Contacts of the helix formed by residues 657 - 668 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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655A GLY 5.9 0.4 - - - +
656A CYS* 1.3 73.8 - - - +
658A LEU* 1.3 66.8 + - - +
659A ASN* 4.3 6.6 - - - +
660A LYS* 3.4 23.4 + - - +
661A LYS* 3.1 26.0 + - - +
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Residues in contact with LEU 658 (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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624A VAL* 3.5 27.1 - - + -
625A PRO 4.7 2.5 - - - +
626A VAL* 4.4 28.4 + - + +
656A CYS 4.0 0.2 + - - -
657A THR* 1.3 73.1 - - - +
659A ASN* 1.3 65.4 + - - +
661A LYS* 3.2 7.8 + - - +
662A ILE* 2.9 52.3 + - + +
675A VAL* 3.9 27.6 - - + -
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Residues in contact with ASN 659 (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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657A THR* 3.3 5.4 - - - +
658A LEU* 1.3 85.4 - - - +
660A LYS* 1.3 56.4 + - - +
662A ILE* 3.6 14.3 + - - +
663A ARG* 2.9 28.9 + - - +
689A ARG* 5.9 0.7 + - - -
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Residues in contact with LYS 660 (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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656A CYS* 2.7 40.2 - - + +
657A THR* 3.4 30.4 + - - +
658A LEU 3.3 0.4 - - - -
659A ASN* 1.3 76.0 - - - +
661A LYS* 1.3 63.8 + - + +
662A ILE 3.3 0.4 - - - -
663A ARG* 3.9 7.6 - - + -
664A ASN* 2.9 53.4 + - - +
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Residues in contact with LYS 661 (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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622A MET* 6.1 0.2 - - - +
624A VAL* 3.5 31.0 - - + +
625A PRO* 4.2 13.3 + - - +
626A VAL 5.8 0.6 + - - -
651A ASP* 3.5 51.0 + - - +
652A LEU 3.8 2.6 + - - -
653A ASP 2.8 32.0 + - - +
654A PRO* 5.0 1.0 - - - +
656A CYS* 3.4 24.9 + - + +
657A THR 3.1 16.9 + - - +
658A LEU* 3.2 7.4 + - - +
660A LYS* 1.3 76.6 - - + +
662A ILE* 1.3 60.0 + - - +
664A ASN* 3.8 3.5 - - - +
665A ALA* 2.9 30.4 + - - +
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Residues in contact with ILE 662 (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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624A VAL* 5.3 1.3 - - + -
658A LEU* 2.9 48.4 + - + +
659A ASN* 3.7 13.0 - - - +
661A LYS* 1.3 74.3 - - + +
663A ARG* 1.3 59.7 + - - +
665A ALA* 3.2 7.4 + - - +
666A GLN* 2.9 56.4 + - + +
673A ILE* 4.3 22.2 - - + -
675A VAL* 4.0 14.1 - - + -
689A ARG* 4.2 29.2 - - - +
693A ASN* 4.9 0.7 - - - +
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Residues in contact with ARG 663 (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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659A ASN 2.9 19.8 + - - +
660A LYS* 4.1 7.2 - - - +
662A ILE* 1.3 76.3 - - - +
664A ASN* 1.3 59.4 + - - +
666A GLN* 3.3 25.4 + - - +
667A LEU* 2.9 69.5 + - + +
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Residues in contact with ASN 664 (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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651A ASP* 5.8 2.0 - - - +
660A LYS* 2.9 47.8 + - - +
661A LYS* 4.0 4.6 - - - +
663A ARG* 1.3 77.9 - - - +
665A ALA* 1.3 59.9 + - - +
667A LEU* 3.3 19.1 + - - +
668A ALA* 2.9 29.6 + - - +
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Residues in contact with ALA 665 (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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622A MET* 3.8 24.5 - - + -
624A VAL* 5.7 0.7 - - + -
661A LYS 2.9 19.8 + - - +
662A ILE* 3.2 5.6 + - - +
664A ASN* 1.3 76.1 - - - +
666A GLN* 1.3 57.3 + - - +
668A ALA* 3.2 2.6 + - - -
669A GLN 3.1 8.3 + - - -
670A TYR* 3.0 35.4 + - + -
673A ILE* 3.8 24.2 - - + -
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Residues in contact with GLN 666 (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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662A ILE* 2.9 32.2 + - - +
663A ARG* 3.5 34.6 + - - +
665A ALA* 1.3 77.5 - - - +
667A LEU* 1.3 59.3 + - - +
669A GLN* 3.4 20.3 + - - +
670A TYR 5.0 0.2 - - - +
673A ILE* 4.0 8.7 - - + +
689A ARG* 4.0 2.2 - - - +
690A THR 3.4 13.3 + - - +
691A ARG* 3.6 32.3 - - - +
693A ASN* 3.0 47.4 + - - +
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Residues in contact with LEU 667 (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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663A ARG* 2.9 60.1 + - + +
664A ASN* 3.7 21.3 - - - +
665A ALA 3.2 0.2 - - - -
666A GLN* 1.3 74.0 - - - +
668A ALA* 1.3 56.9 + - - +
669A GLN* 3.1 21.5 + - - +
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Residues in contact with ALA 668 (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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330A GLN* 4.5 3.8 + - - +
619A ARG* 3.2 28.7 + - - +
664A ASN 2.9 17.6 + - - +
665A ALA* 3.2 5.6 + - - +
667A LEU* 1.3 74.7 - - - +
669A GLN* 1.3 69.4 + - - +
670A TYR* 3.4 19.1 - - + -
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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