Contacts of the helix formed by residues 553 - 567 (chain A) in PDB entry 5KMO
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 ALA 553 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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548A GLU* 5.3 13.9 + - - +
552A SER* 1.3 74.6 - - - +
554A ARG* 1.4 55.0 + - - +
555A GLN 3.3 2.7 - - - -
556A ASP* 3.2 22.5 + - + +
557A PHE* 2.8 32.6 + - - +
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Residues in contact with ARG 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548A GLU* 5.6 11.4 - - + +
552A SER* 5.3 5.8 - - - +
553A ALA* 1.4 79.4 - - - +
555A GLN* 1.3 64.5 + - - +
557A PHE* 3.4 10.4 - - - +
558A GLN* 3.0 33.6 + - - +
580A THR* 5.5 1.4 + - - +
582A GLY 5.0 0.2 + - - -
583A ARG* 3.2 56.0 - - - +
585A LEU* 3.5 43.1 - - + +
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Residues in contact with GLN 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A SER* 2.8 41.4 + - - +
554A ARG* 1.3 89.6 + - - +
556A ASP* 1.4 71.1 + - - +
557A PHE 3.4 0.2 - - - -
558A GLN* 3.5 7.2 + - - +
559A ARG* 3.3 22.5 + - - +
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Residues in contact with ASP 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A SER 3.7 6.8 - - - +
553A ALA* 3.2 33.7 + - + +
555A GLN* 1.4 82.8 - - - +
557A PHE* 1.3 60.7 + - - +
559A ARG* 3.7 6.0 + - - +
560A GLU* 3.2 37.7 + - - +
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Residues in contact with PHE 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546A LEU* 3.6 47.8 - - + -
553A ALA 2.8 15.4 + - - +
554A ARG* 3.4 12.1 - - - +
556A ASP* 1.3 76.1 - - - +
558A GLN* 1.3 80.2 + - + +
560A GLU* 3.4 9.3 + - - +
561A ALA* 2.9 26.2 + - + +
578A VAL* 3.7 33.4 - - + -
579A CYS 5.3 0.2 - - - -
580A THR* 4.4 6.3 - - + -
585A LEU* 3.6 40.8 - - + -
586A LEU 4.0 3.8 - - - -
587A MET* 3.6 15.2 - - + +
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Residues in contact with GLN 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A ALA* 4.5 10.2 - - - +
502A VAL* 4.7 7.8 - - - +
504A HIS* 5.2 5.5 + - - -
554A ARG* 3.0 20.4 + - + +
555A GLN* 3.8 9.2 - - - +
556A ASP 3.3 0.4 - - - -
557A PHE* 1.3 92.9 - - + +
559A ARG* 1.3 59.5 + - - +
561A ALA* 3.3 7.7 + - - +
562A GLU* 3.0 52.6 + - - +
578A VAL* 4.6 6.3 - - - +
580A THR* 4.1 16.2 - - - +
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Residues in contact with ARG 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555A GLN 3.3 14.1 + - - +
556A ASP* 4.1 5.6 - - - +
557A PHE 3.5 0.2 - - - -
558A GLN* 1.3 74.5 - - - +
560A GLU* 1.4 60.1 + - - +
562A GLU* 3.4 16.3 + - - +
563A LEU* 3.0 28.2 + - - +
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Residues in contact with GLU 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546A LEU* 5.8 4.2 - - - +
556A ASP* 3.2 29.2 + - - +
557A PHE* 3.6 8.9 - - - +
559A ARG* 1.4 77.0 - - - +
561A ALA* 1.4 55.2 + - - +
563A LEU* 3.2 16.6 + - + +
564A LEU* 2.9 39.8 + - + +
587A MET* 4.3 9.5 - - + +
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Residues in contact with ALA 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502A VAL* 3.9 13.2 - - + -
557A PHE* 2.9 16.2 + - + +
558A GLN* 3.4 13.9 - - - +
560A GLU* 1.4 76.3 - - - +
562A GLU* 1.4 53.1 + - - +
564A LEU 3.4 0.5 + - - -
565A THR* 2.7 36.9 + - - -
575A PHE* 3.6 7.7 - - + -
578A VAL* 3.9 28.9 - - + -
587A MET* 3.9 10.3 - - + +
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Residues in contact with GLU 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A ALA* 4.0 22.9 - - - +
501A CYS* 5.4 3.7 - - - +
502A VAL* 3.8 18.6 - - + -
558A GLN* 3.0 40.3 + - - +
559A ARG* 3.5 15.6 - - - +
561A ALA* 1.4 73.2 - - - +
563A LEU* 1.3 61.8 + - - +
565A THR* 3.6 5.0 + - - -
566A MET* 3.4 26.7 + - - +
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Residues in contact with LEU 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A ARG 3.0 16.7 + - - +
560A GLU* 3.2 15.5 + - + +
562A GLU* 1.3 75.4 - - - +
564A LEU* 1.4 67.6 + - + +
566A MET* 3.2 35.9 - - + +
567A LEU* 3.3 24.4 + - + +
646A PHE* 3.9 37.5 - - + -
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Residues in contact with LEU 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560A GLU* 2.9 22.1 + - + +
561A ALA 3.4 1.3 + - - +
563A LEU* 1.4 77.8 - - + +
565A THR* 1.4 59.4 + - - +
567A LEU* 3.1 35.6 - - + +
568A GLN* 3.6 9.0 - - - +
572A ILE* 6.6 0.4 - - + -
575A PHE* 3.7 23.0 - - + +
587A MET* 3.8 28.7 - - + -
589A PHE* 3.8 28.3 - - + -
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Residues in contact with THR 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501A CYS* 3.6 39.0 - - - +
502A VAL* 3.7 14.9 - - - +
503A HIS* 4.9 2.7 + - + +
561A ALA 2.7 22.5 + - - -
562A GLU* 3.7 8.5 - - - -
563A LEU 3.3 0.4 - - - -
564A LEU* 1.4 73.8 - - - +
566A MET* 1.4 63.0 + - - +
568A GLN* 3.2 21.6 - - - +
575A PHE* 3.7 14.3 - - - -
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Residues in contact with MET 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562A GLU 3.4 14.3 + - - +
563A LEU* 3.2 26.2 + - + +
565A THR* 1.4 79.3 - - - +
567A LEU* 1.4 71.1 + - + +
568A GLN* 3.4 3.8 + - - +
640A TYR* 3.3 12.1 + - - -
644A LEU* 4.4 16.3 - - + +
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Residues in contact with LEU 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563A LEU* 3.3 25.6 + - + +
564A LEU* 3.1 19.8 - - + +
565A THR 3.4 0.2 - - - -
566A MET* 1.4 83.3 - - + +
568A GLN* 1.3 72.0 + - - +
569A HIS 4.3 0.4 - - - -
572A ILE* 4.0 19.8 - - + +
573A VAL 5.1 0.3 - - - +
640A TYR* 3.4 14.4 - - + -
641A LEU* 4.0 16.2 - - + -
644A LEU* 3.9 21.5 - - + -
646A PHE* 3.9 46.7 - - + -
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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