Contacts of the helix formed by residues 575 - 593 (chain A) in PDB entry 1P4J
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 ARG 575 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A GLN* 4.4 0.2 - - - -
571A HIS 3.4 2.7 + - - -
572A GLU* 3.0 22.7 + - - +
573A TYR 3.7 7.2 - - - +
574A LYS* 1.3 80.3 - - - +
576A GLN* 1.3 62.2 + - - +
577A LEU* 2.8 10.1 - - - +
578A LEU* 2.9 37.6 + - + +
579A ASN 3.6 3.1 + - - -
666A ILE* 3.0 33.7 + - - +
667A SER 3.5 10.9 + - - -
668A THR* 3.2 23.7 + - - +
691A THR* 3.6 11.7 - - - +
713A MET* 5.0 0.2 - - - +
771A PHE* 3.4 14.3 + - + -
772A LYS 3.4 19.6 + - - -
773A VAL* 4.0 22.1 - - + +
776A ASP* 2.9 35.9 + - - +
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Residues in contact with GLN 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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566A GLN* 3.6 25.3 + - + +
568A LYS* 3.4 25.1 + - - +
569A ARG 3.1 24.4 + - - -
570A ILE* 3.9 22.6 - - + +
571A HIS 2.9 33.7 + - - +
574A LYS* 3.8 7.8 - - - +
575A ARG* 1.3 73.1 - - - +
577A LEU* 1.3 56.6 + - - +
579A ASN* 3.1 6.5 + - - +
580A CYS* 3.0 29.9 + - - -
605A ILE* 4.2 14.9 - - + +
606A GLY 5.4 0.4 + - - -
619A ILE* 4.1 19.0 - - + +
623A ILE* 4.8 2.5 - - + -
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Residues in contact with LEU 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A GLU* 5.7 2.9 - - + -
575A ARG* 2.8 3.3 - - - -
576A GLN* 1.3 77.3 - - - +
578A LEU* 1.3 64.7 + - - +
580A CYS* 3.2 6.4 + - + +
581A LEU* 3.0 29.8 + - + +
615A MET* 5.7 0.4 - - - -
619A ILE* 4.0 33.8 - - + +
622A LEU* 3.7 28.9 - - + -
761A ILE* 4.1 17.5 - - + -
764A MET* 3.5 32.1 - - + -
765A LEU* 3.9 18.4 - - + -
773A VAL* 4.5 16.2 - - + -
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Residues in contact with LEU 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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575A ARG* 2.9 49.2 + - + +
577A LEU* 1.3 78.2 - - - +
579A ASN* 1.3 62.2 + - - +
581A LEU* 3.3 6.1 + - + +
582A HIS 3.2 16.5 + - - -
666A ILE* 4.2 11.4 - - + -
711A PHE* 4.3 11.0 - - + -
773A VAL* 3.7 34.8 - - + +
776A ASP* 4.3 3.4 - - + -
777A TYR* 4.0 23.3 - - + -
780A TYR* 3.4 35.9 - - + -
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Residues in contact with ASN 579 (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 ASP* 4.8 1.1 + - - +
566A GLN* 3.1 36.2 + - - +
575A ARG 3.6 1.8 + - - -
576A GLN 3.2 9.9 - - - +
578A LEU* 1.3 80.2 - - - +
580A CYS* 1.3 63.0 + - - +
582A HIS* 3.1 9.9 + - - +
583A VAL* 3.0 32.0 + - - +
603A VAL* 4.1 10.1 - - - +
605A ILE* 3.7 17.2 - - + +
664A GLU* 4.0 13.6 + - - +
666A ILE* 4.0 3.9 - - + +
780A TYR* 3.7 21.7 + - - +
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Residues in contact with CYS 580 (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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576A GLN 3.0 20.5 + - - -
577A LEU* 3.4 13.0 - - + +
579A ASN* 1.3 77.3 - - - +
581A LEU* 1.3 63.8 + - + +
583A VAL* 3.2 9.5 + - - +
584A ILE* 3.0 30.9 + - + +
605A ILE* 4.7 6.1 - - - -
619A ILE* 5.1 1.6 - - - -
622A LEU* 4.1 19.1 - - + -
623A ILE* 3.7 31.2 - - - -
