Contacts of the helix formed by residues 657 - 669 (chain A) in PDB entry 3KN5
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 SER 657 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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518A GLU* 2.8 37.1 + - - -
655A ASN 3.5 2.9 + - - -
656A VAL* 1.3 79.4 - - - +
658A GLN* 1.3 63.2 + - - +
659A GLU* 3.5 13.8 + - - -
660A ALA* 3.5 15.8 + - - +
661A LYS* 3.3 19.1 + - - +
686A TRP* 3.8 3.6 + - - -
694A SER* 6.2 2.7 - - - -
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Residues in contact with GLN 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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657A SER* 1.3 73.6 - - - +
659A GLU* 1.3 72.2 + - - +
661A LYS* 3.2 22.5 + - - +
662A ASP* 2.9 67.0 + - - +
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Residues in contact with GLU 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 SER* 3.5 10.7 - - - -
658A GLN* 1.3 95.3 + - - +
660A ALA* 1.3 56.5 + - - +
662A ASP* 3.5 7.4 + - - +
663A LEU* 2.9 28.4 + - - +
684A ASN* 5.0 1.4 + - - +
685A GLU* 4.0 30.2 - - + +
686A TRP* 4.0 26.7 - - + +
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Residues in contact with ALA 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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518A GLU* 4.3 0.7 - - - +
612A LEU* 4.9 0.8 - - - +
616A LEU* 3.6 27.8 - - + -
656A VAL* 3.9 10.1 - - + -
657A SER* 3.5 16.3 + - - +
658A GLN 3.2 0.2 - - - -
659A GLU* 1.3 77.0 - - - +
661A LYS* 1.3 67.0 + - - +
663A LEU* 3.0 8.3 + - - +
664A ILE* 2.9 29.4 + - - +
686A TRP* 3.8 21.7 - - + +
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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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648A PHE* 3.5 62.3 - - + -
653A TRP* 3.0 34.6 + - + -
654A LYS 5.0 2.2 + - - -
656A VAL* 2.4 33.6 + - + +
657A SER 3.3 9.7 + - - +
658A GLN* 3.2 27.6 + - - +
660A ALA* 1.3 77.6 - - - +
662A ASP* 1.3 59.5 + - - +
664A ILE* 3.5 1.9 + - - +
665A GLN* 3.0 27.0 + - - +
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Residues in contact with ASP 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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658A GLN* 2.9 54.0 + - - +
659A GLU* 3.8 7.2 - - - +
661A LYS* 1.3 75.1 - - - +
663A LEU* 1.3 64.9 + - - +
665A GLN* 3.0 24.4 - - - +
666A GLY* 3.1 6.8 + - - -
676A LEU* 5.7 0.2 - - - +
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Residues in contact with LEU 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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525A MET* 5.3 0.9 - - + -
612A LEU* 3.8 17.7 - - + -
659A GLU 2.9 17.8 + - - +
660A ALA* 3.4 5.2 - - - +
662A ASP* 1.3 72.7 - - - +
664A ILE* 1.3 67.8 + - - +
666A GLY* 3.1 12.5 + - - -
667A LEU* 3.3 15.0 + - + +
676A LEU* 3.6 25.7 - - + +
681A LEU* 3.7 16.2 - - + -
684A ASN* 3.6 34.1 - - - +
686A TRP* 3.7 24.7 - - + -
687A LEU* 3.8 14.1 - - + -
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Residues in contact with ILE 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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609A GLY* 4.5 2.0 - - - +
612A LEU* 3.7 22.2 - - + -
613A TYR* 3.8 20.2 - - + +
616A LEU* 4.1 12.8 - - + -
646A PHE* 4.8 0.2 - - + -
648A PHE* 3.7 21.5 - - + -
653A TRP* 3.5 35.2 - - + -
660A ALA 2.9 17.1 + - - +
661A LYS 3.6 5.8 - - - +
663A LEU* 1.3 75.3 - - - +
665A GLN* 1.3 58.2 + - - +
667A LEU* 3.0 9.2 + - - +
668A LEU* 2.8 54.6 + - + +
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Residues in contact with GLN 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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646A PHE* 3.7 33.2 - - + -
648A PHE* 4.7 7.6 - - + -
661A LYS 3.0 15.7 + - - +
662A ASP* 3.0 22.2 - - - +
664A ILE* 1.3 78.1 - - - +
666A GLY* 1.3 60.4 + - - +
669A THR* 3.2 27.4 + - - -
674A LYS* 3.2 36.7 + - - +
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Residues in contact with GLY 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 ASP 3.1 6.2 + - - -
663A LEU 3.1 8.3 + - - -
665A GLN* 1.3 81.5 - - - +
667A LEU* 1.3 58.6 - - - +
669A THR* 3.9 2.6 - - - +
674A LYS* 4.6 7.9 - - - -
675A ARG* 3.4 9.7 - - - +
676A LEU* 2.7 46.7 + - - +
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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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525A MET* 5.7 2.5 - - - -
529A VAL* 6.5 0.4 - - + -
605A LEU* 3.4 41.9 - - + +
606A TRP* 3.6 22.5 + - - -
608A LEU* 4.2 10.3 - - + +
609A GLY* 3.7 30.5 - - - +
612A LEU* 5.0 5.8 - - + -
663A LEU* 3.3 31.4 + - + +
664A ILE* 3.0 8.7 + - - +
666A GLY* 1.3 78.5 - - - +
668A LEU* 1.3 63.7 + - - +
669A THR 3.3 5.4 + - - +
675A ARG* 5.6 0.3 - - - +
676A LEU* 4.5 13.0 - - + +
681A LEU* 4.2 16.2 - - + -
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Residues in contact with LEU 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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606A TRP* 3.3 40.5 + - + +
609A GLY 3.9 4.7 - - - -
610A VAL* 3.7 33.0 - - + +
613A TYR* 4.1 12.1 - - + -
621A PRO* 4.0 24.5 - - + -
622A PHE* 4.4 8.0 - - + -
641A ILE 5.6 0.5 - - - +
644A GLY* 5.5 1.2 - - - -
646A PHE* 3.7 35.1 - - + -
664A ILE* 2.8 35.5 + - + +
667A LEU* 1.3 75.3 - - - +
669A THR* 1.3 64.7 + - - +
670A VAL* 3.6 4.2 + - - +
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Residues in contact with THR 669 (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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606A TRP* 4.7 1.7 - - - -
644A GLY* 5.6 5.1 - - - -
646A PHE* 4.1 11.2 - - - -
665A GLN* 3.2 19.6 + - - +
666A GLY* 3.9 5.2 - - - +
667A LEU 3.7 6.9 - - - +
668A LEU* 1.3 80.2 - - - +
670A VAL* 1.3 59.9 + - - +
671A ASP* 3.6 17.8 - - - +
674A LYS* 3.7 21.8 - - + +
675A ARG* 3.2 49.4 - - + +
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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