Contacts of the helix formed by residues 559 - 577 (chain A) in PDB entry 3ODX
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 559 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519A GLN* 3.0 35.9 - - + +
523A LEU* 5.2 6.5 - - + -
555A LYS 3.0 24.2 - - - +
556A ASP* 3.0 15.5 - - - +
558A ILE* 1.3 89.8 - - + +
560A THR* 1.3 61.7 + - - -
561A GLU 3.3 1.1 - - - -
562A MET* 3.6 6.4 + - - +
563A GLN* 3.4 27.8 + - - +
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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
----------------------------------------------------------
431A HIS* 4.2 14.9 + - - -
434A MET* 4.6 15.3 - - + +
435A LEU* 5.1 6.2 - - - +
552A LEU* 4.8 11.7 - - + -
556A ASP 3.6 12.8 - - - +
557A MET* 2.7 28.2 + - - +
559A PRO* 1.3 77.0 - - - +
561A GLU* 1.3 63.0 + - - +
563A GLN* 2.9 23.9 + - - +
564A ARG* 2.8 30.7 + - - +
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Residues in contact with GLU 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A HIS* 2.7 33.2 + - + -
435A LEU* 3.8 4.1 - - + +
467A LEU* 3.2 28.1 - - + +
471A HIS* 2.8 25.3 + - - -
512A SER* 2.8 29.0 + - - +
515A PHE* 3.9 24.9 - - + -
516A CYS* 3.6 11.9 - - - -
558A ILE 3.9 1.8 + - - +
559A PRO 3.3 0.4 - - - -
560A THR* 1.3 81.5 + - - +
562A MET* 1.3 65.8 + - - +
564A ARG* 3.3 2.8 + - - +
565A LEU* 3.1 21.9 + - - +
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Residues in contact with MET 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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516A CYS* 3.7 22.2 - - + -
519A GLN* 3.8 24.1 + - - +
558A ILE 5.1 0.2 + - - -
559A PRO 3.6 7.8 + - - +
560A THR 3.2 0.6 - - - -
561A GLU* 1.3 78.0 - - - +
563A GLN* 1.3 68.5 + - + +
565A LEU* 2.7 18.7 + - - +
566A THR* 3.1 21.3 + - + +
599A LEU* 4.9 5.6 - - - -
602A VAL* 4.0 11.9 - - + -
603A ASN* 3.7 21.3 - - - +
606A VAL* 3.7 33.4 - - + -
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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
----------------------------------------------------------
556A ASP 5.6 0.6 + - - -
559A PRO* 3.4 20.6 + - - +
560A THR* 2.9 29.6 + - - +
562A MET* 1.3 79.2 - - + +
564A ARG* 1.3 64.9 + - - +
566A THR* 2.6 28.5 + - - -
567A LYS* 3.2 23.7 + - + +
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Residues in contact with ARG 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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424A LEU* 3.4 8.1 + - - +
427A THR* 2.6 37.5 + - - -
428A GLU* 2.5 48.0 + - - +
431A HIS* 3.6 36.3 - - + +
471A HIS* 4.2 2.0 - - + -
560A THR 2.8 15.3 + - - +
561A GLU 3.4 9.0 - - - +
563A GLN* 1.3 72.3 - - - +
565A LEU* 1.3 64.3 + - + +
567A LYS* 2.8 30.4 + - - +
568A TYR* 3.1 38.1 + - + +
571A LEU* 3.9 13.5 - - - +
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Residues in contact with LEU 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A HIS* 4.9 0.7 - - + -
508A PHE* 4.1 20.2 - - + -
512A SER* 3.5 29.4 - - - +
516A CYS* 4.5 6.1 - - - -
561A GLU* 3.1 20.6 + - - +
562A MET* 2.7 15.5 + - - +
564A ARG* 1.3 72.8 - - - +
566A THR* 1.3 59.6 - - - +
567A LYS 3.2 0.9 + - - -
568A TYR* 3.4 16.7 + - + +
569A PRO* 3.3 17.3 - - - +
595A CYS 5.0 1.4 - - - +
598A ILE* 4.4 15.9 - - + -
599A LEU* 3.6 18.3 - - + +
602A VAL* 3.7 38.8 - - + -
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Residues in contact with THR 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 MET* 3.1 20.4 + - + +
563A GLN* 2.6 23.7 + - - -
565A LEU* 1.3 76.1 - - - +
567A LYS* 1.3 75.3 + - - +
568A TYR 3.4 0.2 - - - -
569A PRO* 3.8 6.0 - - - +
570A LEU* 3.5 21.3 - - - +
599A LEU* 3.6 31.1 - - + +
603A ASN* 5.6 4.3 - - - +
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Residues in contact with LYS 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 GLN* 3.2 27.6 + - + +
564A ARG* 2.8 29.2 + - - +
566A THR* 1.3 100.9 + - - +
568A TYR* 1.3 63.6 + - - +
569A PRO 3.5 0.4 - - - -
570A LEU* 3.2 21.3 + - + +
571A LEU* 3.0 30.2 + - + +
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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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424A LEU* 4.0 12.6 - - + -
428A GLU* 2.4 29.9 + - - -
471A HIS* 3.0 26.9 + + - -
474A PHE* 3.9 5.2 - + - -
499A ARG* 3.8 25.2 + - - -
500A PHE* 3.8 17.9 - + - -
