Contacts of the helix formed by residues 557 - 566 (chain D) in PDB entry 1KPS
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 557 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504D PHE* 4.1 10.8 - - + -
511D SER* 3.7 41.1 - - - +
512D ASN* 4.0 15.7 - - - +
514D PHE* 5.3 1.6 - - + -
515D LEU* 3.5 31.3 - - + +
553D PHE* 3.6 19.7 - - + -
554D PRO* 2.8 38.0 + - + +
556D ALA* 1.3 81.3 - - + +
558D ALA* 1.3 67.4 + - - +
559D PRO 3.5 0.4 - - - -
560D LEU* 3.1 14.2 + - + -
561D LEU* 3.2 9.7 + - - +
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Residues in contact with ALA 558 (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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553D PHE* 4.0 11.6 - - + -
555D LYS 3.0 14.4 + - - +
557D LEU* 1.3 75.9 - - - +
559D PRO* 1.3 60.8 - - + +
561D LEU* 3.0 7.0 + - - +
562D LEU* 2.7 35.7 + - - +
586D LEU* 4.2 12.7 - - + +
589D ILE* 3.8 38.8 - - + -
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Residues in contact with PRO 559 (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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135C THR* 3.9 9.0 - - + -
139C GLN* 3.2 24.1 - - - +
555D LYS 3.6 6.7 - - - +
556D ALA* 3.8 12.8 - - - +
557D LEU 3.7 0.4 - - - -
558D ALA* 1.3 95.7 - - + +
560D LEU* 1.3 58.4 + - + +
562D LEU* 3.4 12.3 - - + +
563D ALA* 2.8 30.3 + - - +
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Residues in contact with LEU 560 (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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131C ALA* 3.4 33.0 - - + +
132C GLU* 3.7 11.9 - - + +
135C THR* 3.0 32.1 - - + +
512D ASN* 4.0 26.0 - - - +
515D LEU* 3.3 26.5 - - + -
519D LEU* 4.3 2.4 - - + +
556D ALA 4.1 17.5 - - - +
557D LEU* 3.1 4.9 + - + +
559D PRO* 1.3 75.3 - - + +
561D LEU* 1.3 69.0 + - - +
563D ALA* 3.4 0.9 + - - +
564D PHE* 3.3 28.2 + - - +
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Residues in contact with LEU 561 (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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515D LEU* 3.7 26.9 - - + +
518D LEU* 5.1 0.2 - - + -
519D LEU* 3.8 19.3 - - + -
522D MET* 4.5 2.2 - - + -
544D LEU* 4.1 33.4 - - + -
548D VAL* 3.8 28.7 - - + -
553D PHE* 4.8 6.1 - - + -
557D LEU 3.2 8.5 + - - +
558D ALA* 3.0 9.3 + - - +
560D LEU* 1.3 75.3 - - - +
562D LEU* 1.3 70.1 + - - +
564D PHE* 3.0 4.3 + - - +
565D VAL* 3.0 41.0 + - + +
582D LEU* 4.8 1.6 - - + -
586D LEU* 4.2 12.1 - - + -
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Residues in contact with LEU 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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580B HIS* 4.7 3.8 - - + -
584B GLN* 6.1 0.7 - - - +
139C GLN* 3.4 21.8 - - - +
558D ALA 2.7 16.0 + - - +
559D PRO* 3.4 10.3 - - + +
561D LEU* 1.3 76.8 - - - +
563D ALA* 1.3 54.6 - - - +
565D VAL* 3.1 0.9 + - - -
566D THR* 2.7 42.4 + - + +
583D LEU* 3.8 11.9 - - + -
586D LEU* 3.4 44.1 - - + +
587D TYR* 3.7 46.7 - - + -
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Residues in contact with ALA 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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575B CYS* 5.6 1.5 - - - -
134C TYR* 3.8 14.6 + - + -
135C THR* 3.4 28.7 - - - +
138C CYS* 5.8 2.7 - - + -
139C GLN* 3.8 11.4 - - + +
559D PRO 2.8 21.7 + - - +
560D LEU 3.6 2.9 - - - +
561D LEU 3.2 0.4 + - - -
562D LEU* 1.3 75.1 - - - +
564D PHE* 1.3 64.0 + - + +
566D THR* 3.9 8.6 - - - +
567D LYS* 3.3 24.9 + - - +
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Residues in contact with PHE 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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128C PRO* 4.4 8.5 - - + -
130C GLN 4.1 3.4 - - - -
131C ALA* 3.7 38.6 - - + -
134C TYR* 3.3 36.1 - + + -
135C THR* 4.3 2.0 - - - -
519D LEU* 3.5 21.3 - - + -
524D LEU* 3.4 48.0 - - + +
525D LEU* 3.7 30.1 - - + -
560D LEU 3.3 15.3 - - - -
561D LEU 3.0 6.5 + - - +
563D ALA* 1.3 78.7 - - + +
565D VAL* 1.3 64.0 + - - +
567D LYS* 3.9 17.8 - - + +
572D LEU* 4.8 3.6 - - - +
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Residues in contact with VAL 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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524D LEU* 4.8 7.6 - - + -
541D LEU* 4.7 6.5 - - + -
544D LEU* 5.5 0.2 - - + -
561D LEU* 3.0 37.7 + - + +
562D LEU* 3.8 3.1 - - - +
564D PHE* 1.3 78.1 - - - +
566D THR* 1.3 59.3 + - - +
567D LYS 3.1 10.3 + - - +
572D LEU* 3.2 36.7 - - + +
579D ARG* 3.6 14.1 + - + +
582D LEU* 3.9 33.0 - - + -
583D LEU* 3.4 25.4 - - + -
586D LEU* 4.5 1.6 - - + -
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Residues in contact with THR 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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566B THR* 5.0 0.5 + - - -
579B ARG* 3.6 12.0 + - - -
580B HIS* 6.1 0.7 - - - +
583B LEU* 4.3 10.9 - - - +
139C GLN* 4.8 3.6 - - - +
562D LEU* 2.7 33.7 + - + +
563D ALA* 3.9 9.2 - - - +
565D VAL* 1.3 74.9 - - - +
567D LYS* 1.3 65.3 + - - +
568D PRO* 3.2 9.2 - - - +
579D ARG* 4.2 9.8 + - - +
583D LEU* 3.7 21.5 - - - +
587D TYR* 3.2 28.4 + - - +
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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