Contacts of the helix formed by residues 418 - 432 (chain A) in PDB entry 1OHV
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 418 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416A THR* 3.2 6.6 + - - -
417A PRO* 1.3 83.8 - - - +
419A GLU* 1.3 64.8 + - - +
420A SER* 3.1 12.4 + - - +
421A ILE* 2.9 37.1 + - - +
422A ARG 3.1 16.8 + - - -
442A LYS* 3.7 15.0 - - - -
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Residues in contact with GLU 419 (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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203A LYS* 5.3 6.6 + - - +
418A ASP* 1.3 74.2 - - - +
420A SER* 1.3 57.7 + - - +
422A ARG* 3.3 15.3 + - - +
423A ASN* 3.0 45.9 + - - +
441A ASP* 3.4 30.4 - - + +
442A LYS* 4.0 3.6 - - - +
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Residues in contact with SER 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A ASP* 3.1 11.0 + - - -
419A GLU* 1.3 80.3 - - - +
421A ILE* 1.3 59.2 + - - +
423A ASN* 3.5 6.5 + - - +
424A LYS* 3.1 28.5 + - - +
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Residues in contact with ILE 421 (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 PHE* 4.8 11.2 - - + -
416A THR* 4.2 0.7 - - - -
417A PRO* 3.9 31.0 - - + -
418A ASP* 2.9 34.5 + - - +
420A SER* 1.3 75.7 - - - +
422A ARG* 1.3 67.7 + - - +
424A LYS* 3.2 6.4 + - - +
425A LEU* 2.9 43.1 + - + +
471A PHE* 4.2 26.9 - - + -
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Residues in contact with ARG 422 (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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203A LYS* 5.3 3.2 - - - +
416A THR* 3.3 20.1 + - - +
418A ASP 3.1 8.7 + - - +
419A GLU* 3.3 22.3 + - - +
421A ILE* 1.3 77.0 - - - +
423A ASN* 1.3 84.9 + - - +
425A LEU* 3.3 2.3 + - - +
426A ILE* 3.1 50.3 + - - +
438A GLY* 4.2 4.9 - - - -
439A CYS 3.2 19.8 + - - +
440A GLY 3.4 13.5 + - - -
441A ASP 3.4 16.9 + - - -
442A LYS* 3.7 13.7 - - - +
443A SER 3.0 34.6 + - - +
444A ILE* 3.8 10.3 - - + +
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Residues in contact with ASN 423 (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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419A GLU* 3.0 35.4 + - - +
420A SER* 3.9 6.3 - - - +
422A ARG* 1.3 103.1 + - - +
424A LYS* 1.3 57.1 + - - +
426A ILE* 3.5 8.3 + - - +
427A SER* 2.9 29.5 + - - -
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Residues in contact with LYS 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A SER 3.1 18.2 + - - +
421A ILE* 3.2 6.5 + - - +
423A ASN* 1.3 74.3 - - - +
425A LEU* 1.3 59.6 + - - +
427A SER* 3.2 7.2 + - - -
428A ILE* 2.8 44.0 + - + +
471A PHE* 3.9 25.4 - - + -
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Residues in contact with LEU 425 (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 PHE* 4.9 7.2 - - + -
402A ILE* 5.0 2.5 - - + -
416A THR* 4.0 19.5 - - + -
421A ILE* 2.9 35.1 + - + +
422A ARG 3.8 3.4 - - - +
424A LYS* 1.3 72.1 - - - +
426A ILE* 1.3 61.5 + - - +
428A ILE* 3.8 3.2 - - - +
429A ALA* 2.9 31.0 + - - +
444A ILE* 3.9 9.9 - - + -
464A PHE* 4.2 22.4 - - + -
467A ILE* 4.1 18.4 - - + -
468A LEU* 4.2 19.7 - - + -
471A PHE* 3.9 30.7 - - + -
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Residues in contact with ILE 426 (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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422A ARG* 3.1 43.2 + - - +
423A ASN* 3.7 9.2 - - - +
424A LYS 3.3 0.2 - - - -
425A LEU* 1.3 74.8 - - - +
427A SER* 1.3 65.6 + - - +
429A ALA* 3.4 5.8 + - - +
430A ARG* 3.0 38.6 + - + +
434A VAL 4.6 0.7 - - - +
435A MET* 5.9 1.3 - - + -
436A LEU* 3.9 29.5 + - + +
437A GLY 3.8 6.1 - - - +
438A GLY* 3.6 24.7 - - - +
444A ILE* 4.1 13.9 - - + -
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Residues in contact with SER 427 (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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22A VAL 5.6 1.6 + - - +
423A ASN 2.9 19.2 + - - -
424A LYS* 3.5 8.7 - - - -
426A ILE* 1.3 79.3 - - - +
428A ILE* 1.3 64.2 + - - +
430A ARG* 3.4 19.0 + - - +
431A ASN* 3.2 32.3 + - - -
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Residues in contact with ILE 428 (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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424A LYS* 2.8 36.6 + - + +
425A LEU* 3.8 5.2 - - - +
427A SER* 1.3 75.9 - - - +
429A ALA* 1.3 68.2 + - - +
431A ASN* 3.1 11.4 + - - +
432A LYS* 3.0 29.8 + - + +
467A ILE* 3.6 36.1 - - + -
471A PHE* 4.7 12.1 - - + -
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Residues in contact with ALA 429 (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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425A LEU 2.9 17.5 + - - +
426A ILE 3.7 4.0 - - - +
428A ILE* 1.3 75.8 - - - +
430A ARG* 1.3 61.7 + - - +
432A LYS* 3.0 10.7 + - - +
433A GLY 3.1 1.4 + - - -
434A VAL* 2.9 38.8 + - + +
436A LEU* 3.7 23.6 - - + -
463A ILE* 5.8 0.4 - - + -
464A PHE* 4.4 5.6 - - + -
467A ILE* 3.5 18.8 - - + +
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Residues in contact with ARG 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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18A MET* 3.4 13.0 - - - +
22A VAL* 3.3 48.8 + - + +
23A PRO* 4.0 9.1 - - - +
44A HIS* 4.1 35.7 + - - +
45A PHE* 4.0 5.3 - - - -
65A MET* 3.9 17.5 - - - +
426A ILE* 3.0 29.6 + - + +
427A SER* 3.6 17.9 + - - +
428A ILE 3.1 0.2 - - - -
429A ALA* 1.3 77.2 - - - +
431A ASN* 1.3 61.9 + - - +
433A GLY* 3.1 12.3 + - - -
434A VAL 3.1 11.5 + - - +
435A MET* 3.9 22.3 - - + +
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Residues in contact with ASN 431 (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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18A MET* 3.5 24.6 - - - +
20A THR 5.0 1.8 - - - +
21A GLU* 3.6 12.9 - - - +
22A VAL* 2.8 40.3 + - - +
427A SER* 3.2 19.7 + - - -
428A ILE* 3.1 15.0 + - + +
430A ARG* 1.3 78.0 - - - +
432A LYS* 1.3 60.3 + - + +
433A GLY 3.4 0.2 - - - -
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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
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16A PRO* 4.7 2.3 - - - +
18A MET* 4.1 6.0 - - - +
428A ILE* 3.0 21.5 + - + +
429A ALA 3.0 10.9 + - - +
431A ASN* 1.3 81.2 - - + +
433A GLY* 1.3 55.1 + - - +
434A VAL 3.7 0.2 - - - -
463A ILE* 3.7 37.0 - - + +
466A ASP* 6.2 3.6 - - - -
467A ILE* 3.8 24.2 - - + +
470A ASP* 6.1 1.1 - - - -
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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