Contacts of the helix formed by residues 558 - 577 (chain A) in PDB entry 4MZ7
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 ASP 558 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491A VAL* 5.5 1.2 - - - +
556A LYS* 3.5 9.6 + - - +
557A VAL* 1.3 86.1 + - - +
559A ARG* 1.3 63.8 + - - +
560A LYS* 3.2 16.2 + - - +
561A SER* 2.7 45.3 + - - -
562A LEU* 3.0 23.2 + - - +
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Residues in contact with ARG 559 (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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557A VAL 4.0 0.4 + - - -
558A ASP* 1.3 74.4 - - - +
560A LYS* 1.3 63.9 + - + +
562A LEU* 4.0 6.7 - - - +
563A TYR* 3.2 27.4 + - + +
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Residues in contact with LYS 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A ASP* 4.2 31.0 + - + +
491A VAL* 3.4 28.8 - - + +
558A ASP* 3.2 8.8 + - - +
559A ARG* 1.3 82.0 - - + +
561A SER* 1.3 64.6 + - - +
563A TYR* 3.7 7.6 + - - +
564A ALA* 3.2 16.5 + - - +
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Residues in contact with SER 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A VAL* 3.7 14.6 - - - +
493A LEU* 3.4 14.8 - - - +
554A CYS* 4.3 0.2 - - - -
556A LYS* 3.5 43.6 + - - -
558A ASP* 2.7 37.8 + - - -
560A LYS* 1.3 72.7 - - - +
562A LEU* 1.3 58.5 + - - +
564A ALA* 3.5 0.6 + - - -
565A ALA* 2.8 28.9 + - - +
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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
----------------------------------------------------------
455A LYS* 3.8 40.2 - - + -
456A TYR 4.2 10.3 - - - +
457A VAL* 4.3 13.7 - - + -
554A CYS* 5.0 2.0 - - + -
556A LYS 4.4 5.1 + - - +
557A VAL 5.2 3.1 - - - +
558A ASP 3.0 18.4 + - - +
559A ARG* 4.0 7.0 - - - +
561A SER* 1.3 75.9 - - - +
563A TYR* 1.3 65.9 + - - +
565A ALA* 3.2 6.3 + - + +
566A ARG* 2.9 62.1 + - - +
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Residues in contact with TYR 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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487A VAL* 3.4 20.5 - - + +
488A LEU 4.0 17.6 + - - -
489A LEU* 4.6 3.4 - - + -
490A ASP* 5.6 9.9 - - + -
559A ARG* 3.2 17.0 + - + +
560A LYS* 4.0 6.7 - - - +
562A LEU* 1.3 76.4 - - - +
564A ALA* 1.3 67.5 + - + +
566A ARG* 3.3 17.4 + - - +
567A GLN* 3.0 56.3 + - + +
587A ILE 4.6 6.5 - - - -
589A PRO* 5.7 4.9 - - + +
590A LEU* 4.6 8.3 - - - +
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Residues in contact with ALA 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A LEU* 4.0 19.7 - - + -
490A ASP 5.7 0.7 - - - +
491A VAL* 3.7 28.3 - - + +
493A LEU* 3.9 8.1 - - + -
560A LYS 3.2 16.2 + - - +
561A SER 3.5 5.2 - - - +
563A TYR* 1.3 80.4 - - + +
565A ALA* 1.3 63.1 + - - +
567A GLN* 3.0 14.2 + - - +
568A TYR* 3.1 21.0 + - + -
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Residues in contact with ALA 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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457A VAL* 3.6 12.1 - - + +
493A LEU* 3.5 10.3 - - + +
498A PHE* 3.8 16.8 - - + -
554A CYS* 3.8 27.8 - - + -
561A SER 2.8 21.7 + - - +
562A LEU* 3.2 6.7 + - - +
564A ALA* 1.3 72.3 - - - +
566A ARG* 1.3 57.6 + - - +
568A TYR* 3.5 2.1 + - - +
569A PHE* 3.0 30.1 + - - +
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Residues in contact with ARG 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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456A TYR 4.6 7.9 + - - -
457A VAL* 3.7 21.9 + - + +
562A LEU* 2.9 55.5 + - - +
563A TYR* 3.4 14.7 - - - +
564A ALA 3.1 0.2 - - - -
565A ALA* 1.3 76.1 - - - +
567A GLN* 1.3 65.5 + - - +
569A PHE* 3.3 1.2 + - - +
570A VAL* 3.0 36.0 + - - +
587A ILE* 3.8 50.2 - - + +
588A ALA* 4.7 0.2 - - - -
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Residues in contact with GLN 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A PRO* 3.7 21.6 - - + +
487A VAL* 4.2 9.7 - - + +
489A LEU* 3.8 22.0 - - + -
563A TYR* 3.0 52.2 + - + +
564A ALA 3.0 4.4 + - - +
566A ARG* 1.3 75.5 - - - +
568A TYR* 1.3 63.9 + - - +
570A VAL* 4.1 0.7 - - - +
571A GLN* 3.0 27.7 + - - +
587A ILE 3.2 23.0 + - - -
588A ALA* 3.6 9.2 - - - +
589A PRO* 4.8 1.6 - - - +
590A LEU* 5.2 1.4 + - - +
591A ILE* 3.5 26.1 - - + +
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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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480A VAL* 3.4 32.0 - - + +
481A ALA* 3.6 18.8 - - - -
483A ALA* 3.7 22.2 - - - +
485A PRO* 3.8 14.5 - - + +
489A LEU* 3.9 22.5 - - + +
491A VAL 4.6 0.4 - - - -
492A LYS* 3.7 18.1 + - - +
493A LEU* 3.5 47.0 + - + -
