Contacts of the helix formed by residues 607 - 615 (chain A) in PDB entry 4N78
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 ASN 607 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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603A THR* 2.9 39.6 + - - +
604A HIS* 3.1 4.3 - - - +
606A ILE* 1.3 85.1 - - - +
608A PHE* 1.3 60.7 + - - +
609A SER* 3.3 3.1 - - - -
610A GLU* 3.2 17.7 + - + +
611A THR* 2.8 27.7 + - - +
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Residues in contact with PHE 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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394A ALA* 3.9 12.3 - - + -
398A LEU* 4.0 29.6 - - + -
465A MET* 3.8 36.8 - - + -
469A GLU* 4.2 21.3 - - + -
472A PHE* 3.4 31.6 - + + -
473A ASN* 3.7 17.0 + - - +
476A ILE* 4.3 16.6 - - + -
604A HIS 3.8 5.2 - - - -
605A LEU* 3.1 15.1 + - + +
606A ILE 3.3 2.8 + - - -
607A ASN* 1.3 74.5 - - - +
609A SER* 1.3 59.3 + - - +
611A THR* 3.1 3.4 + - - -
612A LEU* 2.7 52.2 + - + +
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Residues in contact with SER 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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469A GLU* 3.3 31.6 + - - -
473A ASN* 5.2 0.2 + - - -
607A ASN 3.3 0.8 - - - -
608A PHE* 1.3 84.9 - - - +
610A GLU* 1.3 64.7 + - - +
612A LEU* 3.4 12.4 + - - +
613A GLN* 3.4 25.2 + - - +
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Residues in contact with GLU 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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607A ASN* 3.2 22.0 + - + +
609A SER* 1.3 80.9 + - - +
611A THR* 1.3 63.2 + - - +
613A GLN* 3.5 20.8 + - - +
614A GLN* 3.3 40.2 + - + +
681A ARG* 5.7 4.9 + - - +
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Residues in contact with THR 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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255A LEU* 3.4 33.9 - - + -
256A THR* 4.7 4.0 - - + -
398A LEU* 4.0 11.9 - - + -
604A HIS* 2.6 41.1 + - + -
607A ASN* 2.8 15.4 + - - +
608A PHE* 3.6 4.3 - - - -
610A GLU* 1.3 74.8 - - - +
612A LEU* 1.3 66.5 + - - +
614A GLN* 3.3 11.1 + - - +
615A CYS* 3.1 27.4 + - - -
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Residues in contact with LEU 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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398A LEU* 3.7 18.3 - - + +
401A LEU* 3.5 31.6 - - + -
462A GLN* 3.9 21.3 - - + +
465A MET* 3.9 11.4 - - + -
466A GLY* 3.8 31.2 - - - +
469A GLU* 5.9 1.3 - - - +
608A PHE* 2.7 33.2 + - + +
609A SER* 3.6 8.7 - - - +
610A GLU 3.3 0.2 - - - -
611A THR* 1.3 73.2 - - - +
613A GLN* 1.3 63.7 + - + +
615A CYS* 3.2 10.0 + - - +
616A CYS* 3.3 23.5 - - - -
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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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462A GLN* 4.4 15.9 + - - +
609A SER* 3.4 20.0 + - - +
610A GLU* 3.8 22.4 + - - +
611A THR 3.3 0.4 - - - -
612A LEU* 1.3 78.2 - - + +
614A GLN* 1.3 64.2 + - + +
616A CYS 3.1 13.5 + - - -
617A ASP* 3.3 14.4 + - - +
676A HIS* 5.3 11.6 - - - -
681A ARG* 5.2 7.8 + - - -
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Residues in contact with GLN 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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256A THR* 3.7 26.1 + - + +
257A PRO* 3.7 16.1 - - - +
258A SER* 5.5 2.3 + - - +
259A GLU* 5.5 1.4 - - - +
604A HIS* 5.4 4.5 - - - -
610A GLU* 3.3 30.6 + - + +
611A THR* 3.8 9.3 + - - +
612A LEU 3.3 0.8 - - - -
613A GLN* 1.3 78.1 - - + +
615A CYS* 1.3 57.9 + - - +
616A CYS 3.3 0.2 - - - -
617A ASP* 4.2 14.4 + - - +
681A ARG* 5.5 8.2 - - - +
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Residues in contact with CYS 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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255A LEU* 4.1 16.6 - - - -
256A THR* 3.8 18.4 - - - -
257A PRO* 4.2 7.0 - - - -
398A LEU* 3.7 33.0 - - + +
401A LEU* 3.3 18.7 - - + +
402A SER* 3.8 10.5 + - - +
405A SER* 2.8 20.4 + - - -
611A THR* 3.1 26.6 + - - +
612A LEU 3.7 5.4 - - - +
613A GLN 3.1 0.4 - - - -
614A GLN* 1.3 76.3 - - - +
616A CYS* 1.3 60.7 + - - +
617A ASP 3.6 0.9 - - - -
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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