Contacts of the helix formed by residues 555 - 578 (chain A) in PDB entry 3N00
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 555 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A ASP* 2.8 18.3 + - - +
553A MET* 4.2 1.1 - - - -
554A GLU* 1.3 73.9 - - + +
556A SER* 1.3 60.5 + - - +
557A ALA* 3.4 18.9 + - - +
558A SER* 2.5 50.1 + - - +
559A VAL* 3.5 4.7 + - - +
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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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550A ARG* 3.1 38.3 + - - +
553A MET* 3.6 23.9 + - - +
554A GLU 3.8 2.0 + - - -
555A ASN* 1.3 73.4 + - - +
557A ALA* 1.3 62.8 + - - +
559A VAL* 3.3 4.0 + - - +
560A GLU* 3.0 23.0 + - - +
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Residues in contact with ALA 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A ASN* 3.2 13.6 + - - +
556A SER* 1.3 77.9 - - - +
558A SER* 1.3 57.4 + - - +
560A GLU* 3.2 10.5 + - - +
561A GLN* 2.9 40.9 + - - +
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Residues in contact with SER 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A LEU* 3.6 24.6 - - - +
467A ASP* 4.1 2.9 + - - -
555A ASN* 2.5 45.5 + - - +
557A ALA* 1.3 75.9 - - - +
559A VAL* 1.3 64.0 + - - +
561A GLN* 3.4 11.1 + - - +
562A LEU* 3.2 21.8 + - - +
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Residues in contact with VAL 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A LEU* 4.0 25.4 - - + -
467A ASP* 4.5 2.7 - - + +
471A LEU* 4.1 19.1 - - + -
546A VAL* 3.9 18.2 - - + +
550A ARG* 3.8 24.0 - - + +
553A MET* 3.6 31.4 - - + -
555A ASN 3.5 8.5 + - - +
556A SER 3.3 8.4 + - - +
557A ALA 3.3 0.2 - - - -
558A SER* 1.3 77.5 + - - +
560A GLU* 1.3 58.4 + - - +
562A LEU* 3.3 6.7 + - + +
563A GLN* 3.0 24.6 + - - +
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Residues in contact with GLU 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A ARG* 3.3 36.3 + - - +
556A SER 3.0 16.2 + - - +
557A ALA* 3.6 9.3 - - - +
558A SER 3.2 0.4 - - - -
559A VAL* 1.3 76.2 - - - +
561A GLN* 1.3 64.1 + - + +
563A GLN* 3.2 8.6 + - - +
564A GLU* 3.0 24.7 + - + +
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Residues in contact with GLN 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A ALA* 2.9 28.6 + - - +
558A SER* 3.9 8.2 - - - +
559A VAL 3.4 0.2 - - - -
560A GLU* 1.3 76.1 - - + +
562A LEU* 1.3 57.2 + - - +
564A GLU* 3.5 6.5 + - - +
565A THR* 3.0 31.8 + - - -
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Residues in contact with LEU 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A ILE* 4.7 2.0 - - + -
458A PRO 3.1 28.0 - - - +
459A GLY* 4.1 10.1 - - - +
460A PHE* 3.9 25.6 - - + +
463A LEU* 4.0 20.6 - - + -
471A LEU* 5.3 0.4 - - + -
546A VAL* 4.0 27.1 - - + -
558A SER 3.2 10.5 + - - +
559A VAL 3.5 9.0 - - - +
560A GLU 3.1 0.4 - - - -
561A GLN* 1.3 76.5 - - - +
563A GLN* 1.3 65.6 + - - +
565A THR* 3.3 11.4 + - + -
566A LEU* 3.1 38.4 + - + +
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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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543A VAL* 5.1 0.6 - - + +
546A VAL* 3.6 20.8 - - + +
547A SER* 3.0 38.6 + - - +
550A ARG* 2.8 29.0 + - - +
559A VAL 3.0 13.8 + - - +
560A GLU* 3.2 13.9 + - - +
