Contacts of the helix formed by residues 556 - 568 (chain A) in PDB entry 4JVS
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 556 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414A LYS* 2.5 45.3 + - - +
554A ALA 3.8 0.8 + - - -
555A MET* 1.3 77.0 - - - +
557A GLY* 1.3 64.1 + - - +
558A ASP* 3.2 3.7 + - - +
559A GLN* 2.9 21.7 + - - +
560A LEU* 3.0 22.9 + - - +
589A GLU* 4.4 3.6 - - - -
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Residues in contact with GLY 557 (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 SER* 1.3 74.3 - - - +
558A ASP* 1.3 57.1 + - - +
560A LEU* 3.1 3.8 + - - +
561A ALA* 2.8 31.9 + - - +
589A GLU* 3.4 39.2 + - - +
590A VAL* 4.6 1.0 - - - -
592A ASP* 5.4 1.3 - - - -
593A SER* 3.1 10.9 - - - -
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Residues in contact with ASP 558 (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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414A LYS 3.6 9.4 - - - +
415A ALA* 3.7 7.3 - - - +
416A ALA* 2.9 37.5 + - + +
421A ALA* 3.9 2.9 - - + -
556A SER* 3.2 8.6 + - - +
557A GLY* 1.3 77.6 - - - +
559A GLN* 1.3 52.7 + - - +
562A THR* 2.7 38.2 + - - -
593A SER* 2.4 33.5 + - - +
598A ALA* 4.3 7.4 - - - +
599A PHE* 3.8 16.0 - - - -
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Residues in contact with GLN 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ALA* 5.5 1.4 + - - +
413A SER 4.7 1.2 + - - -
414A LYS* 3.5 43.8 + - - +
421A ALA* 3.8 13.2 - - + +
422A TYR* 3.1 31.4 + - - +
423A ILE* 3.4 8.0 - - + +
424A ALA 5.7 0.6 - - - +
555A MET* 3.3 31.8 - - + +
556A SER* 2.9 33.8 + - - +
558A ASP* 1.3 75.8 - - - +
560A LEU* 1.3 62.7 + - - +
562A THR* 3.4 5.0 - - - -
563A ILE* 3.1 27.5 + - - +
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Residues in contact with LEU 560 (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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552A LEU* 3.8 38.8 - - + +
555A MET* 4.0 14.6 - - + +
556A SER 3.0 20.5 + - - +
557A GLY 3.1 4.2 + - - +
559A GLN* 1.3 78.4 - - - +
561A ALA* 1.3 56.2 + - - +
563A ILE* 3.1 8.2 + - - +
564A CYS* 3.0 29.8 + - - -
580A ILE* 4.2 15.3 - - + +
586A LEU* 3.7 42.8 - - + +
589A GLU* 3.9 15.7 - - + -
590A VAL* 3.6 14.1 - - + -
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Residues in contact with ALA 561 (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 GLY 2.8 15.9 + - - +
560A LEU* 1.3 73.7 - - - +
562A THR* 1.3 60.5 + - - +
564A CYS* 3.3 7.9 + - - +
565A PHE* 2.9 43.8 + - + -
590A VAL* 4.4 14.1 - - + +
593A SER* 4.2 9.2 - - - -
594A LEU* 5.0 6.3 - - + -
599A PHE* 3.7 26.2 - - + -
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Residues in contact with THR 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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420A HIS* 3.9 18.0 - - + +
421A ALA* 3.0 29.1 + - - +
423A ILE* 3.4 23.1 - - + -
426A TYR* 4.0 16.8 + - + +
558A ASP 2.7 22.5 + - - -
559A GLN 3.4 6.5 - - - -
561A ALA* 1.3 76.0 - - - +
563A ILE* 1.3 60.7 + - - +
565A PHE* 3.6 8.7 + - - +
566A GLU* 3.2 22.0 + - - +
599A PHE* 4.0 7.1 - - - -
602A ARG* 4.7 4.4 + - - +
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Residues in contact with ILE 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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423A ILE* 3.9 16.2 - - + -
