the helix formed by residues 485 - 498 (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 ASP 485 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A SO4 5.5 2.1 + - - -
425A ARG 4.5 4.6 - - - +
427A SER 5.7 2.0 - - - -
428A LEU* 3.6 23.9 - - + +
432A LYS* 4.2 15.9 - - + +
436A LEU* 3.7 20.2 - - + +
483A ARG* 3.5 19.9 - - - +
484A PRO* 1.3 81.1 - - - +
486A CYS* 1.3 64.5 + - - +
487A LEU 3.3 0.2 - - - -
488A PRO* 3.6 8.3 - - - +
489A GLN* 3.4 29.0 + - - +
516A LEU* 5.1 0.2 - - - -
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Residues in contact with CYS 486 (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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478A VAL* 4.7 3.6 - - - -
480A PHE* 3.6 43.3 - - - -
483A ARG* 3.0 15.4 + - + +
485A ASP* 1.3 81.1 + - - +
487A LEU* 1.3 70.1 + - - +
489A GLN* 3.1 13.3 + - + +
490A VAL* 2.9 34.3 + - + +
558A ARG* 3.9 31.4 - - - +
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Residues in contact with LEU 487 (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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480A PHE* 4.3 11.2 - - + -
484A PRO 3.1 9.6 + - - +
486A CYS* 1.3 81.3 - - - +
488A PRO* 1.3 73.8 - - + +
490A VAL* 3.4 8.0 - - - +
491A ALA* 3.0 27.8 + - + +
503A LEU* 3.8 33.9 - - + -
513A ASN* 3.5 47.6 - - + +
516A LEU* 4.0 16.8 - - + -
517A HIS* 4.0 5.4 - - + +
520A THR* 3.9 21.5 - - - +
535A LEU* 4.7 2.2 - - + -
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Residues in contact with PRO 488 (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* 4.3 10.3 - - + +
396A LEU* 4.2 23.3 - - + -
436A LEU* 4.1 18.2 - - + -
440A LEU* 4.0 12.9 - - + +
484A PRO 3.3 10.5 - - - +
485A ASP 3.6 10.8 - - - +
487A LEU* 1.3 99.5 - - + +
489A GLN* 1.3 54.9 + - - +
491A ALA* 4.0 4.9 - - + +
492A ALA* 3.0 31.9 + - - +
516A LEU* 4.0 22.9 - - + -
520A THR* 5.2 0.7 - - - +
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Residues in contact with GLN 489 (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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436A LEU* 3.5 25.6 - - + +
440A LEU* 4.6 4.5 - - + -
485A ASP* 3.4 28.6 + - - +
486A CYS* 3.1 14.2 + - - +
488A PRO* 1.3 75.5 - - - +
490A VAL* 1.3 65.9 + - - +
492A ALA* 4.1 1.0 - - - +
493A LEU* 3.1 29.9 + - - +
558A ARG* 5.9 2.2 - - - +
729A ASP* 5.3 3.3 + - - +
731A TYR* 5.2 5.5 + - - +
736A GLY 5.5 0.4 - - - +
737A ALA* 3.4 24.1 - - + +
738A GLU* 3.2 38.4 + - - +
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Residues in contact with VAL 490 (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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476A LEU* 5.6 0.3 - - - +
478A VAL* 4.2 28.3 - - + -
486A CYS* 2.9 29.0 + - + +
487A LEU* 3.4 7.2 - - - +
489A GLN* 1.3 76.6 - - - +
491A ALA* 1.3 61.8 + - - +
493A LEU* 3.8 1.0 - - - +
494A ALA* 2.9 30.3 + - - +
501A LEU* 4.1 5.2 - - + +
503A LEU* 3.6 26.7 - - + -
558A ARG* 4.7 1.3 - - - +
738A GLU 4.2 2.9 - - - +
739A VAL* 3.9 43.7 - - + +
757A LEU* 5.4 0.3 - - - +
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Residues in contact with ALA 491 (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* 4.9 1.3 - - + -
487A LEU* 3.0 23.1 + - + +
488A PRO* 4.0 3.8 - - + +
490A VAL* 1.3 78.6 - - - +
492A ALA* 1.3 57.0 + - - +
494A ALA* 3.2 2.3 + - - +
495A ILE* 2.9 36.6 + - + +
501A LEU* 3.7 18.6 - - + -
520A THR* 3.8 33.2 - - + +
533A VAL* 4.6 5.2 - - + -
