Contacts of the helix formed by residues 560 - 578 (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 THR 560 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307A TYR* 3.7 5.3 - - - -
473A VAL* 5.4 0.2 - - - +
558A ILE* 3.8 5.9 - - - +
559A GLN* 1.3 93.5 - - + +
561A PRO* 1.3 75.4 - - - +
562A GLU* 3.5 8.5 + - - +
563A GLN* 3.0 35.6 + - - +
564A TYR* 3.2 15.8 + - - +
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Residues in contact with PRO 561 (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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304A TYR* 3.5 44.8 - - + +
307A TYR* 3.6 30.3 - - + -
308A GLU* 4.2 13.2 - - + +
560A THR* 1.3 88.2 - - - +
562A GLU* 1.3 55.5 + - - +
564A TYR* 3.2 1.7 + - - +
565A TYR* 2.9 31.2 + - - +
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Residues in contact with GLU 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A LYS* 4.7 9.2 + - - -
304A TYR* 3.8 22.9 + - - +
472A GLY* 3.4 22.9 - - - -
473A VAL* 3.4 31.0 - - + +
560A THR* 3.2 8.1 + - - +
561A PRO* 1.3 80.2 - - - +
563A GLN* 1.3 57.0 + - - +
565A TYR* 3.8 4.4 - - + +
566A PHE* 2.9 29.8 + - - +
334B GLY* 4.3 18.1 + - - +
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Residues in contact with GLN 563 (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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468A TRP* 4.4 13.5 - - + +
472A GLY 5.9 0.4 + - - -
473A VAL* 4.0 17.3 - - + -
520A GLY* 3.3 32.1 - - - +
521A ARG* 4.0 6.7 - - - +
524A THR* 3.8 14.0 + - - +
558A ILE* 3.8 7.5 - - + -
559A GLN* 2.9 32.6 + - - +
560A THR* 3.0 29.1 + - - +
562A GLU* 1.3 76.3 - - - +
564A TYR* 1.3 62.6 + - - +
566A PHE* 3.4 4.9 + - - +
567A CYS* 3.1 26.0 + - - -
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Residues in contact with TYR 564 (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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303A ILE* 3.6 22.0 - - + -
306A GLU* 2.5 34.7 + - + -
307A TYR* 3.6 46.0 - + + -
310A ILE* 3.4 25.9 - - + +
543A VAL* 4.1 6.7 - - + -
544A PHE* 3.3 21.1 + - - -
547A VAL* 3.8 28.5 - - + -
558A ILE* 3.6 8.9 - - + +
560A THR 3.2 2.6 + - - +
561A PRO 3.5 7.0 - - - +
563A GLN* 1.3 78.7 - - - +
565A TYR* 1.3 62.7 + - - +
567A CYS* 3.1 21.0 + - + +
568A TYR* 3.5 21.9 + + - -
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Residues in contact with TYR 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A VAL* 4.6 9.5 - - + +
299A GLN* 5.6 0.2 - - - -
300A LYS* 3.7 63.9 + - + +
303A ILE* 3.8 32.5 - - + -
304A TYR* 3.7 13.5 - + + -
561A PRO 2.9 16.9 + - - +
562A GLU* 3.9 5.8 - - + +
564A TYR* 1.3 75.8 - - - +
566A PHE* 1.3 58.3 + - - +
568A TYR* 3.1 6.6 + - + +
569A LYS* 2.8 74.3 + - + +
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Residues in contact with PHE 566 (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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468A TRP* 4.7 3.4 - + - -
473A VAL* 3.8 19.7 - - + -
474A PRO* 3.4 40.2 - - + -
477A ALA* 4.0 20.2 - - + -
480A LEU* 3.9 20.6 - - + -
524A THR* 3.6 31.2 - - + -
528A LEU* 4.5 2.9 - - + -
562A GLU 2.9 18.4 + - - +
563A GLN* 3.4 6.1 - - - +
565A TYR* 1.3 77.1 - - - +
567A CYS* 1.4 54.1 + - - +
569A LYS* 4.4 5.2 - - - +
570A ALA* 2.7 45.1 + - + +
704A EDO 3.5 33.7 - - - -
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Residues in contact with CYS 567 (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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524A THR* 4.2 16.6 - - - -
527A SER* 4.3 16.8 - - - -
528A LEU* 4.1 9.6 - - + +
531A CYS* 6.2 2.0 - - - -
543A VAL* 3.9 22.7 - - + -
547A VAL* 5.0 2.0 - - - -
558A ILE* 4.1 23.8 - - - -
563A GLN 3.1 17.7 + - - -
564A TYR* 3.1 12.5 + - - +
566A PHE* 1.4 77.9 - - - +
568A TYR* 1.3 63.3 + - - +
570A ALA* 3.9 3.9 - - - +
571A ILE* 3.3 26.9 + - - +
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Residues in contact with TYR 568 (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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286A MET* 4.9 4.4 - - + +
291A LEU* 3.8 26.7 - - + +
294A TYR* 3.3 30.6 + + - -
295A VAL* 3.5 27.6 - - + -
303A ILE* 3.5 24.2 - - + -
306A GLU* 2.6 29.7 + - - -
543A VAL* 3.8 26.9 - - + -
544A PHE* 4.0 9.7 + - - +
564A TYR* 3.5 25.7 + + - -
565A TYR* 3.1 10.6 + - + +
567A CYS* 1.3 78.1 - - - +
569A LYS* 1.3 64.9 + - + +
571A ILE* 3.3 6.5 + - - +
572A LEU* 3.1 26.2 + - - +
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Residues in contact with LYS 569 (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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295A VAL* 4.8 13.7 - - + +
