Contacts of the helix formed by residues 608 - 626 (chain A) in PDB entry 4OSV
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 GLY 608 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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573A ASP 4.0 9.3 + - - -
606A ASN 3.4 0.2 + - - -
607A GLY* 1.3 72.1 - - - -
609A GLY* 1.3 60.2 + - - +
610A LYS 3.1 2.9 - - - -
611A GLN* 2.8 24.4 + - - +
612A ALA* 3.2 10.4 + - - +
9I C 3.7 43.1 + - - +
10I T 4.1 6.7 + - - +
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Residues in contact with GLY 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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573A ASP 5.4 0.4 + - - -
574A GLY 5.9 0.6 + - - -
578A ALA* 4.3 6.9 - - - +
603A ILE 4.1 9.2 - - - -
604A ALA* 3.5 16.1 - - - -
606A ASN* 3.0 18.0 + - - -
607A GLY 4.4 0.2 - - - -
608A GLY* 1.3 76.5 - - - +
610A LYS* 1.3 62.5 + - - +
612A ALA* 3.3 4.3 + - - +
613A LEU* 3.0 34.4 + - - +
9I C 4.7 1.0 + - - -
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Residues in contact with LYS 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A GLN* 3.8 37.4 + - + +
578A ALA* 4.1 6.5 - - - +
581A THR* 3.1 28.9 - - - +
584A ARG* 4.1 10.8 - - - +
608A GLY 3.1 0.4 + - - -
609A GLY* 1.3 77.8 - - - +
611A GLN* 1.3 70.5 + - - +
613A LEU* 3.5 1.7 + - - +
614A GLU* 3.1 51.8 + - - +
9I C 3.8 21.4 + - - +
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Residues in contact with GLN 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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608A GLY 2.8 13.3 + - - +
610A LYS* 1.3 89.7 - - - +
612A ALA* 1.3 58.7 + - - +
614A GLU* 3.5 10.8 + - - +
615A THR* 2.6 34.4 + - - -
644A LYS* 3.3 34.1 + - + +
9I C 3.0 49.1 + - - +
10I T 3.6 18.8 - - - +
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Residues in contact with ALA 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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603A ILE* 3.7 17.9 - - + +
606A ASN* 6.5 0.4 - - + -
608A GLY 3.2 9.7 + - - +
609A GLY* 3.3 5.8 + - - +
611A GLN* 1.3 78.5 - - - +
613A LEU* 1.3 55.8 + - - +
615A THR* 3.7 2.4 - - - -
616A VAL* 2.9 35.9 + - - +
638A ALA* 3.6 25.8 - - + +
640A HIS 5.3 1.1 - - - +
643A GLY* 4.4 3.6 - - - +
644A LYS* 4.0 19.4 - - - +
647A LEU* 4.1 0.8 - - - +
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Residues in contact with LEU 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A ALA 4.2 1.8 - - - +
581A THR* 3.7 29.4 - - + +
582A VAL* 3.8 15.9 - - + +
585A LEU* 4.1 7.2 - - + +
589A LEU* 3.8 26.9 - - + +
600A VAL* 3.7 25.1 - - + +
603A ILE* 3.7 21.5 - - + -
604A ALA* 3.7 19.5 - - + -
609A GLY 3.0 22.0 + - - +
610A LYS 3.8 3.8 - - - +
612A ALA* 1.3 76.2 - - - +
614A GLU* 1.3 58.6 + - - +
616A VAL* 3.5 4.4 + - - +
617A GLN* 3.1 26.5 + - - +
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Residues in contact with GLU 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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581A THR* 4.2 3.1 - - + -
584A ARG* 3.5 19.7 + - - +
585A LEU* 4.1 20.2 - - + -
610A LYS* 3.1 47.6 + - - +
611A GLN* 4.1 13.9 + - - +
613A LEU* 1.3 75.1 - - - +
615A THR* 1.3 59.2 + - - +
617A GLN* 3.5 9.3 + - - +
618A ARG* 3.1 37.5 + - + +
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Residues in contact with THR 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 GLN 2.6 22.5 + - - -
612A ALA 3.8 3.6 - - - -
613A LEU 3.2 0.2 - - - -
614A GLU* 1.3 76.4 - - - +
616A VAL* 1.3 60.2 + - - +
618A ARG* 3.3 20.6 + - - +
619A LEU* 2.9 53.0 + - + +
644A LYS* 3.2 29.7 - - - +
647A LEU* 3.7 23.1 - - + -
648A GLU* 4.3 2.9 - - + -
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Residues in contact with VAL 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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589A LEU* 4.1 13.0 - - + -
595A LEU* 4.2 2.9 - - + -
603A ILE* 3.8 23.8 - - + -
612A ALA 2.9 22.0 + - - +
613A LEU* 3.7 5.4 - - - +
615A THR* 1.3 72.8 - - - +
617A GLN* 1.3 67.1 + - - +
619A LEU* 5.3 0.7 - - - -
620A LEU* 3.0 55.7 + - + +
634A VAL* 4.5 12.8 - - + -
635A VAL* 5.6 1.1 - - + -
638A ALA* 3.4 29.8 - - + -
647A LEU* 3.8 7.4 - - + +
