Contacts of the helix formed by residues 657 - 668 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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656B CYS* 1.3 76.1 - - - +
658B LEU* 1.3 65.7 + - - +
659B ASN* 4.4 6.2 - - - +
660B LYS* 3.3 25.7 + - - +
661B LYS* 3.1 25.7 + - - +
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Residues in contact with LEU 658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624B VAL* 3.7 22.4 - - + -
625B PRO 4.3 2.2 - - - +
626B VAL* 3.9 47.1 + - + +
656B CYS 4.0 0.6 + - - -
657B THR* 1.3 71.6 - - - +
659B ASN* 1.3 70.5 + - - +
661B LYS* 2.9 12.0 + - - +
662B ILE* 2.9 47.1 + - + +
675B VAL* 3.8 18.4 - - + -
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Residues in contact with ASN 659 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657B THR* 3.4 6.5 + - - +
658B LEU* 1.3 83.8 - - - +
660B LYS* 1.3 56.8 + - - +
662B ILE* 3.7 16.2 - - - +
663B ARG* 2.9 30.5 + - - +
689B ARG* 4.7 7.0 + - - +
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Residues in contact with LYS 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655B GLY 4.9 1.0 + - - -
656B CYS* 2.8 42.3 - - + +
657B THR* 3.3 24.0 + - - +
658B LEU 3.2 0.6 - - - -
659B ASN* 1.3 75.8 - - - +
661B LYS* 1.3 62.0 + - - +
663B ARG* 3.8 4.2 - - + +
664B ASN* 2.9 58.0 + - - +
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Residues in contact with LYS 661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624B VAL* 3.5 35.9 - - + +
625B PRO* 4.6 9.9 + - - +
651B ASP* 3.4 48.3 + - - +
652B LEU 3.8 2.4 - - - -
653B ASP* 2.7 34.8 + - - +
654B PRO* 4.9 1.4 - - - +
656B CYS* 3.5 25.4 + - + +
657B THR 3.1 14.3 + - - +
658B LEU* 2.9 7.7 + - - +
660B LYS* 1.3 74.8 - - - +
662B ILE* 1.3 59.3 + - - +
664B ASN* 3.5 5.8 + - - +
665B ALA* 2.9 31.0 + - - +
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Residues in contact with ILE 662 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624B VAL* 5.0 1.3 - - + +
658B LEU* 2.9 44.9 + - + +
659B ASN* 3.7 11.9 - - - +
661B LYS* 1.3 76.6 - - + +
663B ARG* 1.3 57.2 + - - +
665B ALA* 3.2 8.4 + - - +
666B GLN* 2.9 54.0 + - - +
673B ILE* 4.3 16.9 - - + +
675B VAL* 3.9 19.3 - - + -
689B ARG* 3.8 37.0 - - + +
693B ASN* 4.5 0.4 - - - +
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Residues in contact with ARG 663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659B ASN 2.9 18.9 + - - +
660B LYS* 3.8 6.7 - - - +
662B ILE* 1.3 77.5 - - - +
664B ASN* 1.3 59.7 + - - +
666B GLN* 3.1 27.4 + - - +
667B LEU* 2.9 58.7 + - + +
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Residues in contact with ASN 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651B ASP* 5.6 3.5 + - - +
660B LYS* 2.9 49.3 + - - +
661B LYS* 3.9 5.5 - - - +
663B ARG* 1.3 77.3 - - - +
665B ALA* 1.3 60.8 + - - +
667B LEU* 3.3 17.9 + - - +
668B ALA* 2.9 29.8 + - - +
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Residues in contact with ALA 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622B MET* 3.8 23.3 - - + -
624B VAL* 5.8 1.1 - - + -
661B LYS 2.9 18.6 + - - +
662B ILE* 3.2 5.8 + - - +
664B ASN* 1.3 75.8 - - - +
666B GLN* 1.3 57.7 + - - +
668B ALA* 3.3 3.4 + - - -
669B GLN 3.1 7.1 + - - -
670B TYR* 3.0 35.7 + - + -
673B ILE* 3.6 24.2 - - + -
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Residues in contact with GLN 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662B ILE* 2.9 41.4 + - - +
663B ARG* 3.1 34.3 + - - +
665B ALA* 1.3 75.6 - - - +
667B LEU* 1.3 59.8 + - - +
669B GLN* 3.0 28.6 + - - +
670B TYR 4.8 0.2 - - - +
673B ILE* 4.2 4.9 - - + +
689B ARG* 4.2 0.8 - - - +
690B THR 3.5 12.6 + - - +
691B ARG* 3.7 30.1 - - - +
693B ASN* 2.9 38.5 + - - +
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Residues in contact with LEU 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663B ARG* 2.9 52.9 + - + +
664B ASN* 3.3 19.5 + - - +
666B GLN* 1.3 71.8 - - - +
668B ALA* 1.3 60.3 + - - +
669B GLN* 3.1 17.1 + - - +
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Residues in contact with ALA 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B GLN* 4.5 5.6 + - - +
619B ARG* 3.1 32.8 + - - +
664B ASN 2.9 17.7 + - - +
665B ALA* 3.6 6.5 - - - +
666B GLN 3.2 0.4 - - - -
667B LEU* 1.3 75.3 - - - +
669B GLN* 1.3 65.3 + - - +
670B TYR* 3.4 18.2 - - + -
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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