Contacts of the strand formed by residues 499 - 503 (chain N) in PDB entry 2AS5
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 499 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458N ILE* 2.8 47.6 + - + +
476N VAL* 3.8 23.1 - - + +
478N ARG* 3.7 28.9 - - + +
488N SER* 3.6 21.8 - - - -
489N TYR 3.4 15.5 - - - +
490N GLU* 4.4 3.8 - - + -
498N VAL* 1.3 74.5 - - - +
500N GLU* 1.3 58.5 + - - +
501N ILE* 4.5 3.8 - - + -
515N CYS* 3.8 33.7 - - - +
516N ALA* 4.1 16.4 - - + -
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Residues in contact with GLU 500 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455N GLY* 3.3 34.7 - - - -
456N LEU 3.8 5.4 - - - +
457N GLN* 4.5 3.8 - - + +
487N THR 4.3 0.3 - - - +
488N SER* 3.6 4.2 - - - -
489N TYR* 2.6 76.0 + - + +
491N LYS* 3.2 34.1 + - - +
498N VAL 4.0 2.4 + - - -
499N LEU* 1.3 71.9 - - - +
501N ILE* 1.3 62.6 + - - +
502N PRO* 4.4 1.2 - - - +
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Residues in contact with ILE 501 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455N GLY* 3.6 1.6 - - - -
456N LEU* 2.6 48.1 + - + +
458N ILE* 3.4 26.2 - - + -
486N THR* 3.2 22.0 - - + -
487N THR 3.3 15.9 - - - +
488N SER* 3.4 13.2 - - - -
499N LEU* 4.5 2.5 - - + +
500N GLU* 1.3 77.9 - - - +
502N PRO* 1.3 74.4 - - + +
511N ALA* 4.1 16.2 - - + -
513N ILE* 4.4 5.2 - - + -
515N CYS* 3.3 32.8 - - - -
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Residues in contact with PRO 502 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453N PRO* 5.4 4.3 - - + -
454N LEU 3.6 7.2 - - - +
455N GLY* 4.7 1.3 - - - -
486N THR* 4.7 1.1 - - + -
487N THR* 3.1 36.3 - - - +
500N GLU 4.4 1.1 - - - +
501N ILE* 1.3 99.6 - - + +
503N LEU* 1.3 61.2 + - - +
504N GLU* 4.0 23.9 + - + +
511N ALA* 3.9 7.8 - - - +
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Residues in contact with LEU 503 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410N LEU* 5.0 4.0 - - + -
443N VAL* 4.2 6.7 - - + -
445N LEU* 3.9 29.6 - - + +
453N PRO* 3.4 3.6 - - - +
454N LEU* 2.8 32.5 + - + +
456N LEU* 3.4 38.6 - - + -
502N PRO* 1.3 72.0 - - - +
504N GLU* 1.3 60.5 + - - +
509N MET* 3.7 34.8 - - + +
510N ARG 5.1 0.7 - - - +
511N ALA* 3.2 42.2 - - + +
548N VAL* 4.6 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