Contacts of the helix formed by residues 611 - 622 (chain D) in PDB entry 3KSA
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 LEU 611 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523D TYR* 3.5 18.5 + - + +
527D ARG* 4.2 31.0 - - - +
531D GLU* 6.2 2.9 - - + -
608D ILE* 4.0 14.6 - - + -
610D ASP* 1.3 78.5 - - - +
612D ALA* 1.3 62.5 + - - +
613D ARG 3.3 1.1 - - - -
614D ALA* 3.1 5.8 + - - +
615D GLU* 2.9 28.7 + - + +
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Residues in contact with ALA 612 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610D ASP* 3.7 10.1 - - - +
611D LEU* 1.3 81.2 - - - +
613D ARG* 1.3 56.6 + - - +
615D GLU* 3.5 6.6 + - - +
616D ARG* 2.9 50.8 + - - +
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Residues in contact with ARG 613 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLU* 5.0 12.1 - - + -
608D ILE* 5.6 0.4 - - + -
609D GLU* 5.6 2.0 + - - +
610D ASP* 3.2 38.4 + - + +
611D LEU 3.3 0.4 - - - -
612D ALA* 1.3 72.9 - - - +
614D ALA* 1.3 61.6 - - - +
616D ARG* 3.2 19.6 + - - +
617D ARG* 2.8 32.4 + - - +
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Residues in contact with ALA 614 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 4.2 16.4 - - + -
10B GLU* 5.0 6.9 - - - +
523D TYR* 3.7 20.6 - - + -
608D ILE* 3.4 28.0 - - + +
611D LEU 3.1 9.7 + - - +
613D ARG* 1.3 78.0 - - - +
615D GLU* 1.3 64.1 + - - +
617D ARG* 3.1 4.0 + - - -
618D VAL* 2.8 31.3 + - - +
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Residues in contact with GLU 615 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523D TYR* 2.9 31.9 + - - +
524D ARG* 4.8 7.6 + - - -
527D ARG* 4.6 4.0 + - - -
611D LEU* 2.9 17.2 + - + +
612D ALA* 3.7 8.1 - - - +
614D ALA* 1.3 74.8 - - - +
616D ARG* 1.3 65.3 + - - +
618D VAL* 4.8 0.7 - - - -
619D ASN* 3.0 58.5 + - - +
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Residues in contact with ARG 616 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610D ASP* 5.3 0.2 + - - -
612D ALA* 2.9 44.4 + - - +
613D ARG* 3.3 19.8 - - - +
615D GLU* 1.3 77.2 - - - +
617D ARG* 1.3 55.7 + - - +
619D ASN* 3.5 4.6 + - - +
620D VAL* 2.8 34.6 + - + +
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Residues in contact with ARG 617 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLU* 3.4 44.9 + - + +
11B ASP* 4.5 3.8 - - - +
13B MET* 4.8 4.7 - - + -
14B GLY* 4.2 12.6 - - - +
613D ARG 2.8 20.2 + - - +
614D ALA* 3.7 4.7 - - - +
616D ARG* 1.3 72.3 - - - +
618D VAL* 1.3 68.9 + - + +
620D VAL* 3.1 18.0 + - - +
621D LEU* 3.2 46.1 + - + +
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Residues in contact with VAL 618 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 4.1 21.8 - - + -
13B MET* 3.9 23.1 - - + -
463D ALA* 5.0 3.8 - - + -
520D THR* 3.9 17.5 - - + -
523D TYR* 4.4 13.5 - - + -
524D ARG* 4.7 12.8 - - - -
614D ALA 2.8 25.6 + - - +
615D GLU* 4.1 2.2 - - - +
617D ARG* 1.3 73.6 - - + +
619D ASN* 1.3 67.3 + - - +
622D MET* 2.8 53.1 + - + +
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Residues in contact with ASN 619 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463D ALA* 5.4 2.8 - - - +
524D ARG* 4.3 14.2 + - - -
615D GLU* 3.0 52.1 + - - +
616D ARG* 4.0 4.6 - - - +
618D VAL* 1.3 85.1 - - - +
620D VAL* 1.3 56.4 + - - +
623D GLY* 2.8 29.2 - - - +
624D ASP 4.4 0.2 + - - -
625D LYS* 5.5 2.1 + - - +
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Residues in contact with VAL 620 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616D ARG* 2.8 26.6 + - + +
617D ARG* 3.3 10.5 - - - +
619D ASN* 1.3 75.3 - - - +
621D LEU* 1.3 75.3 + - + +
623D GLY* 3.6 2.8 + - - -
626D VAL 5.5 0.3 + - - -
628D PRO* 3.5 35.8 - - + +
629D ARG* 3.6 29.9 + - - +
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Residues in contact with LEU 621 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B MET* 3.6 34.8 - - + +
14B GLY* 4.5 2.9 - - - +
17B PHE* 3.8 36.5 - - + -
617D ARG* 3.2 43.7 + - + +
618D VAL 4.1 0.4 - - - +
620D VAL* 1.3 83.6 - - + +
622D MET* 1.3 66.7 + - + +
629D ARG* 3.0 39.6 + - + -
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Residues in contact with MET 622 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B MET* 3.6 11.2 - - + -
17B PHE* 4.1 12.3 - - + -
461D ASN* 3.0 34.0 + - - +
463D ALA* 4.1 10.5 - - + +
464D LYS* 3.6 0.2 - - - -
513D HIS* 5.0 3.4 - - - +
516D THR* 3.0 36.6 - - + -
517D LEU* 3.7 26.5 - - + -
520D THR* 3.2 28.5 - - + -
618D VAL* 2.8 25.2 + - + +
621D LEU* 1.3 79.4 - - - +
623D GLY* 1.3 67.4 + - - +
629D ARG* 4.4 1.6 - - - +
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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