Contacts of the helix formed by residues 572 - 589 (chain A) in PDB entry 3P1X
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 ASN 572 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555A PHE* 3.6 12.8 - - - -
570A GLY 3.2 0.7 - - - -
571A SER* 1.3 83.1 - - - +
573A LYS* 1.3 63.2 + - - +
574A LYS* 3.2 17.2 - - - +
575A VAL* 2.9 45.9 - - - +
576A ALA* 3.2 22.0 + - - +
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Residues in contact with LYS 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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543A LEU* 3.9 23.0 - - + +
546A GLU* 4.4 5.0 + - - -
555A PHE* 3.5 41.8 - - + -
557A MSE 4.1 16.0 - - + +
572A ASN* 1.3 70.9 - - - +
574A LYS* 1.3 60.6 + - - +
576A ALA* 3.3 6.8 + - - +
577A LYS* 2.8 32.6 + - - +
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Residues in contact with LYS 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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529A VAL* 5.7 0.3 - - - +
572A ASN* 3.2 10.9 - - - +
573A LYS* 1.3 79.5 - - - +
575A VAL* 1.3 58.2 + - - +
577A LYS* 3.4 7.7 + - - +
578A ALA* 3.0 26.9 + - + +
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Residues in contact with VAL 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A GLY* 3.6 21.1 - - - -
571A SER 3.9 3.1 - - - +
572A ASN* 2.9 40.4 - - - +
574A LYS* 1.3 72.0 - - - +
576A ALA* 1.3 65.1 + - - +
578A ALA* 3.3 9.3 + - + +
579A TYR* 2.9 51.6 + - + -
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Residues in contact with ALA 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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555A PHE* 3.7 23.3 - - + +
557A MSE 3.7 14.5 - - + +
568A GLY* 3.4 25.8 - - - +
569A ALA 3.9 9.0 - - - -
570A GLY 4.0 2.0 - - - +
572A ASN 3.2 14.7 + - - +
573A LYS 3.3 4.9 + - - +
575A VAL* 1.3 81.0 - - - +
577A LYS* 1.3 65.1 + - - +
579A TYR 3.3 1.2 + - - -
580A ALA* 3.1 18.5 + - - +
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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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529A VAL* 3.7 22.0 - - + -
541A TYR* 3.3 41.4 - - + +
557A MSE 3.2 36.8 - - + +
573A LYS 2.8 16.5 + - - +
574A LYS* 3.6 7.0 - - - +
576A ALA* 1.3 77.2 - - - +
578A ALA* 1.3 62.0 + - - +
580A ALA* 3.1 4.9 + - - +
581A ALA* 3.0 18.9 + - - +
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Residues in contact with ALA 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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527A ASN* 6.0 2.0 - - - +
528A PRO* 3.4 28.5 - - + +
529A VAL* 4.2 13.9 - - + +
574A LYS* 3.0 17.5 + - + +
575A VAL* 3.3 12.5 + - + +
577A LYS* 1.3 77.0 - - - +
579A TYR* 1.3 57.4 + - + +
581A ALA 3.3 1.2 + - - -
582A LEU* 2.9 25.1 + - - +
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Residues in contact with TYR 579 (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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567A GLN 3.9 1.0 - - - +
568A GLY* 3.6 20.0 - - - -
569A ALA 3.5 18.4 - - - +
570A GLY* 5.8 0.4 - - - -
575A VAL* 2.9 43.6 + - + +
578A ALA* 1.3 74.7 - - + +
580A ALA* 1.3 60.8 + - - +
582A LEU* 3.3 29.7 + - + +
583A ALA* 2.9 29.6 + - - +
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Residues in contact with ALA 580 (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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541A TYR* 4.4 5.6 - - + -
557A MSE 3.7 17.0 - - + +
559A VAL* 3.7 11.8 - - + +
566A PHE* 3.6 18.0 - - - +
567A GLN* 3.6 13.5 - - - +
568A GLY* 3.5 11.1 - - - +
576A ALA 3.1 13.4 + - - +
577A LYS* 3.1 10.5 + - - +
579A TYR* 1.3 77.9 - - - +
581A ALA* 1.3 61.4 + - - +
583A ALA* 3.4 4.9 + - - +
584A ALA 3.3 14.6 + - - -
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Residues in contact with ALA 581 (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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528A PRO 3.6 30.3 - - - +
