Contacts of the helix formed by residues 509 - 525 (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 ALA 509 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B ASP* 3.4 8.3 - - - +
426B LEU* 3.9 17.0 - - + -
482B SER* 4.0 20.4 - - - +
484B PRO* 4.2 6.5 - - + -
506B GLY 3.2 6.6 + - - +
507B LYS 3.1 1.0 - - - -
508B GLU* 1.3 77.5 - - + +
510B ALA* 1.3 55.4 + - - +
511B HIS 3.4 2.5 - - - -
512B SER 3.1 2.8 + - - -
513B ASN* 2.8 55.6 + - - +
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Residues in contact with ALA 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B ASP* 3.7 2.1 + - - +
506B GLY 3.6 6.1 + - - +
507B LYS* 3.2 21.1 + - + +
508B GLU 3.5 0.6 - - - -
509B ALA* 1.3 75.8 - - - +
511B HIS* 1.3 64.7 + - + +
513B ASN* 3.9 4.6 - - - +
514B ARG* 2.9 30.8 + - - +
535B LEU* 5.9 0.2 - - - +
538B THR* 5.7 2.7 - - - +
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Residues in contact with HIS 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B ALA* 3.2 30.0 - - + +
409B LYS* 3.8 30.9 + - + +
410B ASP* 3.0 20.5 + - - +
413B GLU* 3.5 31.9 + - - -
510B ALA* 1.3 77.0 - - + +
512B SER* 1.3 64.8 + - - +
514B ARG* 3.5 5.5 + - + +
515B ILE* 3.2 24.1 + - - +
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Residues in contact with SER 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B ILE* 5.5 0.7 - - - -
406B ALA* 4.5 3.4 - - - -
407B ASN* 2.9 32.5 + - - +
410B ASP* 2.6 27.2 + - - -
426B LEU* 5.0 0.2 - - - +
428B LEU* 4.6 6.3 - - - -
484B PRO* 3.5 26.5 - - - -
509B ALA 3.1 3.1 + - - -
511B HIS* 1.3 74.2 - - - +
513B ASN* 1.3 62.1 + - - +
515B ILE* 3.2 11.5 - - - +
516B LEU* 3.0 27.5 + - - +
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Residues in contact with ASN 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B PHE* 3.5 31.2 - - - -
484B PRO* 3.5 27.4 - - - +
487B LEU* 3.6 16.6 - - + +
505B GLY* 3.9 14.8 - - - -
506B GLY 4.4 2.6 + - - +
509B ALA* 2.8 36.1 + - - +
510B ALA* 4.1 4.7 - - - +
512B SER* 1.3 72.9 - - - +
514B ARG* 1.3 58.1 + - - +
516B LEU* 4.5 0.4 - - - -
517B HIS* 2.8 34.2 + - - +
535B LEU* 4.5 13.8 - - + +
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Residues in contact with ARG 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B ALA 2.9 21.0 + - - +
511B HIS* 3.7 7.2 - - + +
512B SER 3.2 0.2 - - - -
513B ASN* 1.3 77.6 - - - +
515B ILE* 1.3 58.2 + - - +
517B HIS* 3.5 3.1 + - - +
518B LEU* 2.9 29.7 + - + +
535B LEU* 4.4 15.7 - - + +
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Residues in contact with ILE 515 (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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399B GLN* 5.3 3.1 - - - +
402B GLU* 3.8 42.0 - - + +
403B ILE* 4.0 15.9 - - + +
406B ALA* 3.8 17.7 - - + -
511B HIS 3.2 11.2 + - - +
512B SER* 3.2 13.0 - - - +
514B ARG* 1.3 78.7 - - - +
516B LEU* 1.3 66.2 + - + +
518B LEU* 3.1 16.0 + - + +
519B LEU* 2.9 43.9 + - + +
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Residues in contact with LEU 516 (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* 4.9 1.0 - - - +
396B LEU* 3.8 29.4 - - + -
403B ILE* 4.1 26.5 - - + -
428B LEU* 4.1 11.4 - - + -
433B LEU* 5.0 3.1 - - + -
484B PRO* 3.3 39.0 - - + +
485B ASP* 5.2 0.7 - - - -
487B LEU* 3.9 16.4 - - + -
488B PRO* 4.0 14.3 - - + +
512B SER 3.0 22.6 + - - +
513B ASN* 3.9 2.7 - - - +
515B ILE* 1.3 78.1 - - + +
517B HIS* 1.3 52.5 + - - +
519B LEU* 3.6 5.2 + - + +
520B THR* 2.7 36.9 + - - -
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Residues in contact with HIS 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B LEU* 4.0 10.2 - - + +
503B LEU* 4.3 4.9 - - + -
