Contacts of the helix formed by residues 509 - 526 (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 ALA 509 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410A ASP* 3.3 8.5 - - - +
426A LEU* 3.8 17.3 - - + -
482A SER* 4.0 20.0 - - - +
484A PRO* 4.2 6.5 - - + -
506A GLY 3.2 6.9 + - - +
507A LYS 3.1 0.8 - - - -
508A GLU* 1.3 77.4 - - + +
510A ALA* 1.3 55.8 + - - +
511A HIS 3.2 3.6 + - - -
512A SER 3.2 1.9 + - - -
513A ASN* 2.8 56.1 + - - +
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Residues in contact with ALA 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A ASP* 3.7 2.3 + - - +
506A GLY 3.6 6.3 + - - +
507A LYS* 3.1 20.4 + - - +
508A GLU 3.6 0.6 - - - -
509A ALA* 1.3 76.7 - - - +
511A HIS* 1.3 63.5 + - + +
513A ASN* 4.1 3.9 - - - +
514A ARG* 2.9 31.0 + - - +
535A LEU* 6.0 0.2 - - - +
538A THR* 5.7 3.4 - - - +
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Residues in contact with HIS 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ALA* 3.2 33.3 - - + +
409A LYS* 3.8 24.0 - - + +
410A ASP* 3.0 24.8 + - - +
413A GLU* 3.3 29.2 + - - -
510A ALA* 1.3 78.5 - - + +
512A SER* 1.3 65.5 + - - +
514A ARG* 3.5 6.1 + - - +
515A ILE* 3.2 18.2 + - - +
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Residues in contact with SER 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A ILE 5.4 0.4 - - - -
406A ALA* 4.5 2.7 - - - -
407A ASN* 2.8 33.4 + - - +
410A ASP* 2.6 24.2 + - - -
428A LEU* 4.5 7.9 - - - -
484A PRO* 3.5 26.7 - - - -
509A ALA 3.7 1.3 - - - -
511A HIS* 1.3 74.1 - - - +
513A ASN* 1.3 65.9 + - - +
515A ILE* 3.3 10.2 + - - +
516A LEU* 3.0 28.5 + - - +
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Residues in contact with ASN 513 (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* 3.6 30.3 - - - -
484A PRO* 3.5 26.7 - - - +
487A LEU* 3.5 17.1 - - + +
505A GLY* 3.8 16.2 - - - -
506A GLY 4.3 2.4 + - - +
509A ALA* 2.8 36.0 + - - +
510A ALA* 4.1 4.4 - - - +
512A SER* 1.3 71.4 - - - +
514A ARG* 1.3 57.0 + - - +
516A LEU* 3.3 0.6 + - - -
517A HIS* 2.8 34.6 + - - +
535A LEU* 4.6 12.9 - - + +
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Residues in contact with ARG 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A ALA 2.9 22.5 + - - +
511A HIS* 3.6 7.4 - - - +
513A ASN* 1.3 77.4 - - - +
515A ILE* 1.3 57.7 + - - +
517A HIS* 3.7 3.3 + - - +
518A LEU* 3.0 27.2 + - - +
535A LEU* 4.5 16.5 - - + +
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Residues in contact with ILE 515 (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* 5.1 2.2 - - + +
402A GLU* 3.6 40.4 - - + +
403A ILE* 3.8 23.1 - - + +
406A ALA* 4.0 15.0 - - + -
511A HIS 3.2 13.5 + - - +
512A SER* 3.3 11.9 - - - +
514A ARG* 1.3 78.3 - - - +
516A LEU* 1.3 62.7 + - + +
518A LEU* 3.2 9.4 + - + +
519A LEU* 3.0 48.6 + - + +
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Residues in contact with LEU 516 (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 1.6 - - - +
396A LEU* 3.8 28.9 - - + -
403A ILE* 4.2 24.7 - - + -
428A LEU* 4.0 17.5 - - + -
433A LEU* 4.9 2.9 - - + -
436A LEU* 6.3 0.2 - - + -
484A PRO* 3.2 36.8 - - + +
485A ASP* 5.1 0.4 - - - -
487A LEU* 4.0 16.4 - - + -
488A PRO* 4.0 13.7 - - + -
512A SER 3.0 20.4 + - - +
513A ASN* 3.9 3.4 - - - +
515A ILE* 1.3 77.6 - - + +
517A HIS* 1.3 53.8 + - - +
519A LEU* 3.5 6.1 + - + +
520A THR* 2.7 36.7 + - - -
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Residues in contact with HIS 517 (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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487A LEU* 4.0 7.3 - - + +
503A LEU* 4.2 5.4 - - + -
513A ASN 2.8 18.6 + - - +
514A ARG 3.7 4.1 + - - +
516A LEU* 1.3 74.5 - - - +
518A LEU* 1.3 67.1 + - - +
520A THR* 3.1 8.5 + - - -
521A GLN* 2.9 52.9 + - + +
533A VAL* 3.0 42.5 + - + -
534A GLN* 4.9 0.4 - - - -
535A LEU* 3.6 46.9 + - + +
