Contacts of the helix formed by residues 575 - 592 (chain A) in PDB entry 1K2P
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 SER 575 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518A LEU* 3.8 24.3 - - - +
549A ASP 4.1 17.9 - - - -
550A GLU* 5.5 1.3 - - - -
551A TYR* 5.1 1.1 - - - -
567A GLU* 5.3 1.2 + - - -
573A LYS* 4.8 4.3 - - - -
574A PHE* 1.3 76.5 - - - +
576A SER* 1.3 67.1 + - - +
577A LYS* 3.0 23.3 + - - +
578A SER* 3.0 18.7 + - - -
579A ASP* 3.8 3.6 + - - +
638A ALA* 5.3 3.5 - - - +
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Residues in contact with SER 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A GLU* 4.1 26.8 + - - -
518A LEU* 5.3 3.1 - - - -
549A ASP 5.3 0.6 + - - -
575A SER* 1.3 78.1 + - - +
577A LYS* 1.3 81.8 + - - +
578A SER 3.1 0.4 - - - -
579A ASP* 3.1 12.9 + - - +
580A ILE* 3.1 27.1 + - - +
644A PHE* 4.3 3.1 - - - -
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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
----------------------------------------------------------
513A GLU* 5.0 2.2 - - - -
575A SER* 3.0 10.2 + - - +
576A SER* 1.3 92.3 + - - +
578A SER* 1.3 59.9 + - - +
579A ASP 3.4 0.2 - - - -
580A ILE* 3.7 6.9 - - + +
581A TRP* 3.2 11.4 + - - +
638A ALA* 3.4 27.8 + - + +
639A ASP* 4.5 9.5 + - - +
641A ARG* 2.9 68.7 + - + +
642A PRO 4.0 15.0 - - - +
643A THR* 4.7 14.1 - - - +
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Residues in contact with SER 578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A PRO* 3.9 20.6 - - - +
567A GLU* 4.1 5.7 + - - -
568A VAL* 3.7 9.1 - - - +
573A LYS 3.3 8.3 + - - -
574A PHE* 3.2 19.9 - - - -
575A SER* 3.0 29.0 + - - -
576A SER 3.1 0.6 - - - -
577A LYS* 1.3 75.9 - - - +
579A ASP* 1.3 69.2 + - - +
581A TRP* 3.4 4.5 + - - +
582A ALA* 3.1 21.7 + - - +
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Residues in contact with ASP 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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509A MET* 4.5 4.7 - - - +
512A LEU* 5.4 1.0 - - - +
517A PHE 4.8 0.9 - - - +
518A LEU* 3.6 17.8 - - - +
519A HIS* 2.5 57.5 + - - +
520A ARG* 4.4 0.7 - - - -
522A LEU* 3.9 6.6 - - + +
575A SER 3.8 4.6 + - - +
576A SER* 3.1 11.3 + - - +
578A SER* 1.3 77.5 - - - +
580A ILE* 1.3 55.1 + - - +
582A ALA* 3.6 6.9 - - - +
583A PHE* 2.7 35.7 + - - +
644A PHE* 3.8 18.4 - - + -
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Residues in contact with ILE 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A GLU* 4.2 4.5 - - - +
576A SER 3.1 12.6 + - - +
577A LYS* 3.7 14.8 - - + +
578A SER 3.3 0.2 - - - -
579A ASP* 1.3 78.4 - - - +
581A TRP* 1.3 63.7 + - - +
583A PHE* 3.2 1.4 + - - +
584A GLY 2.9 19.2 + - - -
633A CYS* 3.2 36.6 - - - +
641A ARG* 3.8 17.7 - - + -
642A PRO 3.1 24.7 - - - +
643A THR* 3.9 1.8 - - - -
644A PHE* 3.5 48.2 - - + +
647A LEU* 3.7 18.4 - - + -
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Residues in contact with TRP 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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562A ARG 5.1 1.0 + - - -
563A TRP* 3.5 19.5 - - - +
564A SER 3.5 11.1 + - - +
565A PRO* 3.5 26.9 - - + -