498A PHE* 4.0 6.5 - + + -
564A ALA* 3.1 34.5 + - + -
565A ALA 3.7 5.4 - - - +
567A GLN* 1.3 73.9 - - - +
569A PHE* 1.3 58.4 + - - +
572A TRP* 2.9 30.5 + - - +
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Residues in contact with PHE 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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457A VAL* 3.7 24.7 - - + -
458A GLY* 3.6 15.9 - - - -
459A GLU 3.6 28.7 - - - -
460A THR* 4.2 8.1 - - + -
480A VAL* 4.2 7.8 - - + +
550A ILE 5.1 0.2 - - - -
552A VAL* 3.5 38.6 - - + -
565A ALA 3.0 17.3 + - - +
566A ARG 3.6 2.9 - - - +
567A GLN 3.2 0.2 - - - -
568A TYR* 1.3 77.3 - - - +
570A VAL* 1.3 67.6 + - + +
572A TRP* 3.2 11.3 + + - +
573A CYS* 2.9 46.5 + - - -
581A PRO* 3.5 22.4 - - + -
587A ILE* 4.6 2.7 - - + -
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Residues in contact with VAL 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 ARG 3.0 16.1 + - - +
567A GLN 4.3 0.4 - - - +
569A PHE* 1.3 80.4 - - + +
571A GLN* 1.3 66.5 + - - +
573A CYS* 3.1 7.9 + - - +
574A ALA* 2.9 20.3 + - - +
581A PRO* 4.3 12.6 - - + -
584A GLY* 4.9 1.6 - - - +
587A ILE* 3.7 21.3 - - + -
588A ALA* 3.6 26.2 - - + -
591A ILE* 3.7 17.3 - - + -
592A THR* 4.1 9.9 - - + -
598A TRP* 3.7 23.7 - - + -
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Residues in contact with GLN 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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483A ALA* 4.2 0.7 - - + -
484A LYS 3.8 19.7 + - - +
485A PRO* 3.7 33.4 - - + +
486A LYS* 4.3 3.9 + - - +
567A GLN 3.0 19.0 + - - +
568A TYR 3.8 3.4 - - - +
570A VAL* 1.3 75.8 - - - +
572A TRP* 1.3 56.9 + - - +
574A ALA* 3.2 4.7 + - - +
575A ASP* 2.8 60.7 + - - +
591A ILE* 3.6 11.3 - - + +
594A GLN* 2.6 42.4 + - - +
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Residues in contact with TRP 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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460A THR* 4.5 4.9 - - + -
476A LEU* 4.3 20.0 - - + -
479A GLU* 3.1 50.5 + - + +
480A VAL* 3.5 29.4 - - + -
483A ALA* 4.1 7.4 - - + +
500A VAL* 4.5 8.3 - - + -
550A ILE* 4.0 28.0 - - + -
552A VAL* 4.2 9.4 - - + -
568A TYR 2.9 19.7 + - - +
569A PHE* 3.3 21.1 - + - +
571A GLN* 1.3 75.3 - - - +
573A CYS* 1.3 58.0 + - - +
575A ASP* 3.3 10.7 + - + +
576A ARG* 3.0 43.0 + - + +
578A PHE* 3.6 30.1 - + - -
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Residues in contact with CYS 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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460A THR* 3.6 26.7 - - - -
569A PHE* 2.9 46.1 + - - -
570A VAL* 3.1 9.6 + - - +
572A TRP* 1.3 77.1 - - - +
574A ALA* 1.3 64.7 + - - +
576A ARG 3.4 0.3 + - - -
577A ASN* 3.0 3.8 + - - -
578A PHE* 2.9 36.6 + - + +
579A THR 4.2 4.9 - - - +
581A PRO* 4.1 8.5 - - + -
598A TRP* 3.7 17.7 - - + -
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Residues in contact with ALA 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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570A VAL 2.9 12.7 + - - +
571A GLN* 3.3 12.3 - - - +
573A CYS* 1.3 75.4 - - - +
575A ASP* 1.3 58.0 + - - +
577A ASN 3.0 13.3 + - - -
591A ILE* 5.1 0.7 - - + -
594A GLN* 4.1 23.8 - - + +
595A LYS* 2.8 41.7 + - + -
598A TRP* 3.4 19.6 - - + -
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Residues in contact with ASP 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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483A ALA* 4.1 15.1 - - - +
484A LYS 4.7 1.4 + - - -
571A GLN* 2.8 51.4 + - - +
572A TRP* 3.3 8.4 + - + +
574A ALA* 1.3 71.7 - - - +
576A ARG* 1.3 63.8 + - + +
577A ASN* 3.6 5.9 + - - +
594A GLN* 4.7 0.3 - - - +
595A LYS* 5.2 0.2 - - - +
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Residues in contact with ARG 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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466A ILE* 5.3 14.6 - - - +
468A ILE* 4.8 10.7 - - - +
472A ASP* 5.6 4.6 + - - +
476A LEU* 3.7 17.8 - - - +
479A GLU* 2.9 34.7 + - - -
572A TRP* 3.0 36.7 + - + +
575A ASP* 1.3 79.2 - - + +
577A ASN* 1.3 70.4 + - - +
578A PHE* 3.4 56.8 + - + -
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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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463A THR* 3.0 27.9 + - - -
466A ILE* 5.9 3.7 - - + +
573A CYS 3.6 0.9 - - - -
574A ALA 3.0 12.3 + - - +
575A ASP 4.6 4.5 + - - +
576A ARG* 1.3 82.1 + - - +
578A PHE* 1.3 61.5 - - - +
595A LYS* 2.3 43.1 + - - +
597A GLU* 4.2 7.0 + - - +
598A TRP* 5.5 0.4 - - - -
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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