Contacts of the helix formed by residues 662 - 676 (chain A) in PDB entry 3K5N
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 TYR 662 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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652A LEU* 4.2 26.0 - - + -
655A ARG* 4.4 15.7 - - + +
656A ILE* 4.0 22.0 - - + -
660A GLU 4.5 6.1 - - - -
661A PRO* 1.3 75.7 - - + +
663A GLN* 1.3 95.0 + - + +
664A GLU 3.3 2.9 - - - -
665A TYR* 3.2 14.9 + - + +
666A VAL* 3.3 15.5 + - + +
765A LEU* 3.9 18.1 - - + +
768A ILE* 3.3 42.7 + - + +
769A GLU 4.4 8.5 + - - -
774A THR* 4.0 16.8 + - + -
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Residues in contact with GLN 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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661A PRO* 3.9 2.0 - - - +
662A TYR* 1.3 101.1 + - + +
664A GLU* 1.3 63.7 + - + +
666A VAL* 3.5 10.2 + - - +
667A ARG* 3.6 13.9 + - - +
773A ALA 4.2 18.8 + - - +
774A THR* 3.7 24.9 + - + +
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Residues in contact with GLU 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A PRO 5.7 0.4 - - - -
662A TYR 3.3 0.4 - - - -
663A GLN* 1.3 74.5 - - + +
665A TYR* 1.3 66.6 + - - +
666A VAL 3.1 2.2 - - - -
667A ARG* 3.2 7.2 + - + +
668A GLU* 2.8 38.4 + - + +
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Residues in contact with TYR 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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647A GLN* 4.0 3.3 + - - +
648A PHE* 3.6 32.1 - + - -
651A GLU* 3.0 50.5 + - + +
652A LEU* 4.2 10.3 - - + -
655A ARG* 3.3 49.6 - - - +
662A TYR 3.2 12.1 + - - +
664A GLU* 1.3 79.0 - - - +
666A VAL* 1.3 61.4 + - + +
668A GLU* 3.9 14.7 - - - +
669A THR* 2.3 52.9 + - + +
681A ARG* 5.6 2.3 + - - -
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Residues in contact with VAL 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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648A PHE* 4.0 15.0 - - + -
652A LEU* 3.8 26.7 - - + -
662A TYR* 3.3 17.8 + - + +
663A GLN 3.7 8.3 - - - +
664A GLU 3.1 0.8 - - - -
665A TYR* 1.3 79.7 - - + +
667A ARG* 1.3 63.2 + - + +
669A THR* 3.4 6.9 - - - -
670A ILE* 3.0 28.1 + - + +
765A LEU* 5.5 4.5 - - + -
774A THR* 4.7 15.0 - - + -
775A LEU 5.5 2.5 - - - +
776A MET* 4.0 31.0 - - + -
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Residues in contact with ARG 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 GLN 3.6 9.9 + - - +
664A GLU* 3.2 12.1 + - + +
666A VAL* 1.3 75.5 - - + +
668A GLU* 1.3 58.0 + - + +
669A THR 3.0 1.8 - - - -
670A ILE* 2.8 33.1 + - - +
671A ASP* 2.4 69.7 + - - +
775A LEU* 3.1 28.5 + - - +
777A THR* 2.9 33.9 + - - -
778A GLY* 4.6 1.0 - - - -
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Residues in contact with GLU 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A GLU* 2.8 35.2 - - + +
665A TYR* 3.9 15.4 - - - +
667A ARG* 1.3 75.8 - - + +
669A THR* 1.3 55.1 + - - +
671A ASP* 3.8 11.2 + - - -
672A LYS* 2.5 65.3 + - - +
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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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644A LEU* 4.7 9.9 - - + -
648A PHE* 3.6 28.5 - - + -
665A TYR* 2.3 48.6 + - + +
666A VAL 3.4 6.1 - - - -
667A ARG 3.0 0.2 - - - -
668A GLU* 1.3 79.7 - - - +
670A ILE* 1.3 57.7 + - - +
672A LYS* 4.5 2.9 - - - -
673A LEU* 2.9 29.2 + - - +
678A LEU* 3.6 17.1 - - + +
681A ARG* 5.8 2.2 - - - +
757A LEU* 4.8 7.0 - - + -
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Residues in contact with ILE 670 (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* 6.2 0.4 - - + -
666A VAL* 3.0 23.5 + - + +
667A ARG* 2.8 38.2 + - - +
669A THR* 1.3 82.9 - - - +
671A ASP* 1.3 63.4 + - - +
673A LEU* 3.2 7.8 + - + +
674A MET* 2.9 45.0 + - + +
753A LEU* 3.9 14.1 - - + -
757A LEU* 4.0 20.6 - - + -
776A MET* 3.7 30.3 - - + +
777A THR 4.3 4.0 - - - +
778A GLY* 4.7 0.9 - - - -
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Residues in contact with ASP 671 (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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667A ARG* 2.4 70.3 + - - +
668A GLU* 3.5 9.0 + - - +
670A ILE* 1.3 70.8 - - - +
672A LYS* 1.3 58.7 + - + +
674A MET* 3.8 4.8 - - - +
675A ALA* 2.9 27.8 + - - +
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Residues in contact with LYS 672 (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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668A GLU* 2.5 59.4 + - - +
669A THR* 4.0 2.0 - - - +
671A ASP* 1.3 71.4 - - + +
673A LEU* 1.3 69.2 + - - +
675A ALA* 2.9 16.9 + - - +
676A GLY 3.1 7.8 + - - -
677A GLU* 3.1 35.4 + - + +
678A LEU* 3.8 26.0 - - + -
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Residues in contact with LEU 673 (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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644A LEU* 4.5 7.4 - - + -
669A THR 2.9 18.3 + - - +
670A ILE* 3.3 7.2 - - - +
672A LYS* 1.3 80.6 - - - +
674A MET* 1.3 62.4 + - + +
676A GLY* 3.0 13.0 + - - -
677A GLU 4.3 0.3 + - - -
678A LEU* 3.7 17.2 + - + +
679A ASP* 4.4 1.9 - - - +
682A LEU* 3.9 30.1 - - + -
749A TYR* 3.1 45.2 - - + +
752A TYR* 4.2 16.6 - - + -
753A LEU* 4.4 5.8 - - + +
757A LEU* 3.7 28.5 - - + -
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Residues in contact with MET 674 (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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670A ILE* 2.9 24.2 + - + +
671A ASP* 3.9 5.4 - - - +
673A LEU* 1.3 83.1 - - + +
675A ALA* 1.3 61.6 + - - +
676A GLY 3.0 1.2 + - - -
749A TYR* 3.4 42.2 - - + -
750A GLU* 3.8 9.9 - - - +
753A LEU* 3.9 21.5 - - + -
778A GLY* 3.4 36.1 - - - +
779A GLN* 3.6 38.1 + - + +
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Residues in contact with ALA 675 (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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671A ASP 2.9 18.3 + - - +
672A LYS* 2.9 9.9 + - - +
674A MET* 1.3 77.5 - - - +
676A GLY* 1.3 57.5 + - - +
677A GLU* 3.2 27.9 + - + +
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Residues in contact with GLY 676 (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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673A LEU 3.0 8.6 + - - -
674A MET 3.0 2.2 - - - -
675A ALA* 1.3 78.7 - - - +
677A GLU* 1.3 63.0 + - - +
678A LEU 3.4 2.5 - - - -
679A ASP* 3.5 16.4 + - - +
749A TYR* 3.6 22.0 - - - -
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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