Contacts of the helix formed by residues 588 - 606 (chain A) in PDB entry 3APO
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 588 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585A SER* 3.2 8.3 + - - -
586A PRO 3.3 0.2 - - - -
587A TRP* 1.3 79.1 - - - +
589A HIS* 1.3 58.2 + - - +
590A PRO* 3.4 10.2 - - - +
591A SER* 3.1 26.0 + - - -
592A GLN* 2.9 33.0 + - - +
631A TYR* 3.3 34.3 + - - +
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Residues in contact with HIS 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A TRP 4.0 2.4 + - - -
588A SER* 1.3 70.6 - - - +
590A PRO* 1.4 71.9 - - + +
592A GLN* 3.0 21.4 + - + +
593A VAL* 2.9 55.2 + - + +
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Residues in contact with PRO 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A SER* 3.4 15.5 - - - +
589A HIS* 1.4 99.2 - - + +
591A SER* 1.3 54.4 + - - -
593A VAL* 3.7 9.2 - - + +
594A LEU* 3.0 28.8 + - - +
631A TYR 3.5 12.6 - - - +
632A PRO* 3.5 16.0 - - + +
655A ARG* 4.0 19.3 + - - +
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Residues in contact with SER 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A ASP* 5.3 1.6 - - - +
584A TYR* 3.6 22.7 - - - +
585A SER 3.4 24.5 + - - -
588A SER* 3.1 20.9 + - - -
589A HIS 3.1 0.6 - - - -
590A PRO* 1.3 75.9 - - - +
592A GLN* 1.3 59.9 + - - +
594A LEU* 2.9 18.1 + - - +
595A MET* 3.0 16.2 + - - +
631A TYR* 3.7 0.5 - - - +
632A PRO* 3.5 27.5 - - - +
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Residues in contact with GLN 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A PRO* 2.8 29.3 + - + +
587A TRP* 4.2 11.3 - - - +
588A SER 2.9 20.4 + - - +
589A HIS* 3.0 20.0 + - + +
591A SER* 1.3 74.4 - - - +
593A VAL* 1.3 62.3 + - + +
595A MET* 4.2 5.1 - - - +
596A PRO* 3.2 21.3 - - - +
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Residues in contact with VAL 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A HIS* 2.9 47.8 + - + +
590A PRO* 3.7 9.0 - - + +
592A GLN* 1.3 77.7 - - + +
594A LEU* 1.3 62.5 + - - +
596A PRO* 3.4 16.0 - - - +
597A GLU* 4.1 11.6 - - + +
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Residues in contact with LEU 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A ASP* 3.4 34.8 - - + +
590A PRO 3.0 16.9 + - - +
591A SER* 2.9 6.5 + - - +
593A VAL* 1.3 78.0 - - - +
595A MET* 1.3 52.3 + - - +
597A GLU* 2.7 12.6 + - - -
598A TRP* 2.7 43.3 + - + +
632A PRO* 3.8 19.1 - - + -
634A ILE* 4.0 17.0 - - + -
655A ARG* 3.6 35.4 - - + +
660A LEU* 3.7 19.1 - - + -
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Residues in contact with MET 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A VAL* 5.0 1.6 - - + -
582A ASP* 3.5 23.3 - - - +
584A TYR* 3.7 35.7 - - + -
591A SER 3.0 13.9 + - - +
592A GLN* 4.2 4.9 - - - +
594A LEU* 1.3 74.9 - - - +
596A PRO* 1.4 66.8 - - + +
598A TRP* 3.1 14.1 + - + -
599A LYS* 2.9 62.6 + - - +
613A SER* 4.0 13.7 - - - +
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Residues in contact with PRO 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A GLN 3.2 17.7 - - - +
593A VAL* 3.4 13.7 - - - +
595A MET* 1.4 91.9 - - + +
597A GLU* 1.3 60.3 + - - +
599A LYS* 3.6 9.0 + - + +
600A ARG* 3.2 36.9 + - - +
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Residues in contact with GLU 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A VAL* 4.1 14.0 - - + +
594A LEU* 2.7 14.7 + - + +
596A PRO* 1.3 72.9 - - - +
598A TRP* 1.3 66.3 + - - +
600A ARG* 2.7 37.8 + - - +
601A MET* 3.0 26.7 + - - +
655A ARG 3.6 24.9 - - - +
656A ASP* 3.5 11.3 - - - +
657A ALA* 3.0 26.8 + - - +
660A LEU* 5.1 1.8 - - + -
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Residues in contact with TRP 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A VAL* 3.7 28.3 - - + -