544A PHE* 3.8 18.8 - - + -
547A ILE* 3.9 21.3 - - + -
552A LEU* 4.1 9.2 - - + -
555A MET* 3.7 29.6 - - - -
559A GLN 3.1 13.1 + - - +
560A LEU* 3.1 10.6 + - - +
562A THR* 1.3 73.2 - - - +
564A CYS* 1.3 61.3 + - - +
566A GLU* 3.0 4.3 + - - +
567A GLU* 2.9 36.1 + - + +
576A LEU* 3.7 23.3 - - + -
580A ILE* 3.6 19.5 - - + -
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Residues in contact with CYS 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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560A LEU 3.0 16.5 + - - +
561A ALA* 3.6 8.5 - - - +
563A ILE* 1.3 75.9 - - - +
565A PHE* 1.3 61.8 + - - +
566A GLU 3.2 0.7 + - - -
567A GLU* 3.2 10.7 + - - +
568A LEU* 3.2 15.8 + - - +
577A ILE* 3.9 22.8 - - + +
580A ILE* 3.8 28.5 - - - -
581A LEU* 3.9 19.1 - - - -
590A VAL* 4.4 9.6 - - + -
613A ILE* 3.7 22.4 - - + -
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Residues in contact with PHE 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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561A ALA* 2.9 26.9 + - + +
562A THR 3.9 3.1 - - - +
564A CYS* 1.3 74.2 - - - +
566A GLU* 1.3 59.9 + - - +
568A LEU* 3.8 3.2 + - - -
594A LEU* 3.4 24.9 - - + -
599A PHE* 3.6 34.1 - + + -
602A ARG* 3.6 36.1 - - - +
606A ILE* 3.8 30.7 - - + -
609A LYS* 2.9 49.7 + - + +
610A ARG* 4.2 9.9 - - - -
613A ILE* 3.7 24.0 - - + -
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Residues in contact with GLU 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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420A HIS* 4.3 8.5 - - - -
426A TYR* 2.7 32.8 + - + +
430A VAL* 4.0 8.1 - - - +
434A HIS* 3.0 28.4 + - - -
543A PHE* 3.2 26.2 - - + -
544A PHE* 3.7 18.6 - - + -
562A THR 3.2 13.4 + - - +
563A ILE 3.0 9.5 + - - +
565A PHE* 1.3 76.5 - - - +
567A GLU* 1.3 64.4 + - - +
569A ASN* 3.0 45.4 + - - +
602A ARG* 5.2 2.8 + - - +
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Residues in contact with GLU 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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541A SER* 4.4 5.3 - - - -
542A SER* 4.4 3.8 + - - -
543A PHE* 3.7 20.9 + - - +
544A PHE* 3.1 31.2 - - - -
563A ILE* 2.9 27.5 + - + +
564A CYS 3.2 3.8 + - - +
566A GLU* 1.3 77.4 - - - +
568A LEU* 1.3 57.3 + - - +
569A ASN 3.1 0.2 - - - -
570A ALA* 2.9 30.5 + - - +
572A HIS 4.9 1.2 - - - +
574A SER* 2.5 41.9 + - - +
576A LEU* 3.8 8.5 - - - +
577A ILE* 3.7 26.0 - - + +
616A TRP* 5.9 0.6 - - - -
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Residues in contact with LEU 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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564A CYS 3.2 9.5 + - - +
565A PHE 3.9 8.3 - - - +
566A GLU 3.2 0.8 - - - -
567A GLU* 1.3 73.2 - - - +
569A ASN* 1.3 60.1 + - - +
570A ALA 3.1 14.9 + - - +
577A ILE* 3.7 23.6 - - + -
609A LYS* 3.4 51.7 - - + +
612A LYS* 3.7 30.2 + - + +
613A ILE* 3.5 19.5 - - + -
616A TRP* 3.7 25.4 - - + -
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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
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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