Contacts of the helix formed by residues 597 - 611 (chain A) in PDB entry 1N54
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 HIS 597 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457A MET* 5.5 4.6 - - + +
458A ARG* 5.6 3.3 - - + +
481A PRO* 3.8 30.3 - - + +
559A PHE* 4.1 13.2 - + - -
594A TRP* 2.6 40.6 + + + +
596A ASN* 1.3 82.5 - - - +
598A PRO* 1.4 67.5 - - - +
599A GLN* 4.1 28.5 + - + -
600A MET* 3.2 22.2 + - + +
601A ILE* 2.9 23.4 + - - +
54B GLU* 4.8 7.1 - - + +
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Residues in contact with PRO 598 (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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454A GLU* 4.3 8.3 - - + +
457A MET* 5.6 8.7 - - + -
458A ARG* 4.1 11.0 - - - +
595A ARG 5.0 3.8 - - - +
596A ASN* 3.9 4.5 - - - +
597A HIS* 1.4 85.1 - - - +
599A GLN* 1.3 56.5 + - - +
600A MET 2.9 4.5 - - - -
601A ILE* 2.5 41.0 + - + +
602A ALA* 2.7 13.5 + - - +
634A ARG* 3.8 25.6 - - - +
636A PHE* 3.7 33.2 - - + -
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Residues in contact with GLN 599 (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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458A ARG* 3.5 51.6 - - + +
559A PHE* 3.5 19.2 - - + -
597A HIS* 3.6 13.0 + - + -
598A PRO* 1.3 76.9 - - - +
600A MET* 1.3 55.5 + - - +
602A ALA* 3.6 7.5 - - - +
603A VAL* 2.9 39.6 + - + +
54B GLU* 2.7 39.0 + - - +
57B TYR* 4.0 4.0 - - - +
58B GLU* 3.5 27.8 + - - +
1555B GOL 3.9 9.3 - - - +
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Residues in contact with MET 600 (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 ALA 4.4 4.9 - - - +
558A SER 4.1 9.4 - - - +
559A PHE* 3.4 34.1 - - + -
562A SER* 3.6 21.8 - - - +
594A TRP* 3.5 43.3 - - + -
597A HIS* 3.2 32.5 + - + +
598A PRO 2.7 4.0 + - - -
599A GLN* 1.3 75.0 - - - +
601A ILE* 1.3 65.5 + - - +
603A VAL* 2.9 26.1 - - - +
604A LEU* 3.0 33.8 + - + +
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Residues in contact with ILE 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A MET* 3.6 27.1 - - - -
591A PHE* 4.6 11.4 - - + -
594A TRP* 3.3 31.0 - - + +
595A ARG* 4.2 8.5 - - - -
597A HIS 2.9 10.1 - - - +
598A PRO* 2.5 29.4 + - + +
600A MET* 1.3 72.5 - - - +
602A ALA* 1.3 56.1 + - - +
604A LEU* 3.8 2.2 - - - +
605A VAL* 2.7 36.3 + - - +
622A TRP* 3.9 27.8 - - + -
636A PHE* 4.3 17.5 - - + -
640A ILE* 4.2 6.3 - - + -
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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
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458A ARG* 5.4 1.1 - - - +
598A PRO 2.7 14.5 + - - +
599A GLN* 3.6 12.6 - - - +
601A ILE* 1.3 75.4 - - - +
603A VAL* 1.3 65.2 + - - +
604A LEU 2.9 1.7 + - - -
605A VAL* 3.2 1.7 + - - +
606A ASP* 3.1 21.9 + - - +
636A PHE* 5.8 2.9 - - + -
639A GLU* 4.2 7.6 - - - +
640A ILE* 3.7 27.6 - - + +
1555B GOL 3.8 20.9 - - - +
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Residues in contact with VAL 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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559A PHE* 3.5 28.9 - - + -
563A PHE* 3.4 28.5 - - + -
599A GLN* 2.9 27.4 + - + +
600A MET* 2.9 41.5 - - - +
602A ALA* 1.3 71.2 - - + +
604A LEU* 1.3 60.6 + - + +
606A ASP* 3.4 8.5 - - - +
607A LYS 3.2 17.0 + - - -
57B TYR* 4.1 19.5 - - + -
1555B GOL 4.1 13.0 - - - +
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Residues in contact with LEU 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A LEU* 4.6 9.9 - - + -
562A SER* 4.1 24.2 - - - +
563A PHE* 4.4 7.9 - - + -
566A LEU* 3.9 23.9 - - + +
590A MET* 4.1 17.0 - - + -
594A TRP* 3.8 18.4 - - + +
600A MET* 3.0 47.8 + - + +