562A LEU* 1.3 76.5 - - - +
564A GLU* 1.3 56.9 + - - +
566A LEU* 3.2 3.8 + - - +
567A LEU* 2.9 50.9 + - + +
592A LEU* 5.4 2.3 - - - +
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Residues in contact with GLU 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 GLU* 3.0 18.4 + - + +
561A GLN* 3.8 7.0 - - - +
563A GLN* 1.3 73.8 - - - +
565A THR* 1.3 60.0 + - - +
567A LEU* 3.7 9.9 - - - +
568A ARG* 2.8 32.2 + - - +
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Residues in contact with THR 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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283A PRO* 4.6 10.2 - - + +
288A VAL* 4.2 22.2 - - + -
458A PRO* 5.5 2.5 - - + +
561A GLN 3.0 17.1 + - - -
562A LEU* 3.5 16.8 - - + +
564A GLU* 1.3 77.5 - - - +
566A LEU* 1.3 66.6 + - + +
568A ARG* 3.3 32.7 + - - +
569A ALA* 3.2 20.8 + - - +
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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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288A VAL* 3.9 22.7 - - + -
292A VAL* 4.3 4.3 - - + -
457A ILE* 4.0 26.5 - - + -
458A PRO* 5.0 2.7 - - + +
539A LEU* 4.0 16.4 - - + +
542A ALA* 3.9 15.9 - - + +
543A VAL* 3.8 15.3 - - + +
546A VAL* 3.4 37.0 - - + -
562A LEU* 3.1 20.9 + - + +
563A GLN 3.7 5.6 - - - +
565A THR* 1.3 78.1 - - + +
567A LEU* 1.3 62.1 + - - +
569A ALA* 3.3 5.6 + - - +
570A LEU* 3.0 27.9 + - - +
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Residues in contact with LEU 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A VAL* 3.4 32.8 - - + -
547A SER* 5.1 0.4 - - - +
563A GLN* 2.9 46.3 + - + +
564A GLU* 3.9 7.6 - - - +
566A LEU* 1.3 72.8 - - - +
568A ARG* 1.3 65.1 + - - +
570A LEU* 4.2 4.9 - - + -
571A ARG* 3.1 24.4 + - - +
585A PHE* 3.7 17.0 - - + -
589A LEU* 3.7 28.5 - - + -
592A LEU* 5.6 0.9 - - + -
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Residues in contact with ARG 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A PRO 3.1 26.9 + - - -
284A THR* 5.1 0.2 - - - +
285A VAL* 3.9 26.9 - - + +
288A VAL* 5.3 0.6 - - - +
564A GLU 2.8 18.6 + - - +
565A THR* 3.3 30.2 + - - +
566A LEU 3.2 0.2 - - - -
567A LEU* 1.3 77.8 - - - +
569A ALA* 1.3 60.5 + - - +
571A ARG* 3.3 8.0 + - - +
572A ALA* 3.1 21.7 + - - +
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Residues in contact with ALA 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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285A VAL* 3.9 19.3 - - + +
288A VAL* 3.8 24.2 - - + -
289A ILE* 4.2 10.8 - - + +
539A LEU* 3.7 16.6 - - + +
565A THR 3.2 7.0 + - - +
566A LEU 3.6 7.9 - - - +
567A LEU 3.3 0.2 - - - -
568A ARG* 1.3 80.5 - - - +
570A LEU* 1.3 52.2 + - - +
572A ALA* 3.2 4.0 + - - +
573A LEU* 2.8 35.0 + - - +
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Residues in contact with LEU 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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536A GLU* 3.9 27.1 - - - +
539A LEU* 3.6 20.3 - - + +
540A PHE* 4.1 21.1 - - + +
543A VAL* 4.0 21.1 - - + -
566A LEU 3.0 17.7 + - - +
567A LEU* 3.8 8.7 - - + +
569A ALA* 1.3 75.7 - - - +
571A ARG* 1.3 57.0 + - - +
573A LEU* 3.4 3.2 + - + +
574A VAL* 2.9 41.0 + - + +
585A PHE* 3.8 19.5 - - + -
588A LEU* 4.4 13.9 - - + -
589A LEU* 5.9 1.6 - - + -
