Contacts of the helix formed by residues 633 - 644 (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 633 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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632A THR* 1.3 84.2 + - - +
634A ALA* 1.3 59.3 + - - +
635A VAL* 3.0 26.2 + - - +
636A GLU* 2.9 27.6 + - - -
637A ILE* 2.9 20.6 + - - +
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Residues in contact with ALA 634 (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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633A SER* 1.3 73.6 + - - +
635A VAL* 1.3 57.8 + - + +
637A ILE* 3.9 11.8 - - + +
638A MET* 3.1 30.0 + - - +
717A ALA* 4.8 7.1 - - + +
720A HIS* 4.1 25.4 - - + -
721A ALA* 3.7 10.5 - - + +
724A LYS* 4.2 13.5 - - + -
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Residues in contact with VAL 635 (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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633A SER* 3.0 21.8 - - - +
634A ALA* 1.3 76.9 - - - +
636A GLU* 1.3 68.8 + - + +
638A MET* 3.5 9.8 + - + +
639A LYS* 3.1 35.0 + - + +
724A LYS* 4.6 14.6 - - - +
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Residues in contact with GLU 636 (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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632A THR* 4.5 13.7 - - - +
633A SER* 2.9 17.7 + - - +
635A VAL* 1.3 89.7 - - + +
637A ILE* 1.3 65.6 + - - +
639A LYS* 2.7 46.4 + - - +
640A LYS* 3.1 26.0 + - + +
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Residues in contact with ILE 637 (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 PHE* 4.0 22.7 - - + +
623A GLN 5.0 7.4 - - - +
631A CYS* 5.3 5.4 - - + -
632A THR* 3.8 15.9 + - - +
633A SER 2.9 20.3 + - - +
634A ALA* 3.9 11.2 - - - +
636A GLU* 1.3 74.6 - - - +
638A MET* 1.3 59.4 + - - +
640A LYS* 2.9 14.1 + - - +
641A ILE* 2.8 32.3 + - + +
714A CYS 5.3 0.4 - - - +
717A ALA* 4.0 33.4 - - + +
718A THR* 4.2 21.8 - - + +
721A ALA* 3.9 14.6 - - + -
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Residues in contact with MET 638 (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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634A ALA 3.1 14.1 + - - +
635A VAL* 3.7 10.1 - - + +
636A GLU 3.2 0.2 - - - -
637A ILE* 1.3 79.7 - - - +
639A LYS* 1.3 56.3 + - - +
641A ILE* 3.0 11.6 + - - +
642A LYS* 2.9 44.9 + - + +
721A ALA* 4.0 4.7 - - - +
724A LYS* 3.0 56.3 - - + +
725A TYR* 3.6 33.0 - - + -
728A GLU* 4.6 11.4 - - - +
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Residues in contact with LYS 639 (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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635A VAL* 3.1 24.5 + - + +
636A GLU* 2.7 41.8 + - - +
638A MET* 1.3 75.9 - - - +
640A LYS* 1.3 61.6 + - - +
642A LYS* 3.6 26.6 + - - +
643A LYS* 3.3 23.4 + - - +
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Residues in contact with LYS 640 (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 PHE* 3.2 42.1 - - + +
623A GLN* 4.8 15.1 - - - +
632A THR* 6.2 0.4 - - - +
636A GLU* 3.1 14.3 + - + +
637A ILE* 2.9 11.1 + - - +
639A LYS* 1.3 73.2 - - + +
641A ILE* 1.3 60.2 + - - +
643A LYS* 3.4 1.1 + - - -
644A GLY 2.9 8.1 + - - -
645A ASP* 2.7 71.0 + - + +
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Residues in contact with ILE 641 (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* 4.1 15.3 - - + -
622A PHE* 4.0 27.1 - - + -
637A ILE* 2.8 18.2 + - + +
638A MET* 3.0 9.2 + - - +
640A LYS* 1.3 74.1 - - - +
642A LYS* 1.3 69.0 + - - +
644A GLY* 2.9 15.4 + - - -
668A LEU 5.6 0.5 - - - +
670A VAL* 3.7 21.3 - - + +
718A THR 4.2 3.8 - - - +
721A ALA* 3.9 17.3 - - + +
722A PHE* 3.8 32.8 - - + +
725A TYR* 3.9 29.6 - - + -
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Residues in contact with LYS 642 (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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638A MET* 2.9 32.1 + - + +
639A LYS* 3.6 38.0 - - - +
641A ILE* 1.3 74.1 - - - +
643A LYS* 1.3 59.3 + - - +
644A GLY 3.5 0.3 + - - -
670A VAL* 3.8 12.5 - - - +
725A TYR* 3.8 29.8 - - + -
728A GLU* 5.7 5.8 - - - +
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Residues in contact with LYS 643 (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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639A LYS 3.3 15.9 + - - +
640A LYS* 3.9 3.4 - - - +
641A ILE 3.0 1.0 - - - -
642A LYS* 1.3 79.3 - - + +
644A GLY* 1.3 61.0 + - - +
645A ASP* 4.0 28.5 - - + +
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Residues in contact with GLY 644 (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 PHE* 4.8 0.9 - - - -
640A LYS 3.6 1.3 - - - -
641A ILE 2.9 13.8 + - - -
642A LYS 3.3 1.0 + - - -
643A LYS* 1.3 78.9 - - - +
645A ASP* 1.3 57.0 + - - +
646A PHE* 3.1 39.0 + - - +
668A LEU 5.5 1.6 - - - -
669A THR* 5.6 5.2 - - - -
670A VAL* 5.3 5.2 - - - -
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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