Contacts of the helix formed by residues 605 - 621 (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 ASP 605 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441A LYS* 4.9 9.5 + - - -
603A GLN 2.8 13.5 + - - +
604A ASP* 1.3 75.8 - - - +
606A ILE* 1.3 65.6 + - - +
607A CYS 3.3 2.7 - - - -
608A GLU* 3.0 41.5 + - + +
609A LYS* 3.1 15.4 + - + +
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Residues in contact with ILE 606 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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565A PHE* 3.8 37.5 - - + -
599A PHE 3.8 14.6 - - - +
600A MET* 4.4 7.2 - - - +
602A ARG* 3.7 55.9 + - + +
604A ASP* 3.1 11.2 + - - +
605A ASP* 1.3 77.2 - - - +
607A CYS* 1.3 67.2 + - + +
609A LYS* 4.0 2.4 - - + +
610A ARG* 3.1 43.1 + - - +
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Residues in contact with CYS 607 (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 ASP 3.3 0.8 - - - -
606A ILE* 1.3 82.1 - - + +
608A GLU* 1.3 76.2 + - - +
610A ARG* 3.3 19.0 + - - +
611A ASN* 3.1 36.6 + - - +
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Residues in contact with GLU 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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605A ASP* 3.0 40.6 + - + +
607A CYS* 1.3 92.4 + - + +
609A LYS* 1.3 57.1 + - + +
611A ASN* 3.2 14.5 + - - +
612A LYS* 3.0 26.8 + - - +
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Residues in contact with LYS 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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565A PHE* 2.9 44.3 + - + +
568A LEU* 3.4 29.3 - - + +
569A ASN* 2.6 33.2 + - - +
602A ARG* 5.0 0.2 - - - +
604A ASP* 3.3 38.5 + - - +
605A ASP* 3.1 20.2 + - + +
606A ILE* 4.0 4.5 - - + +
608A GLU* 1.3 73.5 - - + +
610A ARG* 1.3 66.7 + - - +
612A LYS* 3.2 3.1 + - - -
613A ILE* 3.0 29.2 + - - +
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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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565A PHE* 4.2 4.8 - - + -
594A LEU* 3.6 55.7 + - + +
595A ASN* 5.6 4.9 - - - +
599A PHE* 4.6 15.0 + - - +
600A MET* 5.3 2.4 - - - +
606A ILE* 3.1 45.2 + - - +
607A CYS* 3.3 25.1 + - - +
609A LYS* 1.3 78.1 - - - +
611A ASN* 1.3 64.3 + - - +
613A ILE* 3.5 3.2 + - - +
614A CYS* 3.2 34.7 + - - -
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Residues in contact with ASN 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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607A CYS* 3.1 31.4 + - - +
608A GLU* 3.3 12.6 - - - +
609A LYS 3.1 0.8 - - - -
610A ARG* 1.3 77.5 - - - +
612A LYS* 1.3 59.1 + - - +
614A CYS* 3.3 7.2 + - - +
615A GLN* 2.9 37.4 + - + +
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Residues in contact with LYS 612 (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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568A LEU* 3.7 28.7 + - + +
608A GLU 3.0 12.6 + - - +
609A LYS* 3.5 9.2 - - - +
611A ASN* 1.3 74.8 - - - +
613A ILE* 1.3 59.0 + - - +
615A GLN* 3.2 6.0 + - - -
616A TRP* 2.9 83.2 + - + +
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Residues in contact with ILE 613 (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* 6.1 0.2 - - - -
564A CYS* 3.7 26.7 - - + +
565A PHE* 3.7 30.7 - - + -
568A LEU* 3.5 17.3 - - + -
577A ILE* 4.8 3.8 - - + -
581A LEU* 4.0 16.2 - - + +
587A TRP* 3.6 23.8 - - + -
590A VAL* 4.6 3.4 - - + -
594A LEU* 4.0 18.4 - - + -
