Contacts of the helix formed by residues 606 - 612 (chain A) in PDB entry 5OQN
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 LEU 606 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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490A ARG* 3.2 39.3 - - + +
569A GLU* 3.9 19.3 - - - +
570A ALA* 6.1 2.2 - - + -
575A ILE* 3.9 41.5 - - + -
578A CYS* 6.0 7.9 - - + -
579A LEU* 4.7 11.0 - - + -
602A LEU* 3.3 6.9 + - + +
605A THR* 1.3 90.8 + - - +
607A ILE* 1.3 59.7 + - - +
608A THR 3.0 2.5 - - - -
609A PRO* 3.9 12.3 - - + -
610A ALA* 2.5 39.7 + - - +
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Residues in contact with ILE 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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579A LEU* 4.2 11.9 - - + +
582A SER* 5.0 2.0 - - - +
586A LEU* 4.5 5.6 - - + -
599A ILE* 5.5 0.9 - - + +
602A LEU* 4.0 16.7 + - + +
603A MET* 3.4 45.8 + - + +
606A LEU* 1.3 77.4 - - - +
608A THR* 1.3 61.3 + - - +
610A ALA* 3.5 7.2 - - - +
611A VAL* 3.3 22.9 + - + +
622A GLY* 4.1 16.2 - - - +
625A ASN* 3.8 25.8 - - + -
626A LEU* 4.1 19.3 - - + +
629A CYS* 4.0 16.2 - - - -
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Residues in contact with THR 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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603A MET* 3.3 20.7 + - - +
604A ASP* 4.4 7.5 + - - +
606A LEU 3.0 0.8 - - - -
607A ILE* 1.3 76.1 - - - +
609A PRO* 1.3 69.2 - - + +
610A ALA 3.0 3.6 - - - -
611A VAL* 2.8 23.9 + - - +
612A ARG* 3.1 39.1 + - + +
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Residues in contact with PRO 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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569A GLU* 5.1 9.2 - - - +
604A ASP 4.0 4.7 - - - +
605A THR 2.9 29.4 - - - +
606A LEU* 3.8 13.9 - - + +
608A THR* 1.3 95.5 - - + +
610A ALA* 1.3 61.1 + - - +
612A ARG* 3.6 11.1 - - + +
613A ASN* 3.1 23.6 + - - +
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Residues in contact with ALA 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 ILE* 5.0 3.1 - - + -
579A LEU* 3.7 28.9 - - + -
606A LEU* 2.5 24.0 + - - +
607A ILE* 3.5 8.1 - - - +
608A THR 3.0 0.2 + - - -
609A PRO* 1.3 71.8 - - - +
611A VAL* 1.3 64.4 + - - +
613A ASN* 3.3 16.0 + - - +
618A ILE* 3.8 12.6 - - + +
619A ARG* 3.5 14.6 - - - -
622A GLY* 3.8 13.9 - - - -
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Residues in contact with VAL 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 ILE 3.3 16.1 + - - +
608A THR* 2.8 9.4 + - - +
610A ALA* 1.3 76.7 - - - +
612A ARG* 1.3 82.1 + - - +
613A ASN 3.3 2.4 + - - -
619A ARG* 2.8 42.2 + - - +
622A GLY* 4.0 22.0 - - - +
623A VAL* 4.3 10.3 - - + +
626A LEU* 4.0 21.3 - - + -
643A ILE* 4.7 18.2 - - + -
647A CYS* 5.7 5.2 - - - -
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Residues in contact with ARG 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 THR* 3.1 36.7 + - + +
609A PRO* 3.4 8.9 + - + +
610A ALA 3.3 0.2 - - - -
611A VAL* 1.3 106.1 - - - +
613A ASN* 1.3 65.0 + - - +
614A THR* 4.9 3.5 - - - +
619A ARG* 4.8 1.6 - - - +
626A LEU* 6.1 0.6 - - - +
640A ASN* 6.1 2.0 - - - +
643A ILE* 5.4 13.5 - - - +
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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