601A ILE 3.8 2.5 - - - +
603A VAL* 1.3 74.1 - - - +
605A VAL* 1.3 56.1 + - - +
606A ASP 3.1 1.1 - - - -
607A LYS* 3.2 2.0 + - - +
608A MET* 2.5 54.1 + - + +
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Residues in contact with VAL 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A LEU* 4.3 8.1 - - + -
590A MET* 3.9 20.2 - - + -
601A ILE* 2.7 28.7 - - + +
602A ALA 3.2 2.9 + - - +
604A LEU* 1.3 74.5 - - - +
606A ASP* 1.3 67.7 + - - +
608A MET* 3.5 9.8 - - - +
609A ILE* 3.1 21.7 + - + +
614A VAL* 5.1 0.7 - - + -
619A VAL* 3.6 32.5 - - + -
622A TRP* 4.3 7.0 - - + -
640A ILE* 3.9 31.0 - - + -
644A THR* 4.6 3.6 - - - +
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Residues in contact with ASP 606 (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 PHE* 6.1 0.2 - - - -
602A ALA 3.1 12.7 + - - +
603A VAL* 3.4 13.8 - - - +
604A LEU 3.1 0.2 - - - -
605A VAL* 1.3 82.6 - - - +
607A LYS* 1.3 65.4 + - - +
609A ILE* 2.9 15.6 + - - +
610A ARG* 2.9 43.6 + - - +
643A SER* 3.7 6.4 + - - +
647A LYS* 3.0 32.8 + - - +
65B ASP* 3.7 10.9 - - - +
66B ILE 5.1 4.1 - - - +
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Residues in contact with LYS 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A PHE* 3.6 59.9 - - + +
566A LEU* 4.7 11.2 - - + +
603A VAL 3.2 2.2 + - - +
604A LEU 3.2 2.5 + - - +
606A ASP* 1.3 87.4 + - - +
608A MET* 1.3 59.3 + - - +
609A ILE 3.3 0.2 - - - -
610A ARG* 3.9 7.2 - - + +
611A THR* 2.8 41.1 + - + +
1556A GOL 2.7 40.5 + - - +
57B TYR* 5.1 0.2 - - - -
67B LYS 3.2 23.6 + - - -
68B LYS* 5.4 1.2 - - - +
89B TYR* 4.7 2.6 + - - -
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Residues in contact with MET 608 (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* 4.3 20.4 - - + +
573A PHE* 6.2 0.2 - - - -
586A VAL* 3.9 19.3 - - + -
587A LEU* 4.1 4.9 - - + -
590A MET* 3.6 37.9 - - + -
604A LEU* 2.5 40.6 + - + +
605A VAL 3.5 3.6 - - - +
606A ASP 3.0 0.2 + - - -
607A LYS* 1.3 74.8 - - - +
609A ILE* 1.3 55.6 + - - +
611A THR* 3.3 5.1 + - - -
613A ILE* 2.6 50.4 + - + +
614A VAL* 3.3 34.7 + - + -
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Residues in contact with ILE 609 (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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605A VAL* 3.1 9.1 + - + +
606A ASP 2.9 7.9 + - - +
608A MET* 1.3 73.6 - - - +
610A ARG* 1.3 59.1 + - - +
611A THR 3.1 2.5 - - - -
612A GLN* 2.7 27.4 + - - +
614A VAL* 2.9 32.1 - - + +
615A ASP* 3.9 14.6 - - - -
616A CYS* 3.9 11.2 - - - +
619A VAL* 3.5 27.1 - - + -
644A THR* 3.7 27.4 - - + +
647A LYS* 5.0 13.9 - - + -
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Residues in contact with ARG 610 (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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606A ASP* 2.9 37.5 + - - +
607A LYS* 4.1 9.4 - - - +
608A MET 3.5 0.4 - - - -
609A ILE* 1.3 75.0 - - - +
611A THR* 1.3 61.7 + - + +
612A GLN* 3.3 3.8 + - - +
647A LYS* 3.8 28.0 - - + +
1556A GOL 4.7 7.9 - - - +
65B ASP* 3.2 38.2 + - - +
66B ILE 4.9 0.6 + - - -
89B TYR* 3.1 52.0 + - - -
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Residues in contact with THR 611 (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* 5.9 0.2 - - - +
567A ALA* 6.1 7.0 - - + -
570A HIS* 3.4 27.2 + - + -
607A LYS* 2.8 38.9 + - + +
608A MET 3.3 1.0 + - - -
610A ARG* 1.3 79.1 - - + +
612A GLN* 1.3 69.9 + - - +
613A ILE* 3.2 25.0 + - + +
1556A GOL 5.2 5.2 - - - +
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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
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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