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Residues in contact with ARG 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 LEU 3.1 17.1 + - - +
568A ARG* 3.6 7.2 - - - +
569A ALA 3.2 0.2 - - - -
570A LEU* 1.3 74.9 - - - +
572A ALA* 1.3 70.1 + - - +
574A VAL* 3.5 2.1 + - - +
575A LEU* 3.1 48.5 + - + +
585A PHE* 3.7 40.6 - - + -
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Residues in contact with ALA 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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285A VAL* 3.7 23.6 - - + -
289A ILE* 5.1 1.3 - - + -
568A ARG 3.1 11.0 + - - +
569A ALA 3.4 8.1 - - - +
571A ARG* 1.3 78.1 - - - +
573A LEU* 1.3 64.2 + - - +
575A LEU* 2.9 15.9 + - - +
576A LYS* 3.0 15.6 + - - +
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Residues in contact with LEU 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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289A ILE* 3.9 29.1 - - + +
535A GLU* 3.5 59.0 - - + +
536A GLU* 3.7 16.4 - - + +
539A LEU* 4.2 8.7 - - + -
569A ALA 2.8 19.8 + - - +
570A LEU* 3.7 6.3 - - + +
572A ALA* 1.3 73.7 - - - +
574A VAL* 1.3 64.2 + - - +
576A LYS* 3.4 11.8 + - + +
577A ASN* 3.1 39.6 + - - +
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Residues in contact with VAL 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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536A GLU* 3.7 25.8 - - + +
570A LEU* 2.9 24.7 + - + +
571A ARG* 4.0 4.3 - - - +
573A LEU* 1.3 78.3 - - - +
575A LEU* 1.3 61.7 + - + +
577A ASN* 3.8 0.9 - - - +
578A ARG* 3.0 26.9 + - - +
581A GLU 5.1 1.8 - - - +
584A ARG* 3.4 34.3 - - + +
585A PHE* 3.9 16.8 - - + +
588A LEU* 3.9 26.9 - - + -
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Residues in contact with LEU 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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571A ARG* 3.1 52.1 + - + +
572A ALA* 2.9 6.0 + - - +
574A VAL* 1.3 80.3 - - + +
576A LYS* 1.3 63.8 + - - +
577A ASN 3.2 1.3 - - - -
578A ARG 4.5 4.7 - - - +
579A PRO* 3.2 47.9 - - + +
581A GLU 4.9 4.0 - - - +
582A THR* 4.5 16.8 - - + +
585A PHE* 6.2 2.0 - - + -
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Residues in contact with LYS 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 ALA 3.0 12.0 + - - +
573A LEU* 3.7 16.4 - - + +
575A LEU* 1.3 77.5 - - - +
577A ASN* 1.3 79.6 + - - +
579A PRO* 3.8 8.5 - - - +
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Residues in contact with ASN 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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533A THR* 3.8 17.1 + - + +
535A GLU* 5.1 2.5 + - - +
536A GLU* 2.7 42.9 + - - +
573A LEU* 3.1 25.6 + - - +
574A VAL 3.8 1.1 - - - +
576A LYS* 1.3 98.5 - - - +
578A ARG* 1.3 68.3 + - + +
579A PRO* 3.6 4.1 - - - +
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Residues in contact with ARG 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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574A VAL 3.0 13.2 + - - +
575A LEU* 4.5 2.1 - - - +
577A ASN* 1.3 87.3 - - + +
579A PRO* 1.4 64.6 - - - +
580A LEU 3.2 3.6 + - - -
581A GLU* 3.0 54.5 + - + +
584A ARG* 3.7 42.9 - - - +
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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