Contacts of the helix formed by residues 591 - 602 (chain A) in PDB entry 6O0Z
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 591 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516A GLU* 3.4 45.8 - - + +
517A TYR* 4.3 21.3 - - + +
519A THR* 5.4 1.1 - - + -
520A VAL* 3.9 23.6 - - + -
549A VAL* 5.2 2.9 - - + +
553A PHE* 4.7 14.8 + - + +
554A LYS* 4.6 22.0 - - + -
590A SER* 1.3 78.5 + - - +
592A GLY* 1.3 62.2 + - - +
593A THR 3.4 2.2 - - - +
594A TYR* 3.4 18.9 + - + +
595A HIS* 2.9 35.6 + - + -
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Residues in contact with GLY 592 (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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557A ARG* 5.1 2.9 - - - -
590A SER* 3.3 13.5 + - - -
591A LEU* 1.3 74.5 - - - +
593A THR* 1.3 61.8 + - - +
595A HIS* 3.2 11.3 + - - +
596A ASP* 2.9 26.2 + - - +
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Residues in contact with THR 593 (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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511A HIS* 3.7 38.0 + - + +
513A LEU* 4.4 10.7 - - + +
516A GLU* 3.7 26.7 - - + -
591A LEU 4.9 0.2 - - - -
592A GLY* 1.3 73.9 - - - +
594A TYR* 1.3 63.1 + - + +
596A ASP* 4.1 7.2 - - - -
597A LEU* 2.9 37.9 + - - +
620A VAL* 5.2 1.6 - - - +
656A TYR* 3.4 22.9 + - - -
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Residues in contact with TYR 594 (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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513A LEU* 4.5 22.0 - - + -
516A GLU* 6.4 0.2 - - + -
517A TYR* 5.2 11.0 - + + -
554A LYS* 3.6 38.2 + - + +
591A LEU* 3.4 22.8 + - + +
592A GLY 3.2 0.4 - - - -
593A THR* 1.3 82.4 - - + +
595A HIS* 1.3 74.7 + + - +
597A LEU* 3.4 6.0 + - + +
598A LEU* 2.9 31.6 + - + +
604A LYS* 4.7 12.6 + - - +
607A LEU* 3.6 39.7 + - + +
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Residues in contact with HIS 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A PHE 3.7 7.2 - - - -
554A LYS* 3.0 32.5 + - - -
555A THR 4.2 5.2 - - - -
556A ASN 3.1 27.6 - - - -
557A ARG* 4.0 16.7 - - + +
590A SER* 4.8 0.7 - - - -
591A LEU* 2.9 25.3 + - + -
592A GLY* 3.2 8.9 + - - +
594A TYR* 1.3 92.0 - + - +
596A ASP* 1.3 59.5 + - - +
598A LEU* 3.5 6.5 - - + +
599A LYS* 2.9 33.8 + - - +
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Residues in contact with ASP 596 (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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592A GLY 2.9 16.1 + - - +
593A THR* 3.7 6.1 - - - +
594A TYR 3.3 0.2 - - - -
595A HIS* 1.3 77.6 - - - +
597A LEU* 1.3 58.4 + - - +
599A LYS* 3.5 16.6 + - - +
600A ILE* 2.9 32.3 + - - +
654A ARG* 4.0 18.4 - - - +
656A TYR* 3.8 22.6 + - + +
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Residues in contact with LEU 597 (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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513A LEU* 6.0 8.5 - - + -
593A THR* 2.9 32.0 + - - +
594A TYR* 3.9 6.7 - - + +
596A ASP* 1.3 75.7 - - - +
598A LEU* 1.3 63.6 + - - +
600A ILE* 4.0 8.7 - - + -
601A ILE* 3.3 27.9 + - + +
607A LEU* 5.8 4.5 - - + +
616A LEU* 5.9 9.2 - - + -
619A ILE* 5.4 9.6 - - + -
620A VAL* 6.0 5.2 - - + -
623A LEU* 5.3 11.9 - - + -
651A LEU* 5.7 9.9 - - + -
654A ARG* 5.1 4.9 - - - -
656A TYR* 3.6 25.8 - - + +
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Residues in contact with LEU 598 (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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594A TYR* 2.9 32.3 + - + +
595A HIS* 3.5 10.8 - - + +
596A ASP 3.2 0.4 - - - -
597A LEU* 1.3 77.6 - - - +
599A LYS* 1.3 52.4 + - - +
601A ILE 3.5 0.5 + - - -
602A LYS* 2.7 29.5 + - - -
603A ASP 3.2 26.7 + - - +
604A LYS* 5.6 2.5 - - + -
607A LEU* 5.4 4.7 - - + +
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Residues in contact with LYS 599 (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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595A HIS* 2.9 20.1 + - + +
596A ASP* 3.5 19.3 + - - +
598A LEU* 1.3 74.5 - - - +
600A ILE* 1.3 68.5 + - - +
601A ILE 3.4 0.2 - - - -
602A LYS* 3.6 12.6 + - - +
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Residues in contact with ILE 600 (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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596A ASP* 2.9 26.6 + - - +
597A LEU* 4.4 8.3 - - + -
599A LYS* 1.3 83.1 - - - +
601A ILE* 1.3 57.8 + - - +
602A LYS* 3.6 1.6 + - - +
647A VAL* 3.3 23.1 - - - +
650A GLN* 4.6 13.2 - - + +
651A LEU* 4.8 22.7 - - + +
654A ARG* 5.7 5.4 - - - -
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Residues in contact with ILE 601 (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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597A LEU* 3.3 21.1 + - + +
598A LEU 4.3 0.2 - - - +
600A ILE* 1.3 76.1 - - - +
602A LYS* 1.3 65.6 + - - +
603A ASP* 2.9 28.2 - - - +
647A VAL* 3.7 20.2 - - + +
651A LEU* 6.1 2.5 - - + -
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Residues in contact with LYS 602 (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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598A LEU 2.7 16.3 + - - -
599A LYS* 3.6 12.5 + - - +
600A ILE 3.3 4.0 - - - +
601A ILE* 1.3 76.0 - - - +
603A ASP* 1.3 59.3 + - - +
647A VAL* 5.4 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