565A TYR* 2.8 70.5 + - + +
566A PHE* 4.0 3.8 - - - +
568A TYR* 1.3 74.8 - - - +
570A ALA* 1.3 57.6 - - - +
572A LEU* 3.2 13.5 + - + +
573A GLU* 2.8 26.0 + - - +
704A EDO 3.3 27.8 + - - +
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Residues in contact with ALA 570 (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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477A ALA* 3.5 25.0 - - + +
481A ILE* 4.2 3.9 - - + +
528A LEU* 3.7 26.9 - - + -
566A PHE* 2.7 29.5 + - + +
567A CYS 3.9 0.2 - - - +
569A LYS* 1.3 72.5 - - - +
571A ILE* 1.3 58.9 + - - +
573A GLU* 3.6 1.4 - - - +
574A PHE* 2.8 30.8 + - - +
704A EDO 3.5 9.7 + - - -
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Residues in contact with ILE 571 (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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288A ILE* 4.1 8.3 - - + -
291A LEU* 3.6 25.1 - - + -
481A ILE* 5.6 0.2 - - + -
528A LEU* 3.5 20.6 - - + -
531A CYS* 4.2 15.7 - - + -
532A LEU* 3.2 35.7 - - + +
535A LEU* 4.4 5.4 - - + -
541A LEU* 3.9 28.0 - - + -
543A VAL* 5.2 1.6 - - + -
567A CYS 3.3 13.4 + - - +
568A TYR* 3.3 8.9 + - - +
569A LYS 3.3 0.6 - - - -
570A ALA* 1.3 78.9 - - - +
572A LEU* 1.3 55.9 + - - +
574A PHE* 3.3 4.6 + - - +
575A ALA* 2.9 26.7 + - - +
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Residues in contact with LEU 572 (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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288A ILE* 4.5 8.3 - - + +
291A LEU* 3.9 22.9 - - + +
292A VAL* 3.5 36.6 - - + +
295A VAL* 3.9 38.4 - - + -
568A TYR 3.1 15.1 + - - +
569A LYS* 3.2 16.6 + - + +
571A ILE* 1.3 74.9 - - - +
573A GLU* 1.3 56.8 + - - +
575A ALA* 3.4 4.7 + - + +
576A GLU* 3.0 28.1 + - - +
581A VAL* 4.3 4.2 - - + +
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Residues in contact with GLU 573 (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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476A SER* 2.5 27.0 + - - -
477A ALA* 2.7 21.2 + - - +
478A ALA* 4.6 0.9 - - - +
569A LYS 2.8 16.9 + - - +
570A ALA 3.6 4.0 - - - +
572A LEU* 1.3 71.7 - - - +
574A PHE* 1.3 61.4 + - - +
576A GLU* 3.2 8.6 + - + +
577A LYS* 2.8 28.9 + - + +
601A SCN 3.7 14.0 - - - -
704A EDO 2.6 27.0 + - - +
409B ARG* 3.2 43.1 + - - +
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Residues in contact with PHE 574 (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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481A ILE* 3.8 20.9 - - + -
485A ARG* 3.3 28.9 - - - -
532A LEU* 3.7 23.6 - - + -
535A LEU* 3.7 28.7 - - + -
536A GLU* 5.7 10.1 - - + -
570A ALA 2.8 17.7 + - - +
571A ILE* 3.4 6.5 - - - +
573A GLU* 1.3 77.5 - - - +
575A ALA* 1.3 59.5 + - - +
577A LYS* 3.1 2.5 + - - +
578A GLU* 2.8 59.1 + - + +
580A MET* 4.3 9.9 - - + -
601A SCN 3.6 26.5 - - - -
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Residues in contact with ALA 575 (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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288A ILE* 3.8 32.1 - - + -
571A ILE 2.9 16.5 + - - +
572A LEU* 3.5 11.0 - - - +
573A GLU 3.3 0.2 - - - -
574A PHE* 1.3 74.9 - - + +
576A GLU* 1.3 60.4 + - - +
578A GLU 3.3 1.4 + - - -
579A GLY 3.2 4.0 + - - -
580A MET* 2.9 40.7 + - - +
581A VAL* 3.6 16.6 - - + -
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Residues in contact with GLU 576 (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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572A LEU 3.0 13.1 + - - +
573A GLU* 3.4 11.4 - - + +
574A PHE 3.2 0.2 - - - -
575A ALA* 1.3 76.8 - - - +
577A LYS* 1.3 58.1 + - - +
579A GLY* 2.9 19.4 + - - -
581A VAL* 3.6 38.4 - - + +
407B GLY 5.8 0.7 - - - +
408B GLY* 4.3 28.2 - - - +
409B ARG* 6.2 1.8 - - - -
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Residues in contact with LYS 577 (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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478A ALA* 4.8 9.4 - - + -
573A GLU* 2.8 20.9 + - + +
574A PHE 3.6 5.2 - - - +
576A GLU* 1.3 74.9 - - - +
578A GLU* 1.3 64.4 + - + +
579A GLY 3.4 2.6 + - - -
601A SCN 3.4 35.9 - - - +
407B GLY 5.9 4.5 - - - +
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Residues in contact with GLU 578 (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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485A ARG* 3.4 26.7 + - - -
574A PHE* 2.8 46.6 + - + +
575A ALA 3.7 3.6 - - - +
577A LYS* 1.3 83.8 - - + +
579A GLY* 1.3 60.7 + - - +
580A MET* 3.3 25.6 + - + +
601A SCN 5.0 1.2 + - - -
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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