Contacts of the strand formed by residues 442 - 451 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439B MET* 2.9 67.9 + - + +
440B ASN 3.6 1.2 + - - -
441B HIS* 1.3 119.8 - + - +
443B LYS* 1.3 74.7 + - - +
444B LYS* 4.4 7.6 - - + -
463B PHE* 4.2 24.7 - + - -
464B GLN 3.1 15.3 - - - +
465B PHE* 4.0 0.2 - - - -
466B LEU* 4.3 4.8 - - - +
482B ASP* 4.0 6.0 + - - -
483B PHE* 3.5 25.4 - + + -
486B VAL* 3.6 29.2 - - + +
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Residues in contact with LYS 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436B VAL* 4.5 18.4 - - + -
437B GLU 3.3 5.6 - - - +
438B ASN* 4.3 21.1 - - - -
439B MET 5.5 0.7 - - - +
442B TYR* 1.3 79.8 - - - +
444B LYS* 1.3 60.5 + - - +
445B THR* 4.0 4.5 + - - +
462B HIS* 3.6 1.9 + - - +
463B PHE* 3.4 4.3 - - - -
464B GLN* 2.9 48.5 + - + +
466B LEU* 3.7 24.2 - - + -
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Residues in contact with LYS 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B GLY 3.8 0.5 - - - +
436B VAL* 3.3 2.8 - - - -
437B GLU* 2.8 65.8 + - + +
439B MET* 5.5 0.2 - - + -
442B TYR* 4.3 9.6 - - + -
443B LYS* 1.3 72.9 - - - +
445B THR* 1.3 61.0 + - - +
446B THR* 4.2 10.4 + - - +
461B THR* 3.7 20.2 - - + -
462B HIS 3.5 2.9 - - - -
463B PHE* 3.6 28.3 - - + -
486B VAL* 6.0 0.9 - - + -
490B GLN* 3.5 25.4 + - - -
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Residues in contact with THR 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B TRP* 4.2 15.8 + - + -
418B LEU 5.4 0.2 + - - -
433B ASN* 3.5 28.9 - - - +
435B GLY 3.3 9.0 - - - +
436B VAL* 3.8 15.5 - - + +
443B LYS* 4.9 4.0 + - - +
444B LYS* 1.3 75.7 + - - +
446B THR* 1.3 61.9 + - - +
447B LEU* 3.7 21.7 + - + -
461B THR* 3.6 2.8 - - - -
462B HIS* 2.7 56.5 + - - +
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Residues in contact with THR 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433B ASN* 3.7 3.3 - - - -
434B LEU* 2.7 51.2 + - + -
435B GLY* 2.9 16.6 + - - +
444B LYS* 4.2 15.4 + - - +
445B THR* 1.3 73.2 - - - +
447B LEU* 1.3 58.9 + - - +
459B GLN* 3.6 40.6 + - + +
460B VAL 3.8 4.0 - - - +
461B THR* 4.7 6.8 + - - +
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Residues in contact with LEU 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B TRP* 3.6 33.4 - - + -
398B ILE* 5.1 0.2 - - + -
416B TRP* 4.5 11.2 - - + -
417B PRO* 4.3 8.7 - - + -
431B VAL* 4.2 15.0 - - + -
432B THR 3.2 13.9 - - - +
433B ASN* 3.9 8.5 - - + -
434B LEU* 4.2 4.5 - - - -
445B THR* 3.7 26.7 - - + +
446B THR* 1.3 76.5 - - - +
448B GLU* 1.3 60.2 + - - +
449B ILE* 5.4 0.9 - - + -
459B GLN* 3.3 7.8 - - - +
460B VAL* 2.7 50.2 + - + +
462B HIS* 4.0 20.9 - - + -
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Residues in contact with GLU 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B THR* 3.4 1.9 - - - +
431B VAL* 3.3 5.9 - - - +
432B THR* 2.9 45.2 + - - +
434B LEU* 4.0 28.8 - - + +
447B LEU* 1.3 75.2 - - - +
449B ILE* 1.3 70.8 + - - +
450B HIS* 4.0 11.8 - - - +
457B LYS* 3.6 32.6 - - + +
458B ARG 3.4 10.3 - - - +
459B GLN* 4.6 0.7 - - - +
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Residues in contact with ILE 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B TRP* 3.7 23.6 - - + +
390B VAL* 3.4 33.0 - - + -
391B TRP* 3.7 28.5 - - + +
429B LEU* 4.3 20.4 - - + -
430B THR 3.4 7.2 - - - +
431B VAL* 4.4 12.8 - - + -
447B LEU* 5.3 1.1 - - + -
448B GLU* 1.3 76.6 - - - +
450B HIS* 1.3 61.4 + - - +
451B ASN 4.0 0.2 - - - -
457B LYS* 3.4 3.5 - - - -
458B ARG* 2.9 39.5 + - + +
460B VAL* 3.7 24.7 - - + -
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Residues in contact with HIS 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428B PHE 3.3 4.9 - - - +
429B LEU* 3.4 2.2 - - - -
430B THR* 2.8 49.7 + - + +
448B GLU* 4.0 11.2 - - - +
449B ILE* 1.3 73.5 - - - +
451B ASN* 1.3 68.0 + - - +
452B THR* 3.4 30.1 + - + +
455B ARG* 4.6 5.8 - - - -
456B GLN 3.4 16.9 + - - -
457B LYS* 3.5 26.7 - - + +
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Residues in contact with ASN 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B TRP* 3.1 50.5 - - + +
428B PHE* 3.2 38.4 - - - -
429B LEU* 3.9 5.1 - - + +
449B ILE 4.0 1.6 + - - -
450B HIS* 1.3 72.0 + - - +
452B THR* 1.3 53.2 + - - +
453B GLU* 3.0 6.9 + - - +
454B GLU* 3.0 33.4 + - + +
455B ARG* 2.8 27.5 + - - -
456B GLN 2.9 16.7 + - - +
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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