Contacts of the helix formed by residues 609 - 617 (chain A) in PDB entry 3JUE
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 THR 609 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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576A PHE* 3.5 10.6 - - - -
599A ASN* 4.3 6.5 - - - +
600A TRP 3.3 7.4 - - - +
601A VAL* 4.8 0.2 - - + -
607A ASN 4.4 5.2 - - - +
608A ALA* 1.3 78.5 - - - +
610A PRO* 1.3 74.2 - - - +
611A LEU* 3.7 8.8 + - - +
612A ILE* 3.2 29.6 + - + +
613A GLN* 3.0 17.8 + - - +
635A GLN* 3.3 47.7 + - + +
636A ALA 5.1 1.6 - - - +
643A PRO* 5.3 0.5 - - - +
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Residues in contact with PRO 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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575A LEU* 3.9 19.7 - - + -
576A PHE* 4.2 17.3 - - + +
579A SER* 3.5 24.2 - - - +
598A VAL 3.6 20.0 - - - +
600A TRP* 3.2 23.3 - - + +
609A THR* 1.3 88.4 - - - +
611A LEU* 1.3 56.3 + - - +
613A GLN* 3.1 7.2 + - + +
614A ALA* 2.8 25.8 + - - +
626A LEU* 3.5 22.5 - - + +
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Residues in contact with LEU 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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598A VAL 5.1 1.6 + - - +
599A ASN* 6.1 1.1 - - - +
609A THR* 3.3 8.2 + - - +
610A PRO* 1.3 78.5 - - - +
612A ILE* 1.3 54.1 + - - +
614A ALA 3.2 0.9 + - - -
615A THR* 2.7 36.8 + - - -
623A CYS* 3.8 42.6 - - + +
626A LEU* 3.5 14.3 - - + +
627A LEU* 4.2 9.2 - - + -
631A ALA* 4.2 19.1 - - + -
632A ASN 4.0 6.5 - - - +
633A VAL* 4.0 19.5 - - - -
643A PRO* 3.8 31.0 - - + -
659A PHE* 4.1 8.7 - - + -
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Residues in contact with ILE 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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608A ALA* 3.9 16.8 - - + -
609A THR* 3.2 28.0 + - + +
611A LEU* 1.3 76.6 - - - +
613A GLN* 1.3 60.4 - - - +
615A THR* 3.3 7.7 + - - -
616A ALA* 2.9 29.2 + - + +
635A GLN 4.0 9.0 - - - +
636A ALA 4.4 0.7 - - - -
637A ASP* 3.9 20.9 - - + +
641A ARG 3.6 22.9 - - - +
642A GLY 4.7 0.4 - - - -
643A PRO* 4.4 15.0 - - + -
646A HIS* 3.8 35.9 - - + +
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Residues in contact with GLN 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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576A PHE* 3.3 66.1 - - + +
577A ARG* 5.3 1.6 - - - +
579A SER* 3.6 2.7 - - - +
580A GLY* 3.8 22.7 - - - +
581A HIS 4.7 0.2 + - - -
606A ASP* 5.0 4.4 + - - -
608A ALA* 4.8 6.1 - - - +
609A THR 3.0 7.3 + - - +
610A PRO 3.3 8.3 - - - +
612A ILE* 1.3 76.7 - - - +
614A ALA* 1.3 59.7 + - - +
616A ALA* 3.4 11.1 + - - +
617A ALA* 3.0 27.2 + - - +
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Residues in contact with ALA 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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579A SER 3.2 15.9 + - - +
610A PRO 2.8 18.9 + - - +
611A LEU 3.2 4.9 + - - +
613A GLN* 1.3 73.4 - - - +
615A THR* 1.3 59.4 + - - +
617A ALA* 3.2 2.9 + - - +
618A ASN 3.2 3.6 + - - -
619A SER* 3.1 28.1 + - - +
622A ALA* 3.8 21.3 - - + -
623A CYS* 3.7 20.9 - - - +
626A LEU* 4.0 7.9 - - + -
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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 LEU 2.7 19.2 + - - -
612A ILE* 3.4 11.1 - - - -
613A GLN 3.2 0.2 - - - -
614A ALA* 1.3 73.8 - - - +
616A ALA* 1.3 59.6 + - - +
618A ASN* 3.0 16.3 + - - -
623A CYS* 4.0 0.6 - - - -
643A PRO* 3.9 6.8 - - - +
646A HIS* 3.8 14.4 - - + -
647A ALA* 3.6 35.0 - - - +
650A LEU* 4.0 1.3 - - + +
652A HIS* 3.4 14.9 + - - +
655A LEU* 3.6 16.3 - - + +
659A PHE* 3.3 22.7 - - + -
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Residues in contact with ALA 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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581A HIS* 5.5 0.7 - - - +
612A ILE* 2.9 17.8 + - + +
613A GLN* 3.4 14.8 + - - +
615A THR* 1.3 76.1 - - - +
617A ALA* 1.3 58.8 + - - +
618A ASN* 3.2 1.4 + - - +
646A HIS* 5.6 2.8 - - - +
650A LEU* 3.7 21.1 - - + +
652A HIS* 4.5 4.3 - - - -
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Residues in contact with ALA 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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579A SER 4.1 4.5 - - - +
580A GLY 3.9 3.6 - - - -
581A HIS* 3.4 49.1 + - - +
583A PRO* 4.2 12.0 - - + +
613A GLN 3.0 14.2 + - - +
614A ALA* 3.5 6.7 - - - +
615A THR 3.1 0.2 - - - -
616A ALA* 1.3 77.4 - - - +
618A ASN* 1.3 68.4 + - - +
619A SER* 3.3 2.4 + - - -
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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