Contacts of the strand formed by residues 484 - 491 (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 ASP 484 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A TRP* 4.7 12.5 + - - -
422A ALA* 3.8 19.4 - - + +
423A SER 3.1 24.7 - - - +
424A ALA* 3.2 10.6 + - - +
479A GLY 5.0 0.3 - - - +
480A LEU* 3.2 17.2 - - - +
481A CYS* 2.9 22.8 + - - +
482A SER* 2.9 23.6 + - - +
483A PRO* 1.3 76.3 - - - +
485A GLY* 1.3 61.9 + - - +
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Residues in contact with GLY 485 (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 ALA* 3.0 20.0 - - - -
423A SER 2.8 9.1 + - - -
478A ASN* 5.3 0.9 - - - -
479A GLY 5.6 1.1 - - - -
480A LEU* 3.7 20.4 - - - +
484A ASP* 1.3 74.0 - - - +
486A GLU* 1.3 59.5 + - - -
487A TRP* 3.0 33.2 - - - -
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Residues in contact with GLU 486 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A LEU* 5.4 1.0 - - - +
420A VAL* 3.2 26.8 - - + +
421A LEU 2.9 26.7 + - - +
422A ALA* 3.2 19.3 + - - +
478A ASN* 5.3 7.9 + - - +
485A GLY* 1.3 72.1 - - - -
487A TRP* 1.3 67.9 + - - +
488A ARG* 3.6 41.2 + - + +
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Residues in contact with TRP 487 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A LEU* 5.9 2.0 - - + -
419A GLY 3.2 3.2 - - - +
420A VAL* 3.1 6.1 + - - -
421A LEU* 2.9 54.9 + - + +
423A SER* 3.6 20.9 - - - -
425A HIS* 3.2 25.8 - + - -
432A ASP* 2.9 22.6 + - - -
478A ASN* 4.5 11.0 - - - +
485A GLY* 3.0 35.0 - - - -
486A GLU* 1.3 76.5 - - - +
488A ARG* 1.3 60.6 + - - +
489A ARG* 3.9 16.3 + - - +
499A GLU* 2.9 40.2 + - + +
501A PHE* 3.5 29.2 - + + -
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Residues in contact with ARG 488 (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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418A VAL* 5.6 3.8 - - + -
419A GLY 3.3 5.2 - - - +
420A VAL* 3.7 28.0 - - + +
486A GLU* 3.6 35.9 + - + +
487A TRP* 1.3 72.2 - - - +
489A ARG* 1.3 67.6 + - - +
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Residues in contact with ARG 489 (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 TRP* 2.8 42.6 - - - -
404A GLU* 5.2 3.3 + - - +
417A THR 3.9 0.7 - - - +
418A VAL* 3.4 5.3 - - - +
419A GLY* 2.8 40.6 + - - +
421A LEU* 5.5 1.8 - - - +
434A TRP* 3.1 41.2 - - + +
487A TRP* 3.9 15.7 - - + +
488A ARG* 1.3 81.6 - - - +
490A LEU* 1.3 65.5 + - - +
491A GLY 4.0 0.2 + - - -
495A PHE* 4.9 3.0 - - - -
497A THR* 3.5 12.3 - - - +
499A GLU* 3.0 34.8 + - - -
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Residues in contact with LEU 490 (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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416A HIS* 4.5 23.1 - - + +
417A THR 3.8 0.7 - - - -
418A VAL* 3.7 33.0 - - + +
434A TRP* 5.7 1.0 - - - -
489A ARG* 1.3 78.7 - - - +
491A GLY* 1.3 61.1 + - - +
492A ARG* 3.2 15.4 + - + +
495A PHE* 4.1 13.4 - - - -
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Residues in contact with GLY 491 (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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404A GLU* 4.5 10.3 + - - -
406A SER* 3.9 10.1 + - - -
415A ASN 3.8 1.7 - - - +
416A HIS* 3.2 5.7 - - - -
417A THR 2.7 42.9 + - - -
489A ARG 4.0 1.0 + - - -
490A LEU* 1.3 67.5 - - - +
492A ARG* 1.3 68.7 + - - +
495A PHE* 3.6 19.5 - - - -
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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