Contacts of the helix formed by residues 560 - 578 (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 THR 560 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A ASN* 3.4 17.5 + - - +
441A HIS* 4.1 23.8 - - + +
467A SER* 5.5 1.1 - - - +
307B TYR* 3.8 5.4 - - - -
558B ILE* 3.8 5.7 - - - +
559B GLN* 1.3 95.5 - - + +
561B PRO* 1.3 70.1 - - + +
562B GLU* 3.5 4.2 + - - +
563B GLN* 2.9 43.9 + - - +
564B TYR* 3.1 10.0 + - - +
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Residues in contact with PRO 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ASN* 6.1 0.2 - - - +
439A MET 4.2 7.6 - - - +
440A ASN* 3.3 29.4 - - - +
304B TYR* 3.5 37.4 - - + -
307B TYR* 3.6 26.8 - - + +
308B GLU* 3.4 22.2 - - - +
311B ARG* 3.9 5.8 - - - +
560B THR* 1.3 82.4 - - - +
562B GLU* 1.3 55.9 + - - +
564B TYR* 3.2 3.8 + - - +
565B TYR* 2.8 29.1 + - - +
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Residues in contact with GLU 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ASN* 2.9 29.7 + - - +
300B LYS* 5.1 1.6 - - - +
304B TYR* 2.5 34.5 + - - +
560B THR* 4.0 1.6 - - - +
561B PRO* 1.3 73.2 - - - +
563B GLN* 1.3 61.1 + - + +
565B TYR* 3.8 9.1 - - - -
566B PHE* 2.8 34.7 + - + +
569B LYS* 2.5 33.8 + - - -
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Residues in contact with GLN 563 (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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468B TRP* 6.2 2.2 - - + +
520B GLY* 3.4 30.5 - - - -
521B ARG* 4.5 4.8 - - - +
524B THR* 4.1 12.3 + - - +
558B ILE* 3.6 10.7 - - + -
559B GLN* 2.7 38.9 + - - +
560B THR* 2.9 31.2 + - - +
562B GLU* 1.3 76.9 - - - +
564B TYR* 1.3 61.2 + - - +
566B PHE* 3.3 10.7 + - - +
567B CYS* 3.2 25.6 + - - -
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Residues in contact with TYR 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ILE* 3.8 15.3 - - + -
306B GLU* 2.6 41.3 + - + -
307B TYR* 3.6 45.5 - + + -
310B ILE* 3.5 22.9 - - + +
543B VAL* 3.7 15.7 - - + -
544B PHE* 3.2 22.0 + - - +
547B VAL* 3.9 21.3 - - + -
558B ILE* 3.6 7.3 - - + +
560B THR 3.1 5.0 + - - +
561B PRO 3.4 7.6 - - - +
563B GLN* 1.3 72.2 - - - +
565B TYR* 1.3 66.0 + - - +
567B CYS* 3.1 22.0 + - - +
568B TYR* 3.6 21.9 + + - -
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Residues in contact with TYR 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B VAL* 4.2 17.9 - - + +
299B GLN* 4.0 9.0 + - - -
300B LYS* 3.7 34.8 + - + +
303B ILE* 3.7 39.9 - - + -
304B TYR* 3.9 14.6 - + + -
561B PRO 2.8 19.4 + - - +
562B GLU* 3.8 13.5 - - - +
564B TYR* 1.3 73.7 - - - +
566B PHE* 1.3 64.6 + - - +
568B TYR* 3.1 7.5 + - + -
569B LYS* 2.9 60.2 + - + +
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Residues in contact with PHE 566 (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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468B TRP* 4.6 6.5 - + - -
474B PRO* 3.6 43.1 - - + -
477B ALA* 4.0 28.9 - - + -
480B LEU* 3.9 22.0 - - + -
524B THR* 3.6 31.6 - - + -
528B LEU* 4.3 1.6 - - + -
562B GLU* 2.8 24.6 + - + +
563B GLN* 3.3 8.1 - - - +
564B TYR 3.2 0.2 - - - -
565B TYR* 1.3 77.7 - - - +
567B CYS* 1.3 56.3 + - - +
569B LYS* 3.9 17.2 - - + +
570B ALA* 2.8 40.2 + - + +
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Residues in contact with CYS 567 (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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524B THR* 4.0 21.1 - - - -
527B SER* 4.4 17.0 - - - -
528B LEU* 3.8 14.8 - - + +
531B CYS* 6.3 0.9 - - - -
543B VAL* 4.1 19.5 - - + -
547B VAL* 5.1 2.7 - - - -
558B ILE* 4.3 16.6 - - - -
563B GLN 3.2 18.2 + - - -
564B TYR* 3.1 12.7 + - - +
566B PHE* 1.3 79.3 - - - +
568B TYR* 1.3 62.8 + - - +
571B ILE* 3.1 30.6 + - + +
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Residues in contact with TYR 568 (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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286B MET* 4.6 5.6 - - + +
291B LEU* 3.6 29.3 - - + +
294B TYR* 3.5 26.8 + + - -
295B VAL* 3.5 26.5 - - + -
303B ILE* 3.9 17.5 - - + -
306B GLU* 2.6 28.8 + - - -
543B VAL* 3.8 27.6 + - + +
544B PHE* 4.3 4.5 + - - +
564B TYR* 3.6 30.9 + + - -
565B TYR* 3.1 13.6 + - + +
567B CYS* 1.3 81.1 - - - +
569B LYS* 1.3 64.0 + - - +
571B ILE* 3.3 6.7 + - - +
572B LEU* 3.1 27.9 + - - +
