Contacts of the helix formed by residues 549 - 573 (chain A) in PDB entry 2KFN
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 PRO 549 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A ILE* 3.0 14.1 - - + +
548A ASP* 1.3 84.2 - - - +
550A LYS* 1.3 63.2 + - + +
552A LEU* 3.3 11.5 + - + +
553A HIS* 2.9 28.9 + - - +
645A PRO* 4.5 15.9 - - + +
648A ILE* 4.1 22.2 - - + -
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Residues in contact with LYS 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A ASP* 3.0 16.3 + - - +
549A PRO* 1.3 77.9 - - + +
551A VAL* 1.3 66.1 + - - +
553A HIS* 3.0 8.4 + - - +
554A ASN* 2.9 42.3 + - - +
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Residues in contact with VAL 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A ASP* 3.3 35.1 + - + +
550A LYS* 1.3 82.5 - - + +
552A LEU* 1.3 63.5 + - + +
554A ASN* 3.4 11.6 + - - +
555A HIS* 3.1 24.6 + - + +
688A ARG* 4.8 7.3 + - - +
691A GLN* 4.9 9.4 - - + +
692A ALA* 4.2 23.3 - - + +
694A ILE* 6.1 1.1 - - + -
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Residues in contact with LEU 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A ILE* 3.5 32.8 - - + -
548A ASP 3.3 11.4 + - - +
549A PRO 3.3 8.7 + - - +
550A LYS 3.2 0.4 - - - -
551A VAL* 1.3 80.0 - - + +
553A HIS* 1.3 58.4 + - - +
555A HIS* 3.5 7.9 + - - +
556A SER* 3.0 20.6 + - - -
641A THR* 3.0 30.0 - - - +
644A LEU* 4.1 26.0 - - + -
645A PRO* 3.8 23.6 - - + -
688A ARG 5.2 0.2 - - - +
689A ILE* 4.8 15.9 - - + +
692A ALA* 3.6 24.7 - - + -
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Residues in contact with HIS 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A PRO 2.9 14.5 + - - +
550A LYS* 3.0 11.2 + - - +
552A LEU* 1.3 76.0 - - - +
554A ASN* 1.3 67.6 + - - +
556A SER* 3.1 12.3 + - - -
557A GLU* 3.0 52.5 + - + +
641A THR 5.7 0.2 - - - -
645A PRO* 5.4 1.5 - - + +
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Residues in contact with ASN 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A LYS* 2.9 30.7 + - - +
551A VAL* 3.4 11.2 + - - +
553A HIS* 1.3 79.7 - - - +
555A HIS* 1.3 64.1 + - - +
557A GLU* 3.2 9.1 + - - +
558A GLU* 2.9 26.7 + - - +
688A ARG* 4.8 4.3 - - - +
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Residues in contact with HIS 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A VAL* 3.1 17.4 + - + +
552A LEU* 3.6 10.6 - - - +
554A ASN* 1.3 79.0 - - - +
556A SER* 1.3 58.3 + - - +
558A GLU* 3.8 1.4 - - - +
559A LEU* 3.0 54.0 + - + +
636A LEU* 4.5 3.5 - - + +
641A THR* 4.0 8.4 + - + -
685A GLU* 2.8 35.8 + - - -
688A ARG* 3.4 61.0 + - + +
689A ILE* 3.9 22.2 - - + +
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Residues in contact with SER 556 (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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552A LEU 3.0 8.7 + - - -
553A HIS* 3.1 19.6 + - - -
555A HIS* 1.3 75.6 - - - +
557A GLU* 1.3 64.2 + - - +
559A LEU* 3.3 2.6 + - - +
560A THR* 2.9 27.7 + - - -
637A LYS* 3.5 14.7 + - - +
641A THR* 3.2 22.7 - - - -
642A ASP* 3.0 21.4 + - - -
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Residues in contact with GLU 557 (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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553A HIS* 3.0 47.9 + - + +
554A ASN* 3.7 9.0 - - - +
556A SER* 1.3 74.9 - - - +
558A GLU* 1.3 62.9 + - - +
560A THR* 3.2 19.7 + - - -
561A LEU* 3.3 21.1 + - + +
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Residues in contact with GLU 558 (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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554A ASN 2.9 16.6 + - - +
555A HIS* 3.8 4.3 - - - +
557A GLU* 1.3 78.0 - - - +
559A LEU* 1.3 57.5 + - - +
561A LEU* 3.3 14.3 + - + +
562A ARG* 2.9 55.7 + - + +
688A ARG* 2.9 39.3 + - - -
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Residues in contact with LEU 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A HIS* 3.0 45.0 + - + +
556A SER 3.8 4.7 - - - +
557A GLU 3.3 0.2 - - - -
558A GLU* 1.3 74.2 - - - +
560A THR* 1.3 59.9 + - - +
562A ARG* 3.8 15.7 - - - +
563A LEU* 2.9 40.0 + - + +
633A LEU* 3.8 27.1 - - + +
636A LEU* 4.7 5.4 - - + -
637A LYS* 3.8 31.4 - - + +
641A THR* 3.8 16.8 - - - +
685A GLU* 3.5 22.0 - - - +
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Residues in contact with THR 560 (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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556A SER 2.9 21.3 + - - -
557A GLU* 3.3 15.0 + - - -
559A LEU* 1.3 76.3 - - - +
561A LEU* 1.3 63.7 + - + +
563A LEU* 3.4 9.8 + - - +
564A ALA* 3.1 22.8 + - + +
637A LYS* 3.5 16.0 + - - +
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Residues in contact with LEU 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A GLU* 3.3 17.6 + - + +
558A GLU* 3.5 15.5 - - + +
560A THR* 1.3 82.1 - - + +
562A ARG* 1.3 57.7 + - + +
564A ALA* 3.1 9.1 + - + +
565A GLU* 2.9 34.4 + - + +
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Residues in contact with ARG 562 (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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558A GLU* 2.9 49.1 + - + +
