Contacts of the strand formed by residues 449 - 453 (chain A) in PDB entry 2AR0
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 449 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A THR* 4.0 15.0 - - + -
378A TRP* 3.4 48.3 - + + -
379A VAL 3.5 21.3 - - - -
380A TYR* 3.4 34.3 - + + -
403A PHE* 4.0 11.9 - + - -
406A VAL* 3.6 43.6 + - + +
407A TYR* 4.5 2.7 - - - -
417A ARG* 3.9 26.1 - - - +
418A THR 3.6 23.4 + - - +
419A GLU* 3.6 3.2 - - - +
420A GLY 3.2 14.0 + - - -
421A GLU* 3.5 22.0 + - + +
447A SER* 3.1 13.4 + - - +
448A ARG* 1.3 78.5 - - - +
450A ARG* 1.3 64.0 + - - +
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Residues in contact with ARG 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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378A TRP* 3.6 6.7 - - - -
379A VAL 2.9 32.3 + - - +
419A GLU* 3.4 18.3 + - - +
436A GLU 3.0 24.6 + - - -
437A ASN* 2.9 27.9 + - - -
440A THR* 3.2 23.0 + - - +
444A LEU* 3.4 29.7 + - + +
445A ALA* 4.3 0.2 - - - +
447A SER* 4.0 4.5 - - - +
448A ARG 4.1 0.4 - - - -
449A TRP* 1.3 82.6 - - - +
451A LYS* 1.3 61.5 + - - +
452A PHE* 3.6 27.1 - - + -
469A TRP* 3.4 43.4 - - + +
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Residues in contact with LYS 451 (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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376A ASP* 3.0 39.4 + - - +
377A VAL 3.4 7.4 - - - +
378A TRP* 3.5 43.1 - - + +
419A GLU* 3.1 30.1 + - + +
450A ARG* 1.3 74.0 + - - +
452A PHE* 1.3 73.6 + - - +
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Residues in contact with PHE 452 (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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376A ASP* 3.6 4.4 - - - +
377A VAL* 2.8 42.2 + - - +
379A VAL* 4.0 9.2 - - + -
436A GLU* 4.0 22.4 - - + -
450A ARG* 3.6 44.4 - - + -
451A LYS* 1.3 80.0 - - - +
453A SER* 1.3 63.2 + - - +
456A TRP* 3.6 38.8 - + + -
457A ILE* 4.4 3.3 - - + +
467A ILE* 3.6 20.6 - - + -
469A TRP* 3.6 40.4 - + - -
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Residues in contact with SER 453 (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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375A ASP 3.7 1.1 - - - -
376A ASP* 3.5 15.6 + - - -
452A PHE* 1.3 73.0 - - - +
454A ARG* 1.3 60.7 + - - +
455A GLU* 3.9 6.8 + - - +
456A TRP* 3.1 27.5 + - - +
457A ILE* 3.0 31.7 + - - +
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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