508A PHE* 4.2 0.4 - + - -
564A ARG* 3.1 45.9 + - + -
565A LEU* 3.8 21.8 - - + +
567A LYS* 1.3 74.6 - - - +
569A PRO* 1.3 66.7 - - + +
571A LEU* 4.6 2.9 - - + +
572A LEU* 2.8 38.3 + - + +
595A CYS* 3.9 18.6 - - + -
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Residues in contact with PRO 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A LEU 3.3 15.5 - - - +
566A THR 3.8 6.1 - - - +
567A LYS 3.7 1.6 - - - -
568A TYR* 1.3 92.0 - - + +
570A LEU* 1.3 58.0 + - + +
572A LEU* 4.7 1.6 - - + -
573A GLN* 2.7 52.5 + - + +
592A ALA 4.7 3.8 - - - +
595A CYS* 4.0 18.1 - - + +
596A ARG* 3.4 37.0 - - + +
599A LEU* 4.4 10.1 - - + -
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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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566A THR 3.5 20.0 - - - +
567A LYS* 3.2 22.3 + - + +
569A PRO* 1.3 85.1 - - + +
571A LEU* 1.3 64.3 + - + +
573A GLN* 3.8 15.2 - - - +
574A SER* 3.5 19.9 + - - -
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Residues in contact with LEU 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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420A VAL* 3.4 23.8 - - + +
423A GLU* 3.7 38.1 - - + +
424A LEU* 3.9 34.1 - - + +
427A THR* 4.2 2.5 - - + +
564A ARG* 3.9 21.3 - - - +
567A LYS* 3.0 26.1 + - + +
568A TYR* 3.8 4.7 - - - +
570A LEU* 1.3 76.2 - - + +
572A LEU* 1.3 70.6 + - + +
574A SER* 3.3 2.9 + - - -
575A ILE* 3.3 25.6 + - - +
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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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424A LEU* 4.4 25.4 - - + -
496A LEU* 3.4 38.8 - - + -
500A PHE* 4.3 5.6 - - + -
568A TYR* 2.8 31.5 + - + +
571A LEU* 1.3 76.4 - - + +
573A GLN* 1.3 64.2 + - - +
575A ILE* 3.3 6.6 + - + +
576A GLY* 3.1 19.1 + - - -
588A VAL* 3.7 8.8 - - - +
591A ALA* 3.7 5.8 - - + -
592A ALA* 3.5 36.6 - - + +
595A CYS* 3.7 20.2 - - - -
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Residues in contact with GLN 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 PRO* 2.7 37.3 + - + +
570A LEU* 3.8 15.1 - - - +
571A LEU 3.3 0.2 - - - -
572A LEU* 1.3 73.7 - - - +
574A SER* 1.4 57.3 + - - +
576A GLY* 3.7 0.9 + - - -
577A GLN* 3.1 37.7 + - - +
589A GLU* 6.1 0.3 - - - +
592A ALA* 4.0 4.4 - - + +
596A ARG* 3.2 48.7 - - - +
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Residues in contact with SER 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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416A LYS* 5.3 3.6 + - - -
417A ARG* 5.2 0.2 - - - -
420A VAL* 3.6 23.5 - - - +
570A LEU 3.5 9.9 + - - -
571A LEU* 3.3 10.5 + - - -
572A LEU 3.1 0.4 - - - -
573A GLN* 1.4 75.4 - - - +
575A ILE* 1.3 63.9 + - - +
576A GLY 3.4 0.2 - - - -
577A GLN* 3.1 26.2 - - - +
578A ASN* 3.1 30.3 + - - +
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Residues in contact with ILE 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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417A ARG* 4.3 10.9 - - + +
420A VAL* 3.3 29.6 - - + -
421A ILE* 3.6 41.3 - - + -
424A LEU* 4.5 19.7 - - + -
492A ILE* 4.3 12.8 - - + -
496A LEU* 5.4 1.3 - - + -
571A LEU 3.3 13.7 + - - +
572A LEU* 3.3 12.1 + - + +
574A SER* 1.3 79.1 - - - +
576A GLY* 1.3 61.7 + - - +
578A ASN* 3.2 6.3 + - - +
579A THR* 3.0 29.2 + - - +
588A VAL* 4.0 13.2 - - + -
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Residues in contact with GLY 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 3.1 12.0 + - - -
573A GLN* 4.0 1.8 - - - -
575A ILE* 1.3 73.7 - - - +
577A GLN* 1.3 54.4 + - - +
578A ASN 3.0 4.3 - - - -
579A THR* 2.8 22.9 + - - -
585A ARG* 3.3 28.6 - - - +
588A VAL* 3.5 21.4 - - - +
589A GLU* 4.7 10.1 - - - -
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Residues in contact with GLN 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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573A GLN* 3.1 27.7 + - - +
574A SER* 3.1 34.0 - - - +
576A GLY* 1.3 74.1 - - - +
578A ASN* 1.4 66.5 + - - +
579A THR 3.5 1.1 - - - +
585A ARG* 5.1 4.7 - - - +
589A GLU* 5.1 3.4 + - - +
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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
------------------------------------------------------------
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