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Residues in contact with ALA 492 (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* 3.4 18.5 - - + +
392A LEU* 4.8 2.8 - - + +
440A LEU* 3.5 31.0 - - + -
443A ILE* 4.1 13.0 - - + +
488A PRO 3.0 20.0 + - - +
489A GLN 4.1 0.9 - - - +
491A ALA* 1.3 75.6 - - - +
493A LEU* 1.3 57.8 + - - +
495A ILE* 3.5 8.2 + - - +
496A ALA* 3.0 30.3 + - - +
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Residues in contact with LEU 493 (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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443A ILE* 3.8 28.0 - - + -
489A GLN 3.1 20.5 + - - +
490A VAL 4.0 2.9 - - - +
491A ALA 3.2 0.2 - - - -
492A ALA* 1.3 74.2 - - - +
494A ALA* 1.3 57.6 + - - +
496A ALA* 3.5 4.4 + - - +
497A SER* 2.6 34.0 + - - -
735A LEU 4.6 3.1 - - - +
737A ALA* 3.8 5.8 - - + +
738A GLU* 3.4 44.0 - - - +
739A VAL* 3.6 10.8 - - + +
752A VAL 4.1 4.0 - - - +
753A GLY* 4.0 4.5 - - - -
754A LEU* 3.5 32.1 - - + +
757A LEU* 3.7 16.0 - - + +
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Residues in contact with ALA 494 (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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476A LEU* 4.2 8.1 - - + -
490A VAL 2.9 17.9 + - - +
491A ALA 3.6 3.8 - - - +
493A LEU* 1.3 75.9 - - - +
495A ILE* 1.3 67.9 + - + +
497A SER* 3.0 8.0 + - - -
498A GLY 3.0 5.0 + - - -
499A ASN* 2.9 44.7 + - + +
501A LEU* 4.1 23.3 - - + -
533A VAL* 5.6 1.3 - - + -
757A LEU* 4.1 4.6 - - - +
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Residues in contact with ILE 495 (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* 4.0 28.2 - - + +
385A ARG* 3.2 32.4 - - + +
388A ILE* 3.9 18.8 - - + -
389A ILE* 3.8 19.5 - - + -
392A LEU* 5.3 5.2 - - + -
491A ALA* 2.9 27.4 + - + +
492A ALA* 3.7 7.9 - - - +
494A ALA* 1.3 75.6 - - - +
496A ALA* 1.3 63.3 + - - +
498A GLY* 3.2 11.8 + - - -
499A ASN 4.6 0.2 + - - -
520A THR* 4.3 14.1 - - + -
524A LEU* 3.7 29.4 - - + -
533A VAL* 4.6 7.6 - - + -
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Residues in contact with ALA 496 (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* 4.2 10.7 + - - +
389A ILE* 3.6 17.3 - - + -
443A ILE* 3.6 16.2 - - + -
447A SER* 3.9 21.9 + - - +
450A SER* 4.3 4.3 - - - -
451A VAL* 3.6 13.3 - - - +
492A ALA 3.0 19.1 + - - +
493A LEU 3.9 4.7 - - - +
495A ILE* 1.3 76.9 - - - +
497A SER* 1.3 58.7 + - - +
498A GLY 3.4 0.2 - - - -
754A LEU* 4.0 14.8 - - + +
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Residues in contact with SER 497 (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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451A VAL* 3.6 16.3 - - - +
472A PRO* 3.4 19.1 - - - +
493A LEU 2.6 22.7 + - - -
494A ALA* 3.0 5.9 + - - -
496A ALA* 1.3 77.4 - - - +
498A GLY* 1.3 62.3 + - - +
499A ASN* 2.9 24.4 + - - -
754A LEU* 3.9 16.4 - - - -
757A LEU* 3.6 15.0 - - - +
758A LEU* 3.6 13.9 - - - +
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Residues in contact with GLY 498 (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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374A GLY 3.2 21.6 - - - +
377A LEU* 4.4 5.4 - - - -
378A ALA* 3.9 19.8 - - - +
385A ARG* 4.5 3.1 - - - -
451A VAL* 4.1 3.0 - - - +
472A PRO* 3.3 21.4 - - - +
474A GLY 4.7 0.7 - - - +
494A ALA 3.0 3.4 + - - -
495A ILE 3.2 10.3 + - - -
496A ALA 3.4 0.8 - - - -
497A SER* 1.3 78.9 - - - +
499A ASN* 1.3 59.5 + - - +
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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