Contacts of the helix formed by residues 464 - 469 (chain A) in PDB entry 1Y24
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 PRO 464 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A ARG* 3.1 41.3 + - - +
451A ASN* 5.1 7.6 - - - +
460A LEU* 3.2 31.0 - - + +
461A ARG* 3.7 4.5 - - - -
463A VAL* 1.3 91.1 - - + +
465A PRO* 1.3 76.6 - - + +
466A GLY 3.2 1.1 - - - -
467A PRO* 3.2 8.2 - - + +
468A GLY 3.2 7.1 + - - -
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Residues in contact with PRO 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PHE* 4.1 17.5 - - + -
365A LEU* 3.7 10.1 - - + -
444A ASP* 2.8 34.0 - - + +
447A ARG* 4.9 11.4 - - + +
448A ALA* 5.7 3.6 - - + +
451A ASN* 5.0 12.1 - - - +
457A THR* 6.0 0.2 - - + -
461A ARG 3.1 28.5 - - - +
462A GLY 3.3 8.7 - - - +
464A PRO* 1.3 86.2 - - + +
466A GLY* 1.3 55.9 + - - +
468A GLY* 3.0 2.2 + - - -
469A LEU* 2.8 31.4 + - - +
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Residues in contact with GLY 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LEU* 3.9 5.5 - - - +
462A GLY 2.9 18.3 + - - -
463A VAL* 4.5 2.9 - - - -
464A PRO 3.2 0.6 - - - -
465A PRO* 1.3 71.4 - - - +
467A PRO* 1.3 61.5 - - - +
469A LEU* 3.1 30.8 - - - +
470A VAL* 4.7 1.0 + - - +
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Residues in contact with PRO 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ARG* 4.7 2.7 - - - +
463A VAL* 3.0 28.9 - - + +
464A PRO* 3.2 17.7 - - + +
466A GLY* 1.3 77.0 - - - +
468A GLY* 1.3 59.4 + - - +
469A LEU 3.0 5.6 + - - -
470A VAL* 3.0 28.8 + - + +
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Residues in contact with GLY 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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441A TYR* 5.1 0.2 - - - -
442A ALA* 3.0 30.7 + - - -
443A SER 3.8 1.6 + - - -
444A ASP* 3.1 10.4 + - - +
447A ARG* 3.3 29.7 - - - +
464A PRO 3.2 7.5 + - - -
465A PRO 3.0 6.2 + - - -
467A PRO* 1.3 74.1 - - - +
469A LEU* 1.3 54.4 + - - +
470A VAL 3.2 2.4 + - - +
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Residues in contact with LEU 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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364A THR 4.3 5.6 - - - +
365A LEU* 3.4 21.3 - - + -
366A THR* 3.0 73.3 - - - +
371A VAL* 5.8 1.0 - - - +
442A ALA* 3.4 17.1 - - - +
444A ASP* 3.0 26.9 + - - +
465A PRO 2.8 7.5 + - - +
466A GLY* 3.1 26.9 - - - +
468A GLY* 1.3 72.2 - - - +
470A VAL* 1.3 59.8 + - - +
471A TYR* 3.7 0.7 + - - -
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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