Contacts of the helix formed by residues 460 - 469 (chain A) in PDB entry 3H44
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 ARG 460 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325A TYR* 4.8 11.1 - - - -
328A SER* 3.5 26.0 + - - +
330A PRO* 6.0 0.2 - - + -
411A PHE* 5.4 0.2 - - - -
458A GLU* 3.8 21.5 + - + +
459A PHE* 1.3 84.5 - - - +
461A PRO* 1.3 68.5 - - - +
462A ASP* 2.5 43.1 + - - +
463A LEU* 3.1 36.8 + - + +
464A ILE* 3.0 31.5 + - + +
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Residues in contact with PRO 461 (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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406A PRO* 3.6 31.3 - - + +
459A PHE* 3.5 35.2 - - + +
460A ARG* 1.3 89.1 - - - +
462A ASP* 1.3 60.7 + - - +
464A ILE* 4.3 2.2 - - + -
465A GLU* 2.8 35.0 + - - +
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Residues in contact with ASP 462 (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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460A ARG* 2.5 50.4 + - - +
461A PRO* 1.3 77.7 - - - +
463A LEU* 1.3 58.4 + - - +
465A GLU* 3.4 7.0 - - - +
466A MET* 2.7 33.7 + - - +
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Residues in contact with LEU 463 (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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325A TYR* 3.8 47.6 - - + +
328A SER* 3.4 25.4 - - - +
330A PRO* 3.8 15.7 - - + -
460A ARG* 3.1 47.0 + - + +
462A ASP* 1.3 75.3 - - - +
464A ILE* 1.3 70.0 + - - +
465A GLU 3.1 0.9 - - - -
466A MET* 3.0 12.5 + - + -
467A VAL* 2.7 30.2 + - + +
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Residues in contact with ILE 464 (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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328A SER 5.5 4.3 - - - +
330A PRO* 3.7 16.6 - - + +
333A TYR* 3.8 54.1 - - + -
334A LEU* 3.9 14.8 - - + +
406A PRO* 3.9 21.1 - - + -
411A PHE* 5.6 1.6 - - + -
459A PHE* 4.0 22.4 - - + -
460A ARG* 3.0 33.7 + - + +
461A PRO* 3.7 4.5 - - + +
463A LEU* 1.3 74.9 - - - +
465A GLU* 1.3 58.6 + - - +
468A LEU* 3.0 35.0 + - + +
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Residues in contact with GLU 465 (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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402A ARG* 6.5 0.7 - - + -
406A PRO* 4.6 14.5 - - + +
461A PRO* 2.8 21.7 + - - +
462A ASP* 3.4 8.1 - - - +
464A ILE* 1.3 79.5 - - - +
466A MET* 1.3 58.3 + - - +
468A LEU* 3.4 10.9 + - + +
469A ASP* 3.0 29.1 + - + +
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Residues in contact with MET 466 (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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320A PRO* 3.6 36.1 - - + -
322A LEU* 5.1 6.1 - - + -
325A TYR* 5.3 7.0 - - + +
462A ASP 2.7 22.1 + - - +
463A LEU* 3.0 19.5 + - + +
465A GLU* 1.3 69.8 - - - +
467A VAL* 1.3 83.4 + - + +
469A ASP* 3.3 18.1 - - - +
470A LYS* 3.7 27.8 + - + +
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Residues in contact with VAL 467 (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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319A ILE* 4.6 18.6 - - + -
320A PRO* 6.4 0.4 - - + -
322A LEU* 3.9 31.6 - - + -
330A PRO* 4.1 16.2 - - + -
331A GLY* 5.0 1.8 - - - +
334A LEU* 3.6 21.5 - - + -
373A PHE* 4.7 12.6 - - + -
463A LEU* 2.7 22.9 + - - +
466A MET* 1.3 82.8 - - + +
468A LEU* 1.3 57.0 + - - +
470A LYS* 2.6 38.0 + - - +
471A LEU* 3.6 6.7 + - + +
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Residues in contact with LEU 468 (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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334A LEU* 3.8 32.0 - - + +
338A ILE* 5.3 0.9 - - + -
398A ILE* 3.6 28.7 - - + -
401A LEU* 4.2 16.4 - - + +
402A ARG* 2.8 53.7 + - + +
406A PRO* 5.6 4.7 - - + -
464A ILE* 3.0 25.4 + - + +
465A GLU* 3.4 10.5 - - + +
467A VAL* 1.3 75.1 - - - +
469A ASP* 1.3 55.6 + - - +
471A LEU* 3.0 29.9 + - + +
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Residues in contact with ASP 469 (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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402A ARG* 3.7 5.8 - - - +
465A GLU* 3.0 13.5 + - + +
466A MET* 3.3 16.6 - - - +
467A VAL 2.8 1.0 + - - -
468A LEU* 1.3 77.0 - - - +
470A LYS* 1.3 61.2 + - + +
472A ARG* 2.8 64.0 + - - +
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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