Contacts of the helix formed by residues 609 - 616 (chain A) in PDB entry 3NC0
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 PRO 609 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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599A PHE 3.8 3.6 - - - +
600A VAL 3.8 23.3 - - - +
601A GLN 4.6 2.0 - - - +
602A VAL* 3.5 29.3 - - + -
608A MET* 1.3 83.3 - - + +
610A PHE* 1.3 67.5 + - - +
611A ILE* 3.2 18.8 - - + -
612A ASP* 2.9 37.6 + - - +
613A GLU* 4.1 1.6 + - - +
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Residues in contact with PHE 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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559A TRP* 3.5 29.3 - + + -
563A LYS* 3.5 38.1 - - + -
566A VAL* 3.5 24.9 - - + -
567A ASN* 3.5 26.7 - - - -
570A PHE* 4.8 2.0 - + - -
598A HIS 5.2 1.0 + - - -
599A PHE* 3.4 27.4 + + + +
601A GLN 5.3 0.4 + - - -
606A GLU* 6.0 0.4 - - - -
608A MET 3.4 4.4 + - - -
609A PRO* 1.3 70.7 - - - +
611A ILE* 1.3 64.4 + - - +
613A GLU* 2.9 38.0 + - + +
614A ILE* 3.1 47.7 + - + +
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Residues in contact with ILE 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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599A PHE 3.0 22.2 + - - +
600A VAL* 4.3 11.2 - - + -
609A PRO* 3.8 13.5 - - + -
610A PHE* 1.3 74.9 - - - +
612A ASP* 1.3 68.4 + - - +
614A ILE* 3.0 6.4 + - + +
615A LEU* 2.7 64.1 + - + +
637A VAL* 3.6 18.4 - - + -
640A MET* 3.3 33.8 - - + +
641A ILE* 4.1 9.4 - - + -
653A LEU* 3.8 16.2 - - + -
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Residues in contact with ASP 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 MET* 4.2 14.4 - - + +
609A PRO* 2.9 37.8 + - - +
610A PHE 2.9 0.4 + - - -
611A ILE* 1.3 86.5 - - - +
613A GLU* 1.3 58.9 + - + +
615A LEU* 3.2 6.7 + - - +
616A ASN* 2.9 46.6 + - - +
653A LEU* 4.1 12.3 - - - +
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Residues in contact with GLU 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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563A LYS* 4.0 14.7 + - - -
567A ASN* 5.7 0.5 + - - +
606A GLU* 4.5 8.0 - - - +
608A MET* 4.5 31.2 - - + +
609A PRO 4.1 0.9 + - - +
610A PHE* 2.9 36.7 + - + +
612A ASP* 1.3 79.2 - - - +
614A ILE* 1.3 62.5 + - + +
616A ASN* 3.5 3.2 + - - +
617A ASN* 3.0 33.4 + - - +
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Residues in contact with ILE 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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566A VAL* 4.8 0.2 - - + -
570A PHE* 3.8 30.1 - - + -
588A PHE* 4.7 3.4 - - + -
599A PHE* 4.3 4.5 - - + -
610A PHE* 3.1 44.8 + - + +
611A ILE* 3.0 10.0 + - + +
613A GLU* 1.3 77.0 - - - +
615A LEU* 1.3 58.6 + - + +
617A ASN 3.3 3.3 + - - -
618A ILE* 3.1 27.2 + - + +
621A ILE* 4.4 7.2 - - + +
633A PHE* 4.5 8.3 - - + -
637A VAL* 4.1 24.7 - - + -
640A MET* 3.6 26.7 - - + -
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Residues in contact with LEU 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 ILE* 2.7 51.7 + - + +
612A ASP* 3.9 5.2 - - - +
614A ILE* 1.3 69.1 - - + +
616A ASN* 1.3 57.9 + - - +
617A ASN 2.9 10.2 + - - -
618A ILE* 3.6 35.6 + - + +
637A VAL* 4.0 13.7 - - + -
641A ILE* 4.5 2.2 - - + -
653A LEU* 3.8 33.2 - - + +
656A LYS* 3.6 33.9 + - + +
657A TYR* 4.2 14.6 - - + +
660A LEU* 6.1 1.2 - - - +
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Residues in contact with ASN 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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608A MET* 6.3 1.4 - - - +
612A ASP* 2.9 29.7 + - - +
613A GLU* 4.6 1.9 - - - +
614A ILE 3.4 0.2 - - - -
615A LEU* 1.3 75.0 - - - +
617A ASN* 1.3 75.4 + - - +
620A THR* 5.7 0.3 - - - +
656A LYS* 2.9 27.0 + - - +
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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