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Residues in contact with LEU 518 (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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514A ARG 3.0 14.5 + - - +
515A ILE* 3.3 17.0 - - + +
517A HIS* 1.3 79.5 + - - +
519A LEU* 1.3 63.3 + - + +
521A GLN* 3.2 8.9 + - - +
522A GLU* 2.9 33.6 + - + +
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Residues in contact with LEU 519 (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* 4.2 9.0 - - + -
395A LEU* 3.3 33.1 - - + +
396A LEU* 4.7 6.5 - - + -
399A GLN* 3.9 29.2 - - + +
403A ILE* 3.8 34.8 - - + -
515A ILE* 3.0 30.4 + - + +
516A LEU* 3.8 6.7 - - + +
517A HIS 3.2 0.2 - - - -
518A LEU* 1.3 80.5 - - + +
520A THR* 1.3 63.1 + - - +
522A GLU* 3.3 20.0 + - - +
523A ALA* 3.0 20.3 + - - +
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Residues in contact with THR 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A LEU* 4.0 23.4 - - + +
487A LEU* 3.9 11.4 - - - +
488A PRO* 5.2 1.0 - - - +
491A ALA* 3.8 24.5 - - + +
495A ILE* 4.3 9.6 - - + -
516A LEU 2.7 20.2 + - - -
517A HIS* 3.1 11.3 + - - -
519A LEU* 1.3 75.1 - - - +
521A GLN* 1.3 57.4 + - - +
523A ALA* 3.2 4.2 + - - +
524A LEU* 2.9 47.2 + - + +
533A VAL* 4.2 13.7 - - + -
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Residues in contact with GLN 521 (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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517A HIS* 2.9 41.0 + - + +
518A LEU* 3.6 10.2 - - - +
520A THR* 1.3 74.7 - - - +
522A GLU* 1.3 58.9 + - - +
524A LEU* 3.4 8.0 + - + -
525A SER* 2.9 25.3 + - - -
530A LYS* 3.1 56.2 + - + +
531A GLU* 4.9 0.2 - - - +
533A VAL 3.3 14.1 + - - +
534A GLN* 4.5 7.9 - - - +
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Residues in contact with GLU 522 (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* 4.4 8.7 + - - +
395A LEU* 3.7 28.5 - - + +
518A LEU* 2.9 16.7 + - - +
519A LEU* 3.4 23.3 - - - +
521A GLN* 1.3 76.3 - - - +
523A ALA* 1.3 58.6 + - - +
525A SER* 2.6 25.7 + - - +
526A ILE* 4.0 7.6 + - - +
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Residues in contact with ALA 523 (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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388A ILE* 3.4 31.0 - - + +
391A HIS* 3.6 14.5 - - + -
392A LEU* 3.8 23.8 - - + +
495A ILE* 6.1 0.2 - - + -
519A LEU 3.0 13.0 + - - +
520A THR* 3.4 9.0 - - + +
522A GLU* 1.3 76.3 - - - +
524A LEU* 1.3 62.4 + - - +
525A SER 3.4 0.2 + - - -
526A ILE* 3.2 27.9 - - - +
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Residues in contact with LEU 524 (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* 4.4 7.4 - - + -
388A ILE* 3.9 9.4 - - + +
495A ILE* 3.7 31.9 - - + -
520A THR* 2.9 27.1 + - + +
521A GLN* 3.7 7.2 - - + +
523A ALA* 1.3 73.9 - - - +
525A SER* 1.3 65.8 + - - +
526A ILE 3.0 1.2 + - - -
527A HIS* 3.1 11.6 + - - +
528A GLY 3.2 7.3 + - - -
529A VAL* 3.2 49.8 + - + +
530A LYS* 3.7 15.5 - - - +
532A ALA* 4.5 4.5 - - + -
533A VAL* 3.7 27.8 - - + +
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Residues in contact with SER 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A GLN 2.9 15.2 + - - -
522A GLU* 2.6 24.9 + - - +
524A LEU* 1.3 77.0 - - - +
526A ILE* 1.3 60.7 + - - +
528A GLY* 2.9 21.5 + - - +
530A LYS* 3.7 23.3 - - - -
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Residues in contact with ILE 526 (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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387A GLU* 3.9 43.1 - - + +
388A ILE* 4.0 5.8 - - + -
391A HIS* 4.1 26.9 - - + +
522A GLU 4.0 9.6 - - - +
523A ALA 3.2 18.8 - - - +
524A LEU 3.0 1.4 + - - -
525A SER* 1.3 78.4 + - - +
527A HIS* 1.3 80.9 + - + +
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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
------------------------------------------------------------
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