559A LEU* 3.9 10.8 - - - +
560A THR 3.3 0.2 - - - -
561A LEU* 1.3 75.9 - - + +
563A LEU* 1.3 57.6 + - - +
565A GLU* 3.8 7.3 - - + +
566A LEU* 2.9 38.4 + - + +
629A GLU* 4.2 15.0 + - - -
633A LEU* 4.0 30.1 - - + +
685A GLU* 3.0 39.0 + - - +
688A ARG* 4.1 2.4 - - - +
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Residues in contact with LEU 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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559A LEU* 2.9 28.0 + - + +
560A THR* 3.7 7.4 - - - +
561A LEU 3.3 0.2 - - - -
562A ARG* 1.3 73.4 - - - +
564A ALA* 1.3 64.1 + - - +
566A LEU* 4.5 0.4 - - + -
567A GLU* 3.2 12.5 + - - +
630A TYR* 3.1 68.5 + - + +
633A LEU* 3.8 23.3 - - + +
634A ALA* 4.0 19.3 - - + +
637A LYS* 4.4 16.8 - - + -
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Residues in contact with ALA 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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560A THR* 3.1 13.3 + - + +
561A LEU* 3.4 13.5 - - + +
563A LEU* 1.3 76.5 - - - +
565A GLU* 1.3 62.2 + - + +
567A GLU* 3.2 13.5 + - - +
568A LYS* 3.1 32.0 + - - +
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Residues in contact with GLU 565 (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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561A LEU* 2.9 19.7 + - + +
562A ARG* 3.8 8.3 - - + +
564A ALA* 1.3 77.8 - - + +
566A LEU* 1.3 56.9 + - + +
568A LYS* 3.3 17.0 + - - +
569A LYS* 3.0 48.6 + - + +
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Residues in contact with LEU 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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562A ARG* 2.9 26.9 + - + +
563A LEU* 4.6 0.7 - - - -
565A GLU* 1.3 74.1 - - + +
567A GLU* 1.3 65.8 + - - +
569A LYS* 3.2 17.3 + - + +
570A ALA* 3.1 21.8 + - - +
626A VAL* 4.1 30.1 - - + +
629A GLU* 3.4 28.9 - - + +
630A TYR* 3.8 35.4 - - + -
633A LEU* 3.7 20.0 - - + -
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Residues in contact with GLU 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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563A LEU 3.2 17.0 + - - +
564A ALA* 3.2 10.9 + - - +
566A LEU* 1.3 78.2 - - - +
568A LYS* 1.3 62.5 + - + +
570A ALA* 3.3 6.2 + - - +
571A HIS* 3.1 59.6 + - + +
577A GLU* 5.4 0.3 - - - +
578A PHE 4.7 4.2 - - - +
580A LEU* 4.3 18.4 - - + -
630A TYR* 4.4 14.3 + - + -
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Residues in contact with LYS 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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564A ALA* 3.1 22.1 + - - +
565A GLU* 3.5 19.5 - - - +
567A GLU* 1.3 75.8 - - + +
569A LYS* 1.3 59.0 + - - +
571A HIS* 3.1 13.6 + - + +
572A GLU* 2.8 34.8 + - - +
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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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565A GLU* 3.0 34.6 + - - +
566A LEU* 3.2 22.8 + - + +
568A LYS* 1.3 75.4 - - + +
570A ALA* 1.3 58.9 + - - +
572A GLU* 3.9 14.4 - - - +
573A ILE* 3.1 35.1 + - + +
626A VAL* 4.8 15.7 - - + -
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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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566A LEU 3.1 11.6 + - - +
567A GLU* 3.4 11.0 - - - +
568A LYS 3.1 0.2 - - - -
569A LYS* 1.3 75.6 - - - +
571A HIS* 1.3 64.2 + - + +
573A ILE* 3.3 11.8 + - - +
574A ALA* 3.4 10.2 + - - +
578A PHE* 4.0 25.2 - - + -
580A LEU* 4.3 15.0 - - + -
623A LEU* 4.0 23.4 - - + +
626A VAL* 4.1 9.6 - - + +
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Residues in contact with HIS 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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567A GLU* 3.1 51.1 + - + +
568A LYS* 3.1 12.2 + - + +
570A ALA* 1.3 75.4 - - + +
572A GLU* 1.3 61.2 + - - +
574A ALA 3.2 22.5 - - - +
575A GLY* 3.4 6.9 + - - -
576A GLU 3.6 17.0 - - - +
577A GLU* 3.6 28.8 + - + +
578A PHE* 3.3 42.8 + + - -
580A LEU* 5.4 0.4 - - + +
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Residues in contact with GLU 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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568A LYS* 2.8 16.5 + - - +
569A LYS* 3.9 16.8 - - - +
571A HIS* 1.3 75.1 - - - +
573A ILE* 1.3 65.8 + - + +
574A ALA 3.7 5.2 - - - +
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Residues in contact with ILE 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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569A LYS* 3.1 24.0 + - + +
570A ALA 3.7 4.9 - - - +
571A HIS 3.3 0.4 - - - -
572A GLU* 1.3 80.2 - - + +
574A ALA* 1.3 59.5 - - - +
593A LYS* 3.6 26.9 + - - +
622A PRO* 3.9 22.7 - - + +
623A LEU* 3.8 36.6 - - + +
626A VAL* 4.4 11.4 - - + -
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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
------------------------------------------------------------
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