Contacts of the helix formed by residues 629 - 637 (chain A) in PDB entry 4KHQ
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 ALA 629 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406A TYR* 2.9 25.0 + - + +
408A MET* 3.8 30.7 - - + -
627A VAL* 3.3 1.0 + - + -
628A SER* 1.3 72.3 - - - +
630A ASP* 1.3 64.4 + - - +
631A LYS 3.3 2.7 - - - -
632A ILE* 3.3 20.7 + - + -
633A ILE* 3.0 25.8 + - - +
651A LEU* 4.4 9.2 - - + -
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Residues in contact with ASP 630 (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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404A TYR* 5.7 0.7 - - - -
405A LYS* 4.0 20.2 + - - +
406A TYR* 3.0 41.8 + - - +
628A SER* 3.4 15.8 + - - +
629A ALA* 1.3 77.6 - - - +
631A LYS* 1.3 62.6 + - + +
633A ILE* 3.5 2.1 + - - +
634A ASP* 2.9 40.9 + - - +
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Residues in contact with LYS 631 (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 CYS* 4.7 7.3 - - + -
611A THR* 5.6 8.7 - - + +
614A GLU* 2.9 46.9 + - + +
615A ALA 5.1 4.2 + - - -
616A PHE* 4.1 32.2 - - + -
628A SER 4.9 1.4 + - - -
629A ALA 3.3 0.4 - - - -
630A ASP* 1.3 78.3 - - + +
632A ILE* 1.3 61.0 + - - +
633A ILE 3.3 0.2 - - - -
634A ASP* 3.8 9.8 - - + +
635A LYS* 3.0 31.9 + - - +
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Residues in contact with ILE 632 (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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408A MET* 4.7 4.3 - - - -
605A LEU* 4.1 17.7 - - + -
609A CYS* 4.5 15.5 - - - -
616A PHE* 5.0 4.9 - - + -
627A VAL* 5.2 2.0 - - + -
628A SER 4.9 1.6 - - - +
629A ALA* 3.3 27.3 + - + +
631A LYS* 1.3 77.2 - - - +
633A ILE* 1.3 62.9 - - - +
635A LYS* 3.5 15.2 - - - +
636A VAL* 3.9 4.3 + - - +
650A PHE* 4.0 26.5 - - + -
651A LEU* 4.0 10.8 - - + -
654A PHE* 3.5 47.1 - - + -
659A MET* 4.6 6.7 - - - -
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Residues in contact with ILE 633 (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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406A TYR* 3.8 31.9 - - + +
629A ALA 3.0 20.1 + - - +
630A ASP 3.7 4.3 - - - +
632A ILE* 1.3 76.4 - - - +
634A ASP* 1.3 61.8 + - - +
636A VAL* 3.1 7.6 + - - +
637A GLY 2.8 22.5 + - - -
638A GLU* 3.8 28.7 - - + -
641A PHE* 4.3 16.3 - - + -
647A TRP* 4.1 28.5 - - + -
650A PHE* 4.4 3.1 - - + -
651A LEU* 3.9 28.5 - - + -
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Residues in contact with ASP 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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406A TYR* 5.8 1.2 - - - -
630A ASP* 2.9 31.4 + - - +
631A LYS* 3.5 10.5 + - + +
632A ILE 3.4 0.2 - - - -
633A ILE* 1.3 81.4 - - - +
635A LYS* 1.3 64.3 + - - +
636A VAL 3.2 0.2 - - - -
637A GLY* 3.2 14.2 + - - +
638A GLU* 5.0 6.9 + - - +
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Residues in contact with LYS 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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608A VAL 4.8 3.8 - - - +
609A CYS* 2.6 45.9 + - + +
611A THR* 6.0 1.0 - - - +
631A LYS 3.0 17.5 + - - +
632A ILE* 3.5 10.3 - - - +
633A ILE 3.2 0.2 - - - -
634A ASP* 1.3 76.9 - - - +
636A VAL* 1.3 62.9 + - + +
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Residues in contact with VAL 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 ILE 4.1 4.0 - - - +
633A ILE 3.1 6.3 + - - +
634A ASP 4.0 0.2 - - - -
635A LYS* 1.3 82.2 - - + +
637A GLY* 1.3 63.6 + - - +
640A LYS* 3.9 27.7 + - + +
641A PHE* 4.2 16.4 - - + -
650A PHE* 3.5 37.2 - - + -
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Residues in contact with GLY 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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633A ILE 2.8 13.2 + - - -
634A ASP* 3.2 14.8 + - - -
636A VAL* 1.3 82.6 - - - +
638A GLU* 1.3 65.5 + - - -
639A SER* 3.1 5.7 + - - -
640A LYS* 3.3 9.5 + - - +
641A PHE* 3.8 9.6 - - - -
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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