529A VAL* 3.7 3.6 - - - +
532A LEU* 4.1 13.0 - - + +
541A TYR* 3.5 23.5 - - - +
559A VAL* 4.7 0.2 - - - -
577A LYS 3.0 10.5 + - - +
578A ALA 3.7 4.7 - - - +
580A ALA* 1.3 76.6 - - - +
582A LEU* 1.3 59.7 + - - +
584A ALA* 3.0 5.0 + - - +
585A LEU* 2.8 32.9 + - - +
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Residues in contact with LEU 582 (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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528A PRO* 3.9 12.9 - - + +
578A ALA 2.9 17.8 + - - +
579A TYR* 3.5 32.5 - - + +
581A ALA* 1.3 77.2 - - - +
583A ALA* 1.3 56.7 + - - +
585A LEU* 3.2 11.3 + - + +
586A GLU* 2.8 61.5 + - + +
594A LEU* 4.4 33.0 - - + -
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Residues in contact with ALA 583 (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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566A PHE* 3.6 20.1 - - + -
567A GLN 3.8 15.7 - - - +
579A TYR 2.9 16.5 + - - +
580A ALA 3.6 6.3 - - - +
581A ALA 3.2 0.2 - - - -
582A LEU* 1.3 76.4 - - - +
584A ALA* 1.3 64.0 + - - +
586A GLU* 3.4 12.2 + - - +
587A LYS* 3.3 18.0 + - - +
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Residues in contact with ALA 584 (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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532A LEU* 3.8 25.4 - - + -
559A VAL* 4.5 0.9 - - + -
561A VAL* 4.2 8.1 - - + -
566A PHE* 3.6 33.1 - - + -
580A ALA 3.3 7.1 + - - +
581A ALA 3.0 9.5 + - - +
583A ALA* 1.3 78.1 - - - +
585A LEU* 1.3 59.6 + - - +
587A LYS* 3.3 1.7 + - - +
588A LEU* 2.9 36.7 + - + +
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Residues in contact with LEU 585 (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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528A PRO* 3.6 33.0 - - + +
531A GLU* 3.9 17.9 - - + +
532A LEU* 3.7 34.5 - - + +
535A LYS* 5.1 1.6 - - + -
581A ALA 2.8 17.0 + - - +
582A LEU* 3.6 13.0 - - + +
584A ALA* 1.3 78.1 - - - +
586A GLU* 1.3 56.5 + - - +
589A PHE* 2.8 62.7 + - + +
592A THR* 4.3 14.8 - - + +
594A LEU* 6.0 2.7 - - + -
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Residues in contact with GLU 586 (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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582A LEU* 2.8 56.9 + - + +
583A ALA* 3.8 9.0 + - - +
584A ALA 3.3 0.2 - - - -
585A LEU* 1.3 73.8 - - - +
587A LYS* 1.3 61.1 + - - +
590A PRO* 3.7 18.7 - - - +
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Residues in contact with LYS 587 (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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564A GLN* 3.7 16.1 + - - -
566A PHE* 3.7 23.3 - - + -
583A ALA 3.3 13.3 + - - +
584A ALA 3.3 1.2 + - - +
585A LEU 3.2 0.2 - - - -
586A GLU* 1.3 81.7 - - - +
588A LEU* 1.3 73.6 + - + +
589A PHE 3.6 0.2 - - - -
590A PRO* 3.9 9.9 - - - +
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Residues in contact with LEU 588 (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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536A ARG* 5.5 0.4 - - - +
561A VAL* 3.4 39.5 - - + +
562A ASP* 4.2 11.4 - - - +
564A GLN* 4.1 21.3 - - - +
566A PHE* 4.1 13.0 - - + -
584A ALA* 2.9 19.7 + - + +
587A LYS* 1.3 86.3 - - + +
589A PHE* 1.3 90.8 + - + +
590A PRO* 3.4 7.3 - - - +
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Residues in contact with PHE 589 (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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532A LEU* 4.2 12.1 - - + -
535A LYS* 3.6 49.8 - - + -
536A ARG* 3.7 27.4 - - + -
585A LEU* 2.8 43.4 + - + +
588A LEU* 1.3 106.9 - - + +
590A PRO* 1.3 66.7 - - - +
591A ASP 3.2 3.4 - - - -
592A THR* 3.1 31.4 + - - +
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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
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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