Contacts of the strand formed by residues 442 - 451 (chain A) in PDB entry 2PA5
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 TYR 442 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A MET* 2.8 69.3 + - + +
440A ASN 3.8 0.6 - - - -
441A HIS* 1.3 86.9 - - + +
443A LYS* 1.3 72.0 + - - +
444A LYS* 4.4 6.3 - - + +
463A PHE* 4.0 19.3 - + - -
464A GLN 3.1 15.7 - - - +
465A PHE* 4.1 0.2 - - - -
466A LEU* 3.7 8.8 - - - +
482A ASP* 4.9 7.4 - - - -
483A PHE* 3.6 28.7 - + + -
486A VAL* 3.6 42.5 - - + +
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Residues in contact with LYS 443 (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 TRP* 4.4 16.7 - - - +
418A LEU* 4.6 16.1 + - - +
436A VAL* 3.3 30.1 - - + -
437A GLU 3.3 13.2 - - - +
438A ASN* 3.8 20.9 - - - +
442A TYR* 1.3 79.3 - - - +
444A LYS* 1.3 62.6 + - - +
445A THR* 3.7 12.6 + - - +
462A HIS* 3.7 1.7 + - - +
463A PHE* 3.4 4.2 - - - -
464A GLN* 2.9 55.0 + - + +
466A LEU* 4.2 11.0 - - + -
705B EDO 4.3 17.3 + - - +
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Residues in contact with LYS 444 (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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435A GLY 4.0 0.5 - - - +
436A VAL* 3.3 3.1 - - - +
437A GLU* 2.8 46.1 + - + +
439A MET* 4.8 5.2 - - - -
442A TYR* 4.3 10.1 - - + +
443A LYS* 1.3 73.3 - - - +
445A THR* 1.3 64.8 + - - +
446A THR* 4.3 11.0 - - - +
461A THR* 3.8 24.5 - - + -
462A HIS 3.6 3.4 - - - -
463A PHE* 3.7 29.3 - - + -
486A VAL* 6.0 0.4 - - + -
490A GLN* 3.9 16.2 + - - -
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Residues in contact with THR 445 (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 TRP* 4.3 12.1 + - + +
433A ASN* 3.5 28.5 - - - +
435A GLY 3.3 7.6 - - - +
436A VAL* 3.9 3.4 - - + +
443A LYS* 3.7 23.4 - - - +
444A LYS* 1.3 77.4 + - - +
446A THR* 1.3 63.9 + - - +
447A LEU* 3.7 22.1 + - + -
461A THR* 3.7 2.6 - - - +
462A HIS* 2.9 49.1 + - - +
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Residues in contact with THR 446 (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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433A ASN* 3.7 4.2 - - - +
434A LEU* 2.8 45.3 + - + -
435A GLY* 2.9 14.9 + - - +
444A LYS* 4.3 14.9 - - - +
445A THR* 1.3 72.5 - - - +
447A LEU* 1.3 62.6 + - - +
459A GLN* 3.5 31.4 - - + +
460A VAL 3.9 5.8 - - - +
461A THR* 4.8 8.5 + - - +
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Residues in contact with LEU 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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387A TRP* 3.6 29.4 - - + -
398A ILE* 5.1 2.0 - - + -
416A TRP* 4.1 16.4 - - + -
417A PRO* 4.1 11.9 - - + +
431A VAL* 4.1 17.5 - - + -
432A THR 3.3 3.4 - - - +
433A ASN* 3.9 15.7 - - - -
434A LEU* 4.6 3.6 - - - -
445A THR* 3.7 25.1 - - + +
446A THR* 1.3 76.3 - - - +
448A GLU* 1.3 60.5 + - - +
449A ILE* 4.1 0.9 - - + -
459A GLN* 3.2 7.4 - - - +
460A VAL* 2.9 44.9 + - + +
462A HIS* 4.0 22.7 - - + -
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Residues in contact with GLU 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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430A THR 3.5 1.6 - - - +
431A VAL* 3.2 4.9 - - - +
432A THR* 2.8 47.5 + - - +
434A LEU* 3.9 28.1 - - + +
447A LEU* 1.3 74.1 - - - +
449A ILE* 1.3 69.7 + - - +
450A HIS* 4.1 9.2 + - - +
457A LYS* 3.8 40.2 + - + +
458A ARG 3.3 10.3 - - - +
459A GLN* 4.4 5.0 + - + +
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Residues in contact with ILE 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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387A TRP* 3.7 23.6 - - + +
390A VAL* 3.4 34.3 - - + -
391A TRP* 3.7 32.9 - - + +
429A LEU* 4.0 22.2 - - + -
430A THR 3.4 7.2 - - - +
431A VAL* 4.4 12.8 - - + +
447A LEU* 5.5 0.7 - - + -
448A GLU* 1.3 75.5 - - - +
450A HIS* 1.3 61.7 + - - +
457A LYS* 3.3 3.5 - - - -
458A ARG* 2.8 38.2 + - + +
460A VAL* 3.7 20.0 - - + -
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Residues in contact with HIS 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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428A PHE 3.5 0.2 - - - +
429A LEU* 3.5 2.8 - - - -
430A THR* 2.8 46.7 + - + +
432A THR* 6.1 0.4 - - - +
448A GLU* 3.9 11.1 + - - +
449A ILE* 1.3 73.6 - - - +
451A ASN* 1.3 73.4 + - - +
452A THR* 3.5 27.4 + - + +
455A ARG* 4.9 5.6 - - - +
456A GLN 3.5 15.4 + - - -
457A LYS* 3.6 35.8 - - + -
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Residues in contact with ASN 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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391A TRP* 3.3 51.8 - - + +
428A PHE* 3.4 18.2 - - - -
429A LEU* 3.8 17.7 - - + +
449A ILE 4.0 1.8 + - - -
450A HIS* 1.3 71.2 - - - +
452A THR* 1.3 58.5 + - - +
453A GLU* 2.9 21.7 + - - +
454A GLU* 2.9 24.5 + - + +
455A ARG* 2.9 23.4 + - - -
456A GLN 2.8 15.9 + - - +
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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