626A ILE* 4.0 20.9 - - + -
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Residues in contact with LEU 581 (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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577A LEU* 3.0 17.9 + - + +
578A LEU* 3.5 7.9 - - + +
579A ASN 3.2 0.2 - - - -
580A CYS* 1.3 77.7 - - + +
582A HIS* 1.3 56.3 + - - +
584A ILE* 3.5 3.3 + - + -
585A THR* 2.7 33.5 + - - -
738A LEU* 4.1 13.2 - - + -
741A ILE* 3.4 33.2 - - + +
742A ILE* 5.1 3.4 - - + -
745A LEU* 5.0 9.4 - - + -
765A LEU* 5.1 11.4 - - + -
773A VAL* 3.6 28.9 - - + -
774A PHE* 4.1 18.6 - - + -
777A TYR* 4.1 21.3 - - + -
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Residues in contact with HIS 582 (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 ASP* 4.8 2.2 + - - -
578A LEU 3.2 4.6 + - - -
579A ASN* 3.1 12.7 + - - +
581A LEU* 1.3 75.1 - - - +
583A VAL* 1.3 69.0 + - - +
585A THR* 2.9 17.2 + - - -
586A LEU* 2.9 52.9 + - + +
601A ARG* 3.9 10.9 + - - -
603A VAL* 6.0 1.4 - - + +
777A TYR* 4.8 0.6 - - - -
780A TYR* 3.4 26.6 + + + +
781A VAL* 4.2 26.1 + - + +
784A GLN* 3.3 49.6 + - + +
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Residues in contact with VAL 583 (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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579A ASN* 3.0 32.3 + - - +
580A CYS* 3.6 9.6 - - - +
582A HIS* 1.3 78.9 - - - +
584A ILE* 1.3 62.6 + - - +
586A LEU* 3.2 11.1 + - - +
587A TYR* 3.0 19.9 + - - +
603A VAL* 3.8 24.7 - - + -
605A ILE* 5.3 3.4 - - + -
626A ILE* 4.0 17.0 - - + -
630A VAL* 5.0 1.8 - - + -
640A LEU* 4.1 11.4 - - + +
642A VAL* 3.4 31.6 - - + -
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Residues in contact with ILE 584 (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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580A CYS* 3.0 19.4 + - + +
581A LEU* 3.9 5.8 - - + +
583A VAL* 1.3 77.0 - - - +
585A THR* 1.3 57.7 + - - +
587A TYR* 3.2 7.9 + - + +
588A ASN* 2.9 33.6 + - - +
622A LEU* 5.2 1.6 - - + -
626A ILE* 3.8 29.4 - - + -
741A ILE* 3.8 26.9 - - + -
744A GLN* 3.6 24.0 - - - +
745A LEU* 4.5 11.7 - - + -
750A PHE* 3.9 33.4 - - + -
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Residues in contact with THR 585 (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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581A LEU 2.7 18.4 + - - -
582A HIS* 2.9 12.7 + - - -
584A ILE* 1.3 76.8 - - - +
586A LEU* 1.3 64.1 + - + +
588A ASN* 3.4 5.5 + - - +
589A ARG* 3.0 59.6 + - - +
737A GLU* 4.2 9.1 - - + +
741A ILE* 3.2 9.5 - - - +
777A TYR* 2.7 30.9 + - - +
781A VAL* 4.4 11.4 - - + -
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Residues in contact with LEU 586 (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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582A HIS* 2.9 53.6 + - + +
583A VAL* 3.5 10.8 - - - +
585A THR* 1.3 80.8 - - + +
587A TYR* 1.3 63.3 + - - +
589A ARG* 3.4 16.8 + - - +
590A ILE* 3.1 32.9 + - + +
601A ARG* 3.9 26.9 - - - +
603A VAL* 5.5 2.2 - - + -
640A LEU* 4.1 22.2 - - + -
781A VAL* 5.9 0.2 - - + -
