Contacts of the helix formed by residues 526 - 533 (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 MET 526 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480D ILE* 5.7 8.1 - - + +
483D ILE* 3.3 40.6 - - + -
485D ALA* 4.6 0.9 - - + -
486D GLY* 4.7 8.1 - - - +
487D VAL* 5.4 2.5 - - + -
491D PHE* 3.1 44.9 - - + -
521D PHE* 4.0 13.3 + - + -
522D PHE* 3.1 40.4 + - + +
525D TYR* 1.3 77.7 - - + +
527D ARG* 1.3 63.8 + - - +
528D PRO* 3.1 7.0 - - - -
529D LEU* 2.8 39.0 + - + +
530D VAL* 3.4 2.1 + - - +
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Residues in contact with ARG 527 (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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522D PHE 3.1 8.1 + - - -
523D TYR* 2.9 66.5 + - + +
524D ARG* 3.5 20.2 + - - +
525D TYR 2.5 15.1 + - - +
526D MET* 1.3 69.8 - - - +
528D PRO* 1.3 69.5 - - + +
530D VAL* 2.8 7.5 + - + +
531D GLU* 2.8 28.6 + - + +
608D ILE* 5.6 3.6 - - + -
611D LEU* 4.2 31.3 - - + +
615D GLU* 4.6 3.2 + - - -
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Residues in contact with PRO 528 (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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491D PHE* 3.1 33.9 - - + -
493D ILE* 4.0 16.4 - - + +
525D TYR 4.0 4.5 - - - +
526D MET 3.1 5.6 - - - -
527D ARG* 1.3 95.1 - - + +
529D LEU* 1.3 51.3 + - - +
531D GLU* 3.7 7.2 - - + +
532D ALA* 2.7 38.0 + - - +
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Residues in contact with LEU 529 (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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483D ILE* 4.9 0.4 - - + -
491D PHE* 3.4 18.4 - - + -
493D ILE* 5.6 5.8 - - + -
498D TYR 5.8 0.2 - - - +
501D ILE* 3.5 26.5 - - + -
522D PHE* 5.0 4.3 - - + -
526D MET* 2.8 49.0 + - + +
528D PRO* 1.3 82.8 - - - +
530D VAL* 1.3 60.7 + - + +
532D ALA* 3.2 15.7 - - + +
533D GLY 3.3 5.5 + - - -
534D HIS* 3.1 52.4 + - + -
535D VAL* 4.5 12.6 - - + -
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Residues in contact with VAL 530 (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* 4.8 9.4 - - + -
519D LEU* 5.2 2.7 - - + +
522D PHE* 3.6 44.0 - - + +
523D TYR* 3.8 10.3 - - + +
526D MET 4.2 0.7 - - - +
527D ARG* 2.8 10.4 + - + +
529D LEU* 1.3 74.3 - - + +
531D GLU* 1.3 63.7 + - - +
533D GLY* 3.2 10.0 + - - -
534D HIS 5.1 0.2 - - - +
535D VAL* 4.0 17.7 - - + -
606D VAL* 3.5 34.5 - - + +
607D THR* 4.2 4.3 - - - -
608D ILE* 4.0 20.4 - - + +
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Residues in contact with GLU 531 (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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527D ARG* 2.8 24.2 + - + +
528D PRO* 3.8 8.3 - - + +
530D VAL* 1.3 74.1 - - - +
532D ALA* 1.3 62.3 + - - +
533D GLY* 3.5 0.7 + - - -
607D THR* 4.8 7.4 - - - +
608D ILE* 4.1 18.9 + - + +
611D LEU* 6.2 3.1 - - + -
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Residues in contact with ALA 532 (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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493D ILE* 5.7 6.5 - - + -
528D PRO 2.7 18.9 + - - +
529D LEU* 3.2 10.3 - - + +
530D VAL 3.1 0.2 - - - -
531D GLU* 1.3 79.0 - - - +
533D GLY* 1.3 59.2 + - - +
534D HIS* 4.1 19.4 + - + +
605D ARG* 4.0 9.5 + - - -
607D THR* 5.5 0.4 - - - +
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Residues in contact with GLY 533 (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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529D LEU 3.3 0.2 + - - -
530D VAL 3.2 13.3 + - - -
531D GLU 4.4 0.7 - - - -
532D ALA* 1.3 79.3 - - - +
534D HIS* 1.3 68.0 + - - +
535D VAL 3.7 1.8 - - - -
536D TYR* 3.6 12.2 + - - -
605D ARG* 3.4 35.9 + - - -
606D VAL 4.3 9.2 - - - -
607D THR* 4.5 6.3 - - - -
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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