Contacts of the helix formed by residues 557 - 566 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504B PHE* 4.2 7.9 - - + -
511B SER* 3.5 36.6 - - - +
512B ASN* 4.1 20.0 - - - +
514B PHE* 5.3 1.8 - - + -
515B LEU* 3.8 22.7 - - + +
553B PHE* 3.7 18.4 - - + -
554B PRO* 3.0 42.2 - - + +
555B LYS 3.0 0.6 - - - -
556B ALA* 1.3 86.2 - - + +
558B ALA* 1.3 66.2 + - - +
559B PRO* 3.4 1.3 - - - -
560B LEU* 3.1 19.2 + - + +
561B LEU* 3.2 10.7 + - - +
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Residues in contact with ALA 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553B PHE* 4.0 9.1 - - + -
555B LYS 3.3 13.5 + - - +
557B LEU* 1.3 76.1 - - - +
559B PRO* 1.3 59.8 - - + +
561B LEU* 3.2 6.4 + - - +
562B LEU* 2.6 37.2 + - + +
586B LEU* 4.0 16.6 - - + +
589B ILE* 3.9 37.9 - - + -
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Residues in contact with PRO 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A THR* 3.5 11.7 - - + +
139A GLN* 3.4 20.2 + - - +
555B LYS 3.8 7.4 - - - +
556B ALA* 3.8 13.5 - - - +
557B LEU 3.5 1.6 - - - -
558B ALA* 1.3 94.7 - - + +
560B LEU* 1.3 63.0 + - + +
562B LEU* 3.3 13.0 - - + +
563B ALA* 2.9 30.0 + - - +
589B ILE* 5.8 0.2 - - + -
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Residues in contact with LEU 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ALA* 3.2 34.5 - - + +
132A GLU* 3.7 12.6 - - + +
135A THR* 3.0 31.2 - - + +
512B ASN* 3.8 28.5 - - - +
515B LEU* 3.3 25.8 - - + -
516B THR* 6.1 0.4 - - - +
519B LEU* 5.1 0.7 - - - -
556B ALA 4.7 12.3 - - - +
557B LEU* 3.1 6.9 + - + +
559B PRO* 1.3 82.9 - - + +
561B LEU* 1.3 62.3 + - - +
563B ALA* 3.4 1.0 + - - +
564B PHE* 3.1 30.1 + - - -
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Residues in contact with LEU 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515B LEU* 3.9 21.8 - - + +
518B LEU* 6.1 0.2 - - + -
519B LEU* 3.8 23.6 - - + -
522B MET* 4.9 1.8 - - + -
544B LEU* 4.3 33.0 - - + -
548B VAL* 4.1 25.1 - - + -
553B PHE* 4.8 7.2 - - + -
557B LEU 3.2 9.1 + - - +
558B ALA* 3.4 8.7 - - - +
560B LEU* 1.3 77.5 - - - +
562B LEU* 1.3 66.3 + - - +
564B PHE 3.2 2.1 + - - +
565B VAL* 2.9 53.6 + - + +
582B LEU* 5.0 1.6 - - + -
586B LEU* 4.2 10.3 - - + -
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Residues in contact with LEU 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A GLN* 3.4 22.2 - - - +
558B ALA* 2.6 19.5 + - + +
559B PRO* 3.3 13.2 - - + +
561B LEU* 1.3 73.1 - - - +
563B ALA* 1.3 51.2 + - - +
565B VAL 3.6 0.2 - - - -
566B THR* 2.6 45.3 + - + +
583B LEU* 3.4 13.0 - - + -
586B LEU* 3.7 35.4 - - + +
587B TYR* 3.3 52.3 - - + -
580D HIS* 4.9 2.7 - - + -
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Residues in contact with ALA 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A TYR* 3.7 20.3 + - + -
135A THR* 3.4 38.8 - - + +
138A CYS* 5.5 2.9 - - + -
139A GLN* 4.3 8.7 - - + +
559B PRO 2.9 12.8 + - - +
560B LEU 3.6 2.2 - - - +
561B LEU 3.3 0.4 - - - -
562B LEU* 1.3 73.9 - - - +
564B PHE* 1.3 59.2 + - + +
566B THR* 3.5 11.3 - - - +
567B LYS* 3.2 24.4 + - - +
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Residues in contact with PHE 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PRO* 4.1 12.8 - - + -
130A GLN 4.2 3.6 - - - -
131A ALA* 3.7 40.2 - - + -
134A TYR* 3.6 30.3 - + - -
135A THR* 4.2 1.3 - - - -
519B LEU* 3.4 34.8 - - + -
524B LEU* 3.7 40.8 - - + +
525B LEU* 3.9 24.9 - - + -
560B LEU 3.1 21.5 - - - -
561B LEU 3.2 3.7 + - - +
563B ALA* 1.3 76.9 - - - +
565B VAL* 1.3 63.4 + - - +
566B THR 3.2 1.3 - - - -
567B LYS* 3.6 22.6 - - + +
570B GLY* 5.7 1.4 - - - -
572B LEU* 4.8 2.1 - - - +
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Residues in contact with VAL 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524B LEU* 4.8 9.2 - - + -
541B LEU* 4.3 7.2 - - + -
561B LEU* 2.9 52.8 + - + +
562B LEU 3.9 1.6 - - - +
564B PHE* 1.3 79.0 - - - +
566B THR* 1.3 57.6 + - - +
567B LYS 3.3 0.7 - - - -
572B LEU* 3.3 20.6 - - + +
579B ARG* 3.1 31.8 + - + -
582B LEU* 3.7 31.0 - - + -
583B LEU* 4.3 17.0 - - + -
586B LEU* 4.5 2.9 - - + -
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Residues in contact with THR 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A GLN* 5.0 2.9 - - - +
562B LEU* 2.6 37.3 + - + +
563B ALA* 3.5 12.6 - - - +
565B VAL* 1.3 78.0 - - - +
567B LYS* 1.3 50.1 + - - +
568B PRO* 2.7 25.2 - - + +
579B ARG* 4.2 8.1 + - - +
583B LEU* 3.5 22.1 - - - +
587B TYR* 2.9 21.9 + - - +
566D THR* 5.0 0.3 + - - -
579D ARG* 3.5 21.4 + - - +
580D HIS* 6.2 0.7 - - - +
583D LEU* 4.5 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