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Residues in contact with TYR 587 (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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583A VAL 3.0 13.7 + - - +
584A ILE* 3.2 10.5 + - - +
586A LEU* 1.3 76.5 - - - +
588A ASN* 1.3 75.4 + - - +
590A ILE* 3.2 6.4 + - - +
591A LYS* 3.0 45.2 + - + +
629A VAL* 3.7 19.0 - - + +
630A VAL* 3.7 32.5 - - + -
633A ASP* 2.6 34.5 + - + -
636A VAL* 3.7 25.6 - - + -
640A LEU* 4.0 8.0 - - + +
749A PHE* 3.9 30.5 - + - -
750A PHE* 5.1 7.4 - + - -
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Residues in contact with ASN 588 (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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584A ILE* 2.9 25.4 + - - +
585A THR* 3.9 4.4 - - - +
587A TYR* 1.3 89.0 - - - +
589A ARG* 1.3 58.4 + - + +
591A LYS* 3.4 6.4 + - - +
592A LYS* 3.0 29.3 + - - +
737A GLU* 6.0 0.7 - - - +
740A GLN* 3.6 33.2 + - - +
741A ILE* 4.0 8.7 - - - +
744A GLN* 2.9 43.4 + - - -
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Residues in contact with ARG 589 (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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585A THR* 3.0 28.4 + - - +
586A LEU* 3.7 15.6 - - - +
588A ASN* 1.3 76.7 - - + +
590A ILE* 1.3 63.4 + - + +
592A LYS* 3.4 7.3 + - - +
593A GLU* 3.1 24.6 + - - +
596A LYS* 5.8 1.8 + - - +
737A GLU* 2.8 42.2 + - - +
781A VAL* 3.7 25.4 - - - +
785A GLU* 2.9 32.2 + - - +
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Residues in contact with ILE 590 (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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586A LEU* 3.1 18.8 + - + +
587A TYR* 3.2 8.0 + - - +
589A ARG* 1.3 76.8 - - + +
591A LYS* 1.3 60.5 + - - +
593A GLU 3.1 4.6 - - - -
594A PRO* 2.8 36.2 - - + +
598A VAL* 4.4 30.3 - - + -
635A VAL* 4.5 4.9 - - + +
636A VAL* 4.5 24.9 - - + -
639A ARG* 3.7 34.8 - - + +
640A LEU* 4.3 28.9 - - + -
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Residues in contact with LYS 591 (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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587A TYR* 3.0 42.3 + - + +
588A ASN* 3.7 7.9 - - - +
589A ARG 3.4 0.2 - - - -
590A ILE* 1.3 76.6 - - + +
592A LYS* 1.3 61.1 + - - +
594A PRO* 3.6 15.2 - - - +
633A ASP* 2.9 39.4 + - - +
635A VAL* 4.3 20.7 - - + +
636A VAL* 4.8 2.9 - - + -
749A PHE* 6.4 0.4 - - - -
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Residues in contact with LYS 592 (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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588A ASN 3.0 17.6 + - - +
589A ARG* 3.6 8.1 - - - +
590A ILE 3.1 0.2 - - - -
591A LYS* 1.3 79.0 - - - +
593A GLU* 1.3 89.8 + - + +
594A PRO* 3.5 4.4 - - - +
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Residues in contact with GLU 593 (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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589A ARG 3.1 13.0 + - - +
590A ILE* 3.1 7.6 - - - +
592A LYS* 1.3 107.7 + - + +
594A PRO* 1.3 65.5 - - - +
595A ASN 3.4 2.5 - - - -
596A LYS* 3.0 57.3 + - + +
639A ARG* 4.4 0.7 + - - -
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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