Contacts of the helix formed by residues 657 - 668 (chain C) in PDB entry 4P3N
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 657 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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655C GLY 5.8 0.7 - - - +
656C CYS* 1.3 77.2 - - - +
658C LEU* 1.3 67.7 + - - +
659C ASN* 4.4 3.7 + - - +
660C LYS* 3.2 25.4 + - - +
661C LYS* 3.1 20.8 + - - +
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Residues in contact with LEU 658 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624C VAL* 3.8 18.2 - - + -
625C PRO 4.8 1.8 - - - +
626C VAL* 3.9 41.8 + - + +
656C CYS 4.1 0.4 + - - -
657C THR* 1.3 71.5 - - - +
659C ASN* 1.3 70.0 + - - +
661C LYS* 2.8 26.8 + - - +
662C ILE* 2.9 34.3 + - + +
675C VAL* 3.8 21.5 - - + -
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Residues in contact with ASN 659 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657C THR* 3.5 3.6 + - - +
658C LEU* 1.3 90.0 - - - +
660C LYS* 1.3 56.6 + - - +
662C ILE* 3.7 20.8 - - - +
663C ARG* 2.9 30.0 + - - +
689C ARG* 4.2 10.0 + - - +
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Residues in contact with LYS 660 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656C CYS* 3.2 40.9 - - + +
657C THR* 3.2 24.7 + - - +
658C LEU 3.1 0.2 - - - -
659C ASN* 1.3 74.3 - - - +
661C LYS* 1.3 61.8 + - + +
663C ARG* 3.8 3.5 - - - +
664C ASN* 2.9 60.4 + - - +
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Residues in contact with LYS 661 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624C VAL* 3.7 32.4 - - + +
625C PRO* 4.7 11.1 + - - +
651C ASP* 3.3 51.3 + - - +
652C LEU 3.7 2.8 + - - -
653C ASP* 2.7 33.6 + - - +
654C PRO* 5.0 0.4 - - - +
656C CYS* 3.6 24.5 + - + +
657C THR 3.1 17.2 + - - +
658C LEU* 2.8 8.1 + - - +
660C LYS* 1.3 75.0 - - - +
662C ILE* 1.3 58.6 + - - +
664C ASN* 3.5 5.2 + - - +
665C ALA* 2.9 30.8 + - - +
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Residues in contact with ILE 662 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624C VAL* 5.2 2.5 - - + -
658C LEU* 2.9 39.7 + - + +
659C ASN* 3.7 16.8 - - - +
660C LYS 3.3 0.2 - - - -
661C LYS* 1.3 77.3 - - + +
663C ARG* 1.3 57.3 + - - +
665C ALA* 3.3 1.9 + - - -
666C GLN* 2.9 49.9 + - - +
673C ILE* 3.5 22.4 - - + +
675C VAL* 4.0 19.5 - - + -
689C ARG* 3.5 40.2 - - + +
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Residues in contact with ARG 663 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659C ASN 2.9 18.9 + - - +
660C LYS* 3.9 4.7 - - - +
662C ILE* 1.3 76.8 - - - +
664C ASN* 1.3 64.7 + - - +
666C GLN* 3.3 23.6 + - - +
667C LEU* 3.0 60.0 + - + +
693C ASN* 6.3 0.8 - - - +
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Residues in contact with ASN 664 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651C ASP* 5.8 2.5 - - - +
660C LYS* 2.9 54.3 + - - +
661C LYS* 3.9 5.7 - - - +
663C ARG* 1.3 77.6 - - - +
665C ALA* 1.3 60.4 + - - +
667C LEU* 3.3 18.1 + - - +
668C ALA* 2.9 28.2 + - - +
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Residues in contact with ALA 665 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622C MET* 3.8 28.5 - - + -
624C VAL* 5.6 1.3 - - + -
661C LYS 2.9 19.3 + - - +
662C ILE* 3.3 5.6 + - - +
664C ASN* 1.3 76.7 - - - +
666C GLN* 1.3 59.4 + - - +
668C ALA* 3.3 6.8 + - - -
669C GLN 3.2 4.2 + - - -
670C TYR* 3.1 29.9 + - + +
673C ILE* 3.6 20.0 - - + -
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Residues in contact with GLN 666 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662C ILE* 2.9 32.9 + - - +
663C ARG* 3.6 30.0 + - - +
664C ASN 3.2 0.2 - - - -
665C ALA* 1.3 77.1 - - - +
667C LEU* 1.3 59.7 + - - +
669C GLN* 3.2 26.6 + - - +
673C ILE* 3.7 7.0 - - + -
689C ARG* 4.0 2.2 - - - +
690C THR 2.9 24.5 + - - +
691C ARG* 3.3 30.9 - - - +
693C ASN* 2.9 37.0 + - - +
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Residues in contact with LEU 667 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663C ARG* 3.0 54.7 + - + +
664C ASN* 3.6 21.8 - - - +
665C ALA 3.3 0.2 - - - -
666C GLN* 1.3 72.9 - - - +
668C ALA* 1.3 58.2 + - - +
669C GLN* 3.0 19.6 + - - +
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Residues in contact with ALA 668 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330C GLN* 4.4 3.0 + - - +
619C ARG* 3.2 29.2 + - - +
664C ASN 2.9 16.4 + - - +
665C ALA* 3.5 8.1 - - - +
666C GLN 3.2 0.2 - - - -
667C LEU* 1.3 74.8 - - - +
669C GLN* 1.3 69.1 + - - +
670C TYR* 3.6 21.5 - - + -
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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