566A PRO* 3.5 23.8 - - + -
577A LYS 3.2 9.4 + - - +
578A SER 3.6 8.7 - - - +
579A ASP 3.2 0.6 - - - -
580A ILE* 1.3 80.0 - - - +
582A ALA* 1.3 60.9 + - - +
584A GLY 3.1 2.6 + - - -
585A VAL* 3.1 32.1 + - + +
598A TYR* 5.2 2.3 + - - -
610A ILE* 3.2 29.9 - - + +
615A ARG* 3.5 27.1 - - - -
633A CYS* 3.4 14.8 - - - +
634A TRP* 3.2 46.3 + + + -
636A GLU* 3.8 9.0 - - - -
641A ARG* 4.0 6.3 - - - -
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Residues in contact with ALA 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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519A HIS 5.8 0.2 - - - +
522A LEU* 3.4 39.4 - - + +
563A TRP* 3.4 25.6 - - + +
578A SER 3.1 9.6 + - - +
579A ASP* 3.3 9.2 + - - +
581A TRP* 1.3 80.4 - - - +
583A PHE* 1.3 57.3 + - - +
585A VAL* 3.3 4.3 + - - +
586A LEU* 2.9 25.6 + - - +
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Residues in contact with PHE 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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502A CYS* 3.6 26.9 - - - -
505A VAL* 3.8 23.6 - - + -
506A CYS* 3.7 27.6 - - + -
509A MET* 4.6 0.7 - - + -
522A LEU* 3.7 12.1 - - + +
579A ASP 2.7 20.6 + - - +
580A ILE 3.2 3.8 + - - +
582A ALA* 1.3 69.8 - - - +
584A GLY* 1.3 62.3 + - - +
586A LEU* 3.0 9.3 + - + +
587A MET* 2.9 56.2 + - + +
633A CYS* 4.2 4.0 - - - -
644A PHE* 3.7 16.6 - + + -
647A LEU* 3.8 33.9 - - + -
651A ILE* 4.2 7.6 - - + -
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Residues in contact with GLY 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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580A ILE 2.9 10.7 + - - -
581A TRP 3.1 4.9 + - - -
583A PHE* 1.3 78.6 - - - +
585A VAL* 1.3 60.1 + - - +
587A MET* 3.3 12.6 - - - +
588A TRP 3.3 14.4 + - - -
630A MET* 3.7 6.7 - - - +
633A CYS* 3.6 25.6 - - - -
634A TRP* 3.3 16.8 - - - -
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Residues in contact with VAL 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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562A ARG 3.7 13.9 - - - +
563A TRP* 3.3 33.2 - - + +
581A TRP* 3.1 26.3 + - + +
582A ALA 3.6 2.0 - - - +
583A PHE 3.1 0.2 - - - -
584A GLY* 1.3 74.1 - - - +
586A LEU* 1.3 67.7 + - - +
588A TRP* 2.8 15.6 + - - +
589A GLU* 2.9 10.4 + - - +
597A PRO* 3.7 13.7 - - + -
598A TYR* 5.6 2.0 - - - +
616A LEU* 3.6 24.7 - - + -
634A TRP* 3.5 22.0 - - - +
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Residues in contact with LEU 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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482A LEU* 3.8 14.6 - - + -
505A VAL* 3.5 37.2 - - + -
522A LEU* 4.1 11.0 - - + -
523A ALA* 4.8 3.1 - - - +
524A ALA* 3.5 37.9 - - + +
527A CYS* 3.9 14.4 - - - -
582A ALA 2.9 14.4 + - - +
583A PHE* 3.0 15.7 + - + +
585A VAL* 1.3 76.5 - - - +
587A MET* 1.3 56.1 + - + +
589A GLU* 2.9 15.5 + - - +
590A ILE* 2.8 34.6 + - + +
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Residues in contact with MET 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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499A LEU* 4.9 2.0 - - + -
502A CYS* 3.6 32.8 - - + -
583A PHE* 2.9 45.5 + - + +
