Contacts of the strand formed by residues 446 - 450 (chain A) in PDB entry 2AYO
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 TRP 446 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A LEU* 4.9 12.1 - - + -
419A LEU* 3.8 34.8 - - + -
420A GLN 3.2 19.7 + - - -
422A VAL* 4.6 2.0 - - + +
438A TRP* 3.6 22.8 + - + +
439A VAL 3.8 11.0 + - - -
440A LYS* 3.1 57.0 - - + -
444A ASP 3.9 1.5 + - - -
445A GLU* 1.3 73.8 - - - +
447A ILE* 1.3 57.7 + - - +
456A ILE* 3.8 3.4 - - - +
457A VAL* 2.7 54.6 + - + +
458A THR 4.4 4.3 - - - -
459A PRO* 4.4 19.3 - - + -
462A ILE* 2.9 48.0 - - + +
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Residues in contact with ILE 447 (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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102A LEU* 5.6 3.6 - - + -
103A PRO* 3.9 22.2 - - + -
438A TRP* 3.2 10.3 - - - +
439A VAL* 2.9 35.6 + - + +
441A ARG* 3.8 45.1 - - + +
442A LYS* 6.5 2.0 - - + -
445A GLU 5.2 1.6 - - - +
446A TRP* 1.3 73.9 - - - +
448A LYS* 1.3 64.3 + - - +
449A PHE* 3.2 37.9 + - + -
454A VAL* 4.0 9.0 - - + -
455A SER 3.4 13.2 - - - +
456A ILE* 4.6 13.2 - - + -
457A VAL* 4.7 1.3 - - - -
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Residues in contact with LYS 448 (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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436A VAL* 4.0 10.3 - - + -
437A SER 3.8 4.0 - - - -
438A TRP* 3.5 40.8 - - + -
446A TRP 4.2 0.4 + - - -
447A ILE* 1.3 76.6 - - - +
449A PHE* 1.3 52.1 + - - +
450A ASP* 2.6 46.0 + - - -
453A LYS* 3.1 15.0 - - - +
455A SER* 3.1 34.1 + - - +
457A VAL* 4.2 15.5 - - + -
471A TRP* 5.4 8.3 - - - -
472A HIS* 5.6 3.5 + - - -
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Residues in contact with PHE 449 (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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103A PRO* 4.2 7.6 - - + -
104A CYS 4.1 10.8 - - - -
105A GLY* 6.0 0.7 - - - -
117A ALA* 5.8 0.3 - - - -
120A GLN* 2.8 61.9 - - + +
123A ARG* 4.1 15.7 - - - -
436A VAL* 3.8 2.2 - - - +
437A SER* 3.2 35.2 + - - +
439A VAL* 5.1 10.5 - - + -
441A ARG* 3.9 25.1 - - - -
447A ILE* 3.2 35.8 - - + -
448A LYS* 1.3 67.5 - - - +
450A ASP* 1.3 60.5 + - - +
451A ASP 3.7 2.4 + - - -
454A VAL* 3.5 24.0 - - + +
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Residues in contact with ASP 450 (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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434A HIS* 3.2 33.6 + - - -
435A TYR 5.5 0.2 - - - +
436A VAL* 4.1 12.1 - - + +
448A LYS* 2.6 32.4 + - - -
449A PHE* 1.3 71.1 - - - +
451A ASP* 1.3 70.9 + - - +
452A ASP 4.5 0.3 + - - -
453A LYS* 2.4 70.7 + - + +
454A VAL* 4.2 0.5 + - - +
472A HIS* 5.7 0.3 + - - -
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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