609A LYS 3.0 19.7 + - - +
610A ARG* 3.7 4.5 - - - +
612A LYS* 1.3 75.7 - - - +
614A CYS* 1.3 58.5 + - - +
616A TRP* 3.3 8.1 + - - +
617A ARG* 3.0 26.0 + - - +
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Residues in contact with CYS 614 (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 TRP* 4.2 24.2 - - + -
591A ASP* 5.3 3.4 - - - -
594A LEU* 5.0 5.2 - - - -
610A ARG* 3.2 26.0 + - - -
611A ASN* 3.7 9.2 - - - +
613A ILE* 1.3 75.3 - - - +
615A GLN* 1.3 64.0 + - + +
616A TRP 3.0 5.2 + - - -
617A ARG* 3.2 11.7 + - - +
618A GLN* 3.4 14.9 + - - +
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Residues in contact with GLN 615 (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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611A ASN* 2.9 25.4 + - + +
612A LYS* 3.2 7.6 + - + +
614A CYS* 1.3 76.4 - - + +
616A TRP* 1.3 62.8 + - + +
618A GLN* 2.7 62.1 + - - +
619A LEU* 3.5 13.5 - - - +
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Residues in contact with TRP 616 (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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567A GLU 5.9 0.7 - - - -
568A LEU* 3.7 24.2 - - + -
570A ALA 5.7 3.1 - - - -
571A PRO 6.4 0.2 - - - -
572A HIS 4.7 1.8 - - - -
573A PRO* 3.6 44.6 - - + -
577A ILE* 3.8 25.4 - - + -
578A MET* 3.7 18.1 - - + +
581A LEU* 3.9 10.4 - - + +
612A LYS* 2.9 51.6 + - + +
613A ILE* 3.7 5.6 - - - +
614A CYS 3.0 0.4 - - - -
615A GLN* 1.3 82.5 - - + +
617A ARG* 1.3 52.4 + - - +
618A GLN 3.2 1.1 - - - -
619A LEU* 3.4 32.3 - - + +
620A VAL* 2.2 34.6 - - - +
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Residues in contact with ARG 617 (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 37.9 + - + +
582A LYS 4.0 4.8 + - - -
584A ASP* 2.6 47.9 + - - +
587A TRP* 3.4 58.2 - - + +
613A ILE 3.0 16.1 + - - +
614A CYS 3.2 5.6 + - - +
616A TRP* 1.3 76.1 - - - +
618A GLN* 1.3 63.0 + - - +
620A VAL* 2.9 14.9 - - - +
621A GLN* 2.7 57.8 + - - +
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Residues in contact with GLN 618 (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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614A CYS 3.4 6.3 + - - +
615A GLN* 2.7 51.0 + - - +
617A ARG* 1.3 80.7 - - - +
619A LEU* 1.3 75.7 + - + +
620A VAL 3.2 1.0 + - - -
621A GLN* 3.5 25.9 + - - +
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Residues in contact with LEU 619 (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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578A MET* 5.4 5.2 - - + -
615A GLN 3.5 12.8 - - - +
616A TRP* 3.4 43.3 - - + +
618A GLN* 1.3 93.5 - - + +
620A VAL* 1.3 62.4 + - + +
621A GLN 3.8 0.2 - - - -
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Residues in contact with VAL 620 (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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578A MET* 3.6 34.3 - - + +
581A LEU* 4.2 16.2 - - + +
582A LYS* 4.3 26.7 - - + +
616A TRP 2.2 35.7 - - - +
617A ARG* 2.9 18.2 - - - +
619A LEU* 1.3 80.5 - - + +
621A GLN* 1.3 63.4 + - - +
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Residues in contact with GLN 621 (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 LYS* 5.3 5.8 - - - +
584A ASP* 5.3 1.1 - - - +
617A ARG* 2.7 62.4 + - - +
618A GLN* 3.5 23.4 + - - +
619A LEU 3.8 0.8 - - - -
620A VAL* 1.3 76.2 - - - +
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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