Contacts of the helix formed by residues 442 - 454 (chain P) in PDB entry 3HX0
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 GLY 442 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440P HIS 3.4 1.4 + - - -
441P ARG* 1.3 71.5 - - - +
443P ILE* 1.3 61.1 + - - +
444P PHE* 2.8 8.8 + - - +
445P SER* 3.2 16.4 + - - -
446P ARG* 3.6 8.9 + - - +
471P GLN* 4.8 10.0 + - - +
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Residues in contact with ILE 443 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403P ALA* 6.0 0.2 - - + -
406P PHE* 4.5 20.8 - - + -
407P ASN* 5.5 2.7 - - + -
410P LEU* 4.4 24.5 - - + -
432P ILE* 4.2 20.9 - - + -
439P SER 3.6 19.5 - - - +
440P HIS* 2.9 24.7 - - - +
441P ARG 3.3 1.8 + - - +
442P GLY* 1.3 73.7 - - - +
444P PHE* 1.3 60.4 + - - +
445P SER 3.4 0.2 - - - -
446P ARG* 3.9 9.1 - - - +
447P LEU* 2.8 39.7 + - + +
493P VAL* 3.5 26.5 - - + -
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Residues in contact with PHE 444 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440P HIS 4.4 0.4 + - - -
442P GLY 2.8 2.5 + - - +
443P ILE* 1.3 90.5 - - - +
445P SER* 1.3 66.9 + - - +
447P LEU* 3.5 4.7 + - + +
448P LEU* 3.3 46.5 + - + +
463P SER 4.5 2.7 - - - -
464P GLN* 3.9 26.9 - - + -
471P GLN* 3.0 64.8 - - + +
472P LYS 3.9 19.5 - - - -
473P TYR* 4.0 12.8 - - + -
491P ILE* 4.1 10.8 - - + -
493P VAL* 3.8 19.7 - - + -
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Residues in contact with SER 445 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252F HIS* 5.0 11.6 - - - -
442P GLY* 3.2 8.0 + - - -
444P PHE* 1.3 82.9 - - - +
446P ARG* 1.3 67.0 + - - +
447P LEU 3.2 0.5 + - - -
448P LEU* 3.2 8.0 + - - +
449P ASP* 3.1 24.2 + - - +
471P GLN* 5.4 1.1 - - - +
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Residues in contact with ARG 446 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406P PHE* 3.7 28.4 - - + -
442P GLY 3.6 7.6 + - - +
443P ILE* 3.4 10.9 + - - +
445P SER* 1.3 78.1 - - - +
447P LEU* 1.3 62.4 + - - +
449P ASP* 3.5 7.6 + - - +
450P SER* 3.1 22.9 + - - -
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Residues in contact with LEU 447 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399P VAL* 3.7 15.7 - - + +
402P ALA* 4.0 8.5 - - + +
403P ALA* 3.8 31.4 - - + +
406P PHE* 3.9 11.4 - - + -
432P ILE* 3.5 31.6 - - + -
443P ILE* 2.8 28.0 + - + +
444P PHE* 3.7 6.1 - - + +
446P ARG* 1.3 74.0 - - - +
448P LEU* 1.3 61.4 + - + +
450P SER* 3.0 5.4 + - - -
451P LEU* 2.9 48.8 + - + +
491P ILE* 4.5 9.9 - - + -
493P VAL* 6.0 0.4 - - + -
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Residues in contact with LEU 448 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444P PHE* 3.3 43.0 + - + +
445P SER* 3.2 9.7 + - - +
447P LEU* 1.3 79.8 - - + +
449P ASP* 1.3 54.8 + - - +
451P LEU* 4.4 4.7 - - + +
452P ARG* 2.7 56.5 + - - +
457P LEU* 3.9 12.0 - - + +
463P SER 3.8 17.5 - - - +
473P TYR* 3.7 36.8 - - + -
491P ILE* 4.2 15.7 - - + -
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Residues in contact with ASP 449 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290F HIS* 3.1 56.9 + - - +
291F LYS* 4.5 2.8 - - - +
445P SER* 3.1 13.7 + - - +
446P ARG* 3.6 11.9 - - - +
448P LEU* 1.3 75.8 - - - +
450P SER* 1.3 57.6 + - - +
452P ARG* 3.7 13.4 - - - +
453P GLN* 2.8 35.3 + - - +
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Residues in contact with SER 450 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402P ALA* 4.2 8.4 + - - +
406P PHE* 4.3 14.0 - - - -
446P ARG 3.1 13.3 + - - -
447P LEU* 3.0 15.6 + - - -
449P ASP* 1.3 76.9 - - - +
451P LEU* 1.3 57.6 + - - +
453P GLN* 3.2 5.5 + - - +
454P GLU* 2.9 44.7 + - - +
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Residues in contact with LEU 451 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398P THR* 4.1 13.5 - - + +
399P VAL* 3.9 26.7 - - + -
402P ALA* 4.0 12.6 - - + -
447P LEU* 2.9 41.9 + - + +
448P LEU* 4.0 4.7 - - + +
450P SER* 1.3 73.5 - - - +
452P ARG* 1.3 61.5 + - - +
454P GLU* 3.2 25.3 + - - +
456P PHE* 3.1 47.1 + - + -
457P LEU* 3.5 19.4 + - + -
491P ILE* 4.1 11.7 - - + -
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Residues in contact with ARG 452 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290F HIS* 6.1 2.2 - - - +
448P LEU* 2.7 55.4 + - - +
449P ASP* 3.7 16.5 + - - +
451P LEU* 1.3 74.1 - - - +
453P GLN* 1.3 59.6 + - - +
455P GLY* 3.8 7.8 + - - -
457P LEU* 3.7 31.0 - - + +
460P ASP* 3.6 33.0 + - - +
463P SER* 5.1 5.7 + - - -
473P TYR* 5.0 0.2 - - - -
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Residues in contact with GLN 453 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290F HIS* 5.9 6.3 - - + +
449P ASP* 2.8 29.6 + - - +
450P SER* 3.7 4.7 - - - +
452P ARG* 1.3 76.7 - - - +
454P GLU* 1.3 57.2 + - - +
455P GLY 3.2 5.5 + - - -
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Residues in contact with GLU 454 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398P THR* 5.4 4.7 - - - +
402P ALA* 3.8 9.7 - - - +
450P SER* 2.9 42.1 + - - +
451P LEU* 3.2 30.3 - - - +
453P GLN* 1.3 75.9 - - - +
455P GLY* 1.3 58.9 + - - +
456P PHE* 3.4 8.6 + - + +
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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