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Residues in contact with GLN 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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584A ARG* 5.5 0.9 + - - -
585A LEU* 3.5 37.7 - - + +
588A VAL* 4.3 14.8 - - + +
589A LEU* 4.0 17.0 - - + +
593A HIS* 3.5 30.0 + - + -
613A LEU 3.1 18.0 + - - +
614A GLU* 3.6 11.6 - - - +
615A THR 3.3 0.2 - - - -
616A VAL* 1.3 77.7 - - - +
618A ARG* 1.3 64.8 + - + +
619A LEU 3.7 0.2 + - - -
621A PRO* 3.9 5.0 - - - +
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Residues in contact with ARG 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 GLU* 3.1 28.7 + - + +
615A THR* 3.7 20.3 + - - +
617A GLN* 1.3 83.9 - - + +
619A LEU* 1.3 83.6 + - + +
620A LEU 3.6 0.2 - - - -
621A PRO* 4.0 10.6 - - - +
622A VAL* 4.8 2.6 - - - +
644A LYS* 5.4 3.8 - - - +
648A GLU* 3.2 28.3 + - - +
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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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615A THR* 2.9 37.7 + - + +
616A VAL* 5.3 0.4 - - - -
618A ARG* 1.3 100.5 - - + +
620A LEU* 1.3 61.8 + - - +
621A PRO 3.2 2.2 - - - -
622A VAL* 3.2 18.6 + - + +
623A LEU* 2.8 44.4 + - + +
634A VAL* 6.3 0.2 - - + -
647A LEU* 4.1 17.7 - - + +
648A GLU* 4.0 21.1 - - + -
651A GLN* 4.3 12.3 - - + -
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Residues in contact with LEU 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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589A LEU* 5.1 0.2 - - + -
593A HIS* 3.6 37.2 - - + +
595A LEU* 4.0 17.7 - - + -
616A VAL* 3.0 36.4 + - + +
619A LEU* 1.3 76.2 - - - +
621A PRO* 1.3 69.9 - - + +
623A LEU* 4.6 2.7 - - - +
624A CYS* 3.0 56.2 + - - +
631A PRO* 4.2 11.0 - - + +
634A VAL* 3.5 27.3 - - + +
635A VAL* 6.0 0.7 - - + -
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Residues in contact with PRO 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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593A HIS* 4.0 14.4 - - + +
617A GLN 3.9 14.1 - - - +
618A ARG 4.0 9.6 - - - +
619A LEU 3.6 1.8 - - - -
620A LEU* 1.3 96.2 - - + +
622A VAL* 1.3 56.8 + - - +
624A CYS* 4.8 1.1 - - + -
625A GLN* 2.8 56.5 + - + +
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Residues in contact with VAL 622 (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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618A ARG 4.8 2.4 + - - +
619A LEU* 3.3 26.0 - - + +
621A PRO* 1.3 79.9 - - - +
623A LEU* 1.3 60.1 + - - +
625A GLN* 5.0 0.7 - - - -
626A ALA* 2.9 44.5 + - + +
627A HIS* 3.3 7.1 + - - +
651A GLN* 4.0 36.1 - - + +
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Residues in contact with LEU 623 (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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619A LEU* 2.8 39.9 + - + +
620A LEU 4.0 0.4 - - - +
622A VAL* 1.3 78.5 - - - +
624A CYS* 1.3 58.5 + - - +
627A HIS* 3.3 27.9 - - + +
628A GLY 3.2 10.0 + - - -
629A LEU* 3.1 36.2 + - + +
634A VAL* 3.8 19.5 - - + -
637A ILE* 5.9 0.4 - - + -
647A LEU* 4.1 29.8 - - + +
650A VAL* 4.5 9.0 - - + -
651A GLN* 3.7 30.3 - - + +
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Residues in contact with CYS 624 (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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620A LEU* 3.0 43.4 + - - +
621A PRO* 4.1 2.5 - - + +
623A LEU* 1.3 77.6 - - - +
625A GLN* 1.3 62.9 + - + +
628A GLY* 3.2 25.6 + - - -
629A LEU 3.2 20.8 - - - +
630A THR 3.9 1.8 - - - -
631A PRO* 3.8 23.6 - - - -
634A VAL* 4.1 4.3 - - - -
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Residues in contact with GLN 625 (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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621A PRO* 2.8 40.5 + - + +
622A VAL* 5.0 0.7 - - - -
624A CYS* 1.3 78.2 - - + +
626A ALA* 1.3 58.9 + - + +
628A GLY* 4.6 1.4 + - - -
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Residues in contact with ALA 626 (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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622A VAL* 2.9 35.4 + - + +
625A GLN* 1.3 75.9 - - + +
627A HIS* 1.3 70.6 + - + +
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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