Contacts of the strand formed by residues 422 - 427 (chain A) in PDB entry 1YC0
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 LEU 422 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A HIS* 2.8 21.9 + - + +
420A PRO 4.7 1.7 - - - +
421A TRP* 1.3 85.0 - - + +
423A ALA* 1.3 60.6 + - - +
424A ALA 4.4 0.2 + - - -
433A ALA* 4.0 14.8 - - + -
434A GLY 3.2 17.7 - - - +
461A VAL 4.4 2.6 - - - +
462A LEU* 4.1 7.3 - - - +
463A GLY 4.4 9.9 + - - -
464A GLN 5.2 3.2 + - - +
538A ALA* 3.8 24.0 - - + +
539A GLY* 4.4 0.7 - - - -
540A TRP* 4.0 20.3 - - + -
554A LEU* 3.1 39.5 - - + -
600A GLY* 4.1 1.1 - - - -
601A PRO* 3.3 24.2 - - + -
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Residues in contact with ALA 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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421A TRP 4.3 1.8 - - - +
422A LEU* 1.3 76.8 - - - +
424A ALA* 1.3 60.6 + - - +
425A ILE* 4.8 1.1 - - + -
433A ALA* 3.1 12.0 - - - +
434A GLY* 2.9 45.6 + - - +
435A SER* 4.9 0.2 - - - -
442A VAL* 4.1 7.9 - - + -
460A VAL* 4.0 14.8 - - + -
461A VAL 3.6 3.8 - - - -
462A LEU* 3.5 22.4 - - + -
540A TRP* 4.2 4.7 - - - -
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Residues in contact with ALA 424 (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 LEU 4.4 0.2 + - - -
423A ALA* 1.3 71.2 - - - +
425A ILE* 1.3 61.6 + - - +
426A TYR* 3.6 16.1 - - + -
431A PHE* 3.7 17.5 - - + -
459A SER 3.4 1.7 - - - +
460A VAL* 3.3 3.3 - - - -
461A VAL* 2.7 44.2 + - + +
464A GLN* 3.1 30.1 - - - +
540A TRP* 4.1 8.2 - - + -
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Residues in contact with ILE 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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423A ALA* 4.2 3.1 - - + +
424A ALA* 1.3 74.8 - - - +
426A TYR* 1.3 61.2 + - - +
427A ILE* 3.5 26.5 + - + +
431A PHE* 3.4 5.0 - - - -
432A CYS* 2.9 39.2 + - + +
433A ALA 3.3 27.4 - - - +
434A GLY* 4.0 5.4 - - - +
442A VAL* 4.3 3.8 - - + -
444A SER* 3.6 14.4 - - - +
449A PHE* 3.9 14.8 - - + -
458A VAL* 4.1 12.1 - - + -
459A SER 3.4 4.3 - - - +
460A VAL* 4.4 16.8 - - + -
501A ILE* 3.6 21.1 - - + -
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Residues in contact with TYR 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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424A ALA* 3.6 13.7 - - + -
425A ILE* 1.3 68.6 - - - +
427A ILE* 1.3 61.8 + - - +
428A GLY 3.7 6.7 - - - +
430A SER 3.7 5.6 - - - +
431A PHE* 3.7 26.2 - + + -
457A SER 3.4 7.3 - - - +
458A VAL* 3.4 0.3 - - - -
459A SER* 2.8 49.6 + - - +
461A VAL* 3.5 28.7 - - + -
464A GLN* 2.4 30.2 + - - -
467A PHE* 4.0 15.3 - + - -
468A ASN* 3.0 36.6 + - + -
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Residues in contact with ILE 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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425A ILE* 3.6 24.7 - - + +
426A TYR* 1.3 69.2 - - - +
428A GLY* 1.3 59.7 + - - +
429A ASP 3.2 0.5 + - - -
430A SER* 2.8 40.2 + - - +
431A PHE 4.9 1.1 - - - -
432A CYS* 4.2 14.4 - - + +
448A CYS* 3.7 31.9 - - + +
449A PHE* 3.9 24.0 - - + -
453A PRO* 3.5 37.7 - - + -
457A SER* 3.8 2.7 - - - -
458A VAL* 4.6 6.7 - - + +
263I PHE* 5.0 6.5 - - + -
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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