584A GLY* 3.3 8.3 - - - +
585A VAL 3.1 0.2 - - - -
586A LEU* 1.3 74.3 - - - +
588A TRP* 1.3 58.2 + - - +
590A ILE* 3.0 9.8 + - + +
591A TYR* 2.8 34.4 + - + +
626A VAL* 4.5 13.2 - - + +
629A ILE* 3.9 30.7 - - + -
630A MET* 3.6 33.0 - - + -
633A CYS* 5.4 0.4 - - - -
647A LEU* 5.6 0.7 - - - -
651A ILE* 4.9 4.0 - - + -
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Residues in contact with TRP 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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584A GLY 3.3 5.4 + - - +
585A VAL* 2.8 12.0 + - - +
587A MET* 1.3 77.7 - - - +
589A GLU* 1.3 60.4 + - + +
591A TYR* 4.6 2.7 - - - +
592A SER* 2.8 45.6 + - - -
595A LYS* 3.2 31.2 - - + -
596A MET 3.4 25.6 - - - -
597A PRO* 3.6 13.5 - - + -
598A TYR 4.9 0.7 - - - -
599A GLU* 5.7 1.8 - - - -
616A LEU* 3.5 40.3 - - + +
617A TYR* 2.9 61.9 + + - +
619A PRO* 3.8 9.8 - - + +
630A MET* 3.3 30.7 - - + -
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Residues in contact with GLU 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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483A LEU* 4.3 11.4 - - - +
486A LEU* 3.6 2.8 - - + +
524A ALA* 2.9 44.5 + - + +
525A ARG 4.8 0.9 + - - -
563A TRP* 2.8 41.7 + - - +
585A VAL 2.9 13.5 + - - +
586A LEU* 2.9 19.4 + - - +
588A TRP* 1.3 82.4 - - + +
590A ILE* 1.3 60.4 + - - +
592A SER* 3.7 4.9 + - - -
593A LEU 3.4 2.9 + - - -
594A GLY* 2.7 32.8 + - - -
595A LYS 4.0 16.3 - - - +
596A MET* 5.6 0.2 - - - -
597A PRO* 4.4 3.5 - - + +
435B GLY* 6.0 0.2 - - - -
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Residues in contact with ILE 590 (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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482A LEU* 4.2 24.0 - - + -
486A LEU* 3.8 10.9 - - + +
498A LEU* 3.4 47.0 - - + +
501A MET* 3.6 30.5 - - + +
502A CYS* 3.5 28.0 - - - +
505A VAL* 5.1 1.6 - - + -
586A LEU* 2.8 25.9 + - + +
587A MET* 3.0 8.3 + - + +
589A GLU* 1.3 75.2 - - - +
591A TYR* 1.3 60.1 + - + +
593A LEU* 3.0 22.2 + - - +
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Residues in contact with TYR 591 (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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495A THR* 3.5 18.1 + - + +
498A LEU* 3.6 26.0 - - + -
499A LEU* 3.2 35.3 + - + +
502A CYS* 3.8 23.6 - - - -
587A MET* 2.8 27.2 + - + +
588A TRP 4.4 0.2 - - - +
590A ILE* 1.3 73.4 - - + +
592A SER* 1.3 57.0 + - - +
593A LEU 3.0 8.5 + - - -
619A PRO* 3.6 25.3 - - + +
620A HIS* 5.0 0.9 - - - -
621A LEU* 3.0 61.2 - - + +
622A ALA* 3.8 8.5 - - + -
626A VAL* 3.7 26.1 - - + +
630A MET* 5.4 2.7 - - - -
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Residues in contact with SER 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A TRP* 2.8 42.5 + - - -
589A GLU 3.7 1.2 + - - -
591A TYR* 1.3 73.5 - - - +
593A LEU* 1.3 63.8 + - - +
595A LYS* 3.0 51.6 + - - +
617A TYR* 5.0 4.7 - - - -
619A PRO* 3.9 16.7 - - - +
620A HIS* 5.1 12.0 - - - -
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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
------------------------------------------------------------
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