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Residues in contact with LYS 569 (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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295B VAL* 5.8 2.0 - - + -
562B GLU* 2.5 33.2 + - - -
565B TYR* 2.9 59.1 + - + +
566B PHE* 3.8 17.5 - - + +
568B TYR* 1.3 77.9 - - - +
570B ALA* 1.3 57.7 + - - +
572B LEU* 3.3 7.7 + - - +
573B GLU* 2.8 32.0 + - - +
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Residues in contact with ALA 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B ALA* 3.4 32.3 - - + +
481B ILE* 4.9 4.7 - - + +
528B LEU* 4.1 18.2 - - + -
566B PHE* 2.8 30.4 + - + +
567B CYS 3.8 3.8 - - - +
569B LYS* 1.3 73.8 - - - +
571B ILE* 1.3 65.7 + - - +
573B GLU* 3.4 2.3 + - - +
574B PHE* 3.0 26.1 + - - +
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Residues in contact with ILE 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ILE* 4.2 9.9 - - + -
291B LEU* 3.6 20.4 - - + -
481B ILE* 6.1 1.1 - - - -
528B LEU* 3.8 15.3 - - + -
531B CYS* 3.9 20.2 - - + -
532B LEU* 4.8 16.4 - - + -
535B LEU* 5.4 0.7 - - + -
541B LEU* 3.7 37.5 - - + -
543B VAL* 3.9 13.5 - - + -
567B CYS* 3.1 19.8 + - + +
568B TYR* 3.7 4.3 - - - +
569B LYS 3.3 0.2 - - - -
570B ALA* 1.3 77.5 - - - +
572B LEU* 1.3 57.4 + - - +
574B PHE* 3.4 8.4 + - + +
575B ALA* 2.8 28.1 + - - +
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Residues in contact with LEU 572 (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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288B ILE* 4.4 8.1 - - + +
291B LEU* 3.8 24.7 - - + +
292B VAL* 3.6 37.2 - - + +
295B VAL* 3.8 39.7 - - + -
568B TYR 3.1 21.0 + - - +
569B LYS* 3.7 6.7 - - + +
571B ILE* 1.3 75.5 - - - +
573B GLU* 1.3 59.2 + - - +
575B ALA* 3.4 3.6 + - + +
576B GLU* 2.9 30.0 + - - +
581B VAL* 4.8 2.4 - - + +
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Residues in contact with GLU 573 (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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475B SER 4.4 3.4 - - - +
476B SER* 2.7 30.3 + - - -
477B ALA* 2.9 30.4 + - + +
478B ALA* 4.3 6.3 + - + +
569B LYS 2.8 17.8 + - - +
570B ALA* 3.8 5.3 - - - +
571B ILE 3.3 0.2 - - - -
572B LEU* 1.3 76.5 - - - +
574B PHE* 1.3 63.0 + - - +
576B GLU* 3.3 6.9 + - - +
577B LYS* 3.0 26.1 + - + +
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Residues in contact with PHE 574 (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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477B ALA* 5.8 0.4 - - + +
481B ILE* 3.6 41.3 - - + -
532B LEU* 3.9 30.3 - - + -
535B LEU* 4.6 3.8 - - + -
570B ALA 3.0 18.0 + - - +
571B ILE* 3.5 7.0 - - + +
573B GLU* 1.3 77.8 - - - +
575B ALA* 1.3 61.3 + - + +
577B LYS* 3.2 7.1 + - + +
578B GLU* 2.8 61.1 + - + +
580B MET* 3.6 24.7 - - + -
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Residues in contact with ALA 575 (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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288B ILE* 3.7 39.9 - - + -
571B ILE 2.8 20.9 + - - +
572B LEU* 3.5 8.3 - - - +
573B GLU 3.3 0.2 - - - -
574B PHE* 1.3 76.0 - - + +
576B GLU* 1.3 59.5 + - - +
578B GLU 3.3 0.9 + - - -
579B GLY 3.2 3.5 + - - -
580B MET* 2.9 44.0 + - - +
581B VAL* 4.1 4.5 - - + -
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Residues in contact with GLU 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B LEU 2.9 17.1 + - - +
573B GLU* 3.6 6.3 - - - +
575B ALA* 1.3 76.5 - - - +
577B LYS* 1.3 63.2 + - - +
579B GLY* 3.2 13.5 + - - -
581B VAL* 3.9 18.3 - - + +
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Residues in contact with LYS 577 (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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478B ALA* 6.3 3.6 - - + -
573B GLU* 3.0 18.6 + - + +
574B PHE* 3.6 8.3 - - + +
576B GLU* 1.3 76.5 - - - +
578B GLU* 1.3 69.3 + - + +
579B GLY* 3.4 1.2 + - - -
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Residues in contact with GLU 578 (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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574B PHE* 2.8 58.1 + - + +
575B ALA 3.9 1.8 - - - +
576B GLU 3.2 0.2 - - - -
577B LYS* 1.3 83.1 - - + +
579B GLY* 1.3 61.0 + - - +
580B MET* 3.6 22.4 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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