580A MET* 3.7 45.5 - - + -
581A VAL 4.3 1.3 - - - -
582A ASP* 3.5 30.8 - - + +
594A LEU* 2.7 23.3 + - + +
595A MET* 3.1 19.3 + - + +
597A GLU* 1.3 79.2 - - - +
599A LYS* 1.3 56.3 + - - +
601A MET* 3.5 23.4 + - + +
602A ALA* 3.1 27.9 + - - +
611A VAL* 3.3 15.5 - - + +
612A GLY 3.0 18.2 + - - -
634A ILE* 3.6 37.9 - - + -
660A LEU* 4.0 18.4 - - + -
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Residues in contact with LYS 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A HIS* 6.4 2.9 - - + -
556A PRO* 5.4 9.1 - - - +
557A SER* 4.8 2.6 - - - -
558A VAL* 3.8 30.4 + - + +
595A MET* 2.9 47.1 + - + +
596A PRO* 3.9 7.9 - - + +
598A TRP* 1.3 73.9 - - - +
600A ARG* 1.3 64.4 + - - +
602A ALA* 3.5 2.9 + - - +
603A ARG* 3.3 22.7 + - - +
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Residues in contact with ARG 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A PRO* 3.2 26.4 + - - +
597A GLU* 2.7 45.9 + - - +
599A LYS* 1.3 73.0 - - - +
601A MET* 1.3 68.4 + - - +
602A ALA 3.4 0.5 + - - -
603A ARG* 3.4 19.0 + - - +
604A THR* 3.5 15.4 + - - -
657A ALA* 3.7 13.4 - - + +
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Residues in contact with MET 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A MET* 3.8 14.6 - - + -
597A GLU 3.0 19.0 + - - +
598A TRP* 3.6 44.0 - - + +
600A ARG* 1.3 76.3 - - - +
602A ALA* 1.3 58.5 + - - +
604A THR* 2.9 28.7 - - - +
605A LEU* 3.2 20.8 + - + +
611A VAL* 3.9 26.2 - - + -
657A ALA* 3.8 17.6 - - + +
660A LEU* 3.4 29.2 - - + -
661A ARG* 3.9 17.5 - - + +
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Residues in contact with ALA 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A SER* 3.8 18.1 - - - +
558A VAL* 3.7 22.4 - - + -
598A TRP 3.1 14.6 + - - +
599A LYS 3.8 2.5 - - - +
600A ARG 3.3 0.2 - - - -
601A MET* 1.3 78.2 - - - +
603A ARG* 1.3 58.5 + - - +
605A LEU* 3.0 17.8 + - - +
606A THR* 3.3 10.0 + - - -
609A ILE 5.4 0.3 - - - +
611A VAL* 3.8 31.2 - - + +
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Residues in contact with ARG 603 (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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549A PHE* 6.3 0.6 - - - -
552A ASP* 2.9 35.1 + - - -
553A LEU* 6.1 1.4 - - - +
557A SER* 3.5 19.2 + - - +
599A LYS 3.3 11.5 + - - +
600A ARG* 3.7 16.2 - - - +
601A MET 3.3 0.4 - - - -
602A ALA* 1.3 77.6 - - - +
604A THR* 1.3 59.3 + - - +
606A THR* 3.1 18.6 + - - +
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Residues in contact with THR 604 (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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600A ARG 3.5 10.0 + - - -
601A MET* 2.9 18.2 - - - +
603A ARG* 1.3 80.6 - - - +
605A LEU* 1.3 56.7 + - + +
606A THR* 3.5 2.0 + - - +
608A LEU* 4.1 6.4 - - - +
661A ARG* 2.5 64.7 + - + +
769A LYS* 5.3 9.0 + - - -
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Residues in contact with LEU 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A MET* 4.3 9.0 - - - -
601A MET* 3.2 38.1 + - + +
602A ALA* 3.0 10.6 + - - +
604A THR* 1.3 79.3 - - + +
606A THR* 1.3 68.4 + - - +
607A GLY 3.2 0.3 + - - -
608A LEU* 2.7 25.9 + - + -
609A ILE* 3.1 51.6 + - + +
611A VAL* 4.2 10.8 - - + -
661A ARG* 4.1 20.4 - - + +
665A LEU* 4.0 22.9 - - + -
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Residues in contact with THR 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A SER* 4.1 10.0 + - - -
602A ALA 3.3 7.1 + - - -
603A ARG* 3.1 19.9 + - - +
604A THR 3.5 2.8 - - - +
605A LEU* 1.3 76.7 - - - +
607A GLY* 1.3 61.6 + - - +
608A LEU* 3.3 10.9 + - - +
609A ILE 5.2 1.1 - - - -
769A LYS* 5.1 12.4 + - - -
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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