Contacts of the helix formed by residues 561 - 572 (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 ASP 561 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542D LEU* 5.4 1.7 - - - +
543D TYR* 4.2 20.9 + - - -
560D THR* 1.3 75.0 - - - +
562D GLY* 1.3 65.4 + - - +
564D LEU* 2.8 27.0 + - - +
565D GLU* 3.2 6.2 + - - +
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Residues in contact with GLY 562 (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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560D THR* 2.5 7.4 + - - -
561D ASP* 1.3 76.5 - - - +
563D GLU* 1.3 60.8 + - - +
565D GLU* 3.1 17.6 + - - +
566D GLU* 3.5 9.9 + - - +
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Residues in contact with GLU 563 (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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557D TYR 5.4 0.4 - - - +
558D ALA* 3.8 20.4 - - + -
559D TRP* 3.9 12.1 - - + +
560D THR 2.7 17.8 + - - +
562D GLY* 1.3 70.5 - - - -
564D LEU* 1.3 60.9 + - - +
566D GLU* 3.4 7.3 + - - +
567D LEU* 3.0 23.9 + - - +
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Residues in contact with LEU 564 (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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145B PHE 5.4 0.2 - - - +
147B ASP* 5.1 6.7 - - - +
543D TYR* 3.2 50.9 - - + +
545D MET* 4.0 24.5 - - + -
558D ALA* 3.9 6.5 - - + +
560D THR 3.8 0.6 + - - -
561D ASP* 2.8 21.7 + - - +
563D GLU* 1.3 79.2 - - - +
565D GLU* 1.3 53.9 + - - +
567D LEU* 3.1 4.9 + - + -
568D ARG* 2.8 30.4 + - + +
577D LEU* 3.8 25.4 - - + -
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Residues in contact with GLU 565 (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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561D ASP 3.2 5.1 + - - +
562D GLY* 3.1 11.9 + - - +
564D LEU* 1.3 77.4 - - - +
566D GLU* 1.3 57.8 + - - +
568D ARG* 3.2 9.1 + - - +
569D LYS* 2.9 27.9 + - - +
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Residues in contact with GLU 566 (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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562D GLY 3.5 6.5 + - - +
563D GLU* 3.4 10.2 + - - +
564D LEU 3.3 0.4 - - - -
565D GLU* 1.3 73.9 - - - +
567D LEU* 1.3 66.3 + - - +
569D LYS* 3.3 8.2 + - - +
570D GLN* 3.0 23.1 + - - +
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Residues in contact with LEU 567 (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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545D MET* 4.0 18.6 - - + -
556D ALA* 5.1 8.1 - - + -
557D TYR 5.7 3.1 - - - +
558D ALA* 5.0 6.5 - - + -
563D GLU 3.0 14.7 + - - +
564D LEU* 3.5 13.7 - - + +
566D GLU* 1.3 75.6 - - - +
568D ARG* 1.3 58.6 + - - +
570D GLN* 3.2 6.3 + - - +
571D PHE* 3.0 43.2 + - + -
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Residues in contact with ARG 568 (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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147B ASP* 5.4 4.9 - - - +
545D MET* 3.8 25.2 - - + +
564D LEU* 2.8 18.3 + - + +
565D GLU* 3.4 12.6 - - - +
567D LEU* 1.3 70.6 - - - +
569D LYS* 1.3 64.2 + - - +
571D PHE* 3.6 1.3 + - - +
572D GLY* 3.3 23.6 + - - +
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Residues in contact with LYS 569 (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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565D GLU 2.9 13.3 + - - +
566D GLU* 3.3 11.6 + - - +
568D ARG* 1.3 77.2 - - - +
570D GLN* 1.3 66.2 + - - +
572D GLY* 3.3 8.6 + - - -
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Residues in contact with GLN 570 (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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566D GLU 3.0 13.4 + - - +
567D LEU* 3.4 11.0 - - - +
569D LYS* 1.3 78.8 - - - +
571D PHE* 1.3 65.9 - - + +
572D GLY 2.9 6.2 + - - -
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Residues in contact with PHE 571 (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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545D MET* 3.3 32.8 - - + -
546D SER* 3.6 4.7 - - - -
547D LYS* 3.4 32.9 - - + +
554D GLU* 3.0 32.8 - - + -
555D VAL* 3.9 1.6 - - - -
556D ALA* 3.4 34.8 - - + -
567D LEU* 3.0 27.1 + - + +
568D ARG 4.3 2.5 - - - +
570D GLN* 1.3 80.8 - - + +
572D GLY* 1.3 65.7 + - - +
573D LYS 3.0 9.7 + - - +
575D ALA* 3.6 19.0 - - + +
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Residues in contact with GLY 572 (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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545D MET* 5.9 0.5 - - - +
568D ARG 3.3 15.6 + - - +
569D LYS* 3.3 7.1 + - - -
570D GLN 2.9 8.9 + - - -
571D PHE* 1.3 86.6 - - - +
573D LYS* 1.3 62.8 + - - +
575D ALA* 3.8 10.7 + - - +
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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