513B ASN 2.8 22.1 + - - +
514B ARG 3.7 4.1 + - - +
516B LEU* 1.3 71.2 - - - +
518B LEU* 1.3 66.1 + - - +
520B THR* 3.2 6.9 + - - -
521B GLN* 2.9 55.3 + - + +
533B VAL* 2.9 42.3 + - + -
534B GLN* 4.9 0.2 - - - -
535B LEU* 3.7 45.8 + - + +
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Residues in contact with LEU 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B ARG* 2.9 16.9 + - + +
515B ILE* 3.1 21.5 + - + +
517B HIS* 1.3 77.7 + - - +
519B LEU* 1.3 65.6 + - + +
521B GLN* 3.2 10.2 + - + +
522B GLU* 2.9 35.4 + - + +
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Residues in contact with LEU 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU* 3.7 14.8 - - + +
395B LEU* 3.5 33.8 - - + +
396B LEU* 4.8 5.6 - - + -
399B GLN* 3.9 27.6 - - + +
403B ILE* 3.7 35.9 - - + -
515B ILE* 2.9 29.0 + - + +
516B LEU* 4.0 6.1 - - + +
518B LEU* 1.3 78.2 - - + +
520B THR* 1.3 67.0 + - - +
522B GLU* 3.3 20.7 + - - +
523B ALA 3.1 17.3 + - - -
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Residues in contact with THR 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU* 3.7 23.7 - - + +
487B LEU* 3.8 12.3 - - - +
488B PRO* 5.1 1.7 - - - +
491B ALA* 3.8 23.5 - - + +
495B ILE* 4.3 8.5 - - + -
516B LEU 2.7 20.5 + - - -
517B HIS* 3.2 11.6 + - - -
519B LEU* 1.3 74.5 - - - +
521B GLN* 1.3 57.4 + - - +
523B ALA* 3.2 5.0 + - - +
524B LEU* 3.0 44.0 + - + +
533B VAL* 4.2 13.9 - - + -
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Residues in contact with GLN 521 (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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369B MSE 5.9 1.0 - - - +
517B HIS* 2.9 46.0 + - + +
518B LEU* 3.6 9.0 - - + +
520B THR* 1.3 77.2 - - - +
522B GLU* 1.3 55.9 + - - +
524B LEU* 3.4 8.4 + - + +
525B SER* 3.0 23.2 + - - -
530B LYS* 3.2 61.9 + - + +
531B GLU* 4.9 0.2 - - - +
533B VAL 3.2 20.6 + - - +
534B GLN* 4.7 8.1 - - - +
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Residues in contact with GLU 522 (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* 4.1 8.6 + - - +
395B LEU* 3.3 41.3 - - + +
518B LEU* 2.9 22.5 + - + +
519B LEU* 3.3 18.9 + - - +
520B THR 3.3 0.2 - - - -
521B GLN* 1.3 74.4 - - - +
523B ALA* 1.3 60.0 + - - +
525B SER* 2.6 26.2 + - - +
526B ILE* 3.9 7.1 - - - +
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Residues in contact with ALA 523 (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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388B ILE* 3.4 31.9 - - + +
391B HIS* 3.8 14.6 - - + -
392B LEU* 3.8 22.7 - - + +
495B ILE* 6.1 0.2 - - + -
519B LEU 3.1 13.1 + - - +
520B THR 3.5 8.5 - - - +
522B GLU* 1.3 73.8 - - - +
524B LEU* 1.3 65.2 + - - +
525B SER 3.3 0.9 + - - -
526B ILE* 3.3 28.1 + - - +
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Residues in contact with LEU 524 (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* 4.2 7.2 - - + -
388B ILE* 3.9 12.5 - - + +
495B ILE* 3.8 28.5 - - + -
520B THR* 3.0 27.6 + - + +
521B GLN* 3.7 7.4 - - - +
523B ALA* 1.3 76.6 - - - +
525B SER* 1.3 62.6 + - - +
527B HIS* 3.1 12.1 + - - +
529B VAL* 3.2 58.2 + - + +
530B LYS 3.8 9.6 - - - +
532B ALA* 4.5 4.7 - - + -
533B VAL* 3.7 32.1 - - + +
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Residues in contact with SER 525 (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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521B GLN 3.0 15.0 + - - -
522B GLU* 2.6 25.5 + - - +
524B LEU* 1.3 77.8 - - - +
526B ILE* 1.3 64.0 + - - +
528B GLY* 2.9 17.8 + - - +
530B LYS* 4.1 19.3 - - - -
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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