Contacts of the helix formed by residues 577 - 586 (chain A) in PDB entry 3KUT
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 577 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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574A HIS* 3.0 19.8 + - + +
576A THR* 1.3 94.4 - - - +
578A ALA* 1.3 61.5 + - - +
579A GLY 3.4 2.0 - - - -
580A LYS* 3.2 9.0 + - + -
581A ILE* 2.8 42.6 + - + +
611A VAL* 4.1 34.8 - - + -
614A LEU* 4.2 20.4 - - + -
618A GLN* 5.1 7.6 - - - +
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Residues in contact with ALA 578 (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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567A PHE* 3.5 22.7 - - + -
570A ILE* 4.0 9.2 - - - +
571A GLN* 3.5 31.2 - - + +
574A HIS 3.2 7.7 + - - +
575A PRO 3.7 10.0 + - - +
576A THR 3.6 1.4 - - - -
577A LEU* 1.3 77.7 - - - +
579A GLY* 1.3 57.6 + - - +
582A THR* 2.7 37.4 + - - -
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Residues in contact with GLY 579 (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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567A PHE* 3.8 9.2 - - - -
577A LEU 3.4 0.6 - - - -
578A ALA* 1.3 79.0 - - - +
580A LYS* 1.3 57.4 + - - +
583A GLY 3.0 15.2 + - - -
117C GLU* 3.6 19.2 + - - -
118C PHE* 2.9 39.9 + - - +
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Residues in contact with LYS 580 (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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577A LEU* 3.2 10.6 + - + +
579A GLY* 1.3 74.3 - - - +
581A ILE* 1.3 59.8 + - - +
583A GLY* 3.2 2.6 + - - -
584A MET* 2.9 35.6 + - - +
614A LEU* 3.7 33.7 - - + -
618A GLN* 5.7 3.4 - - - +
113C PRO 3.0 28.4 + - - -
114C ASN* 3.8 7.3 + - - +
115C ALA* 2.8 29.4 + - - +
117C GLU* 3.9 26.4 + - - +
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Residues in contact with ILE 581 (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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570A ILE* 3.6 24.0 - - + -
574A HIS* 5.3 2.2 - - + -
577A LEU* 2.8 32.2 + - + +
580A LYS* 1.3 72.1 - - - +
582A THR* 1.3 65.8 + - - +
584A MET* 3.2 7.4 + - - +
585A LEU* 3.0 28.6 + - + +
607A VAL* 4.2 16.6 - - + -
610A ALA* 3.8 45.1 - - + +
611A VAL* 3.8 14.8 - - + +
614A LEU* 3.9 18.8 - - + -
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Residues in contact with THR 582 (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 GLY* 4.2 14.6 - - - +
566A LEU* 4.5 3.1 - - + -
567A PHE* 3.7 16.0 - - + +
570A ILE* 3.6 28.5 - - + +
578A ALA 2.7 23.3 + - - -
581A ILE* 1.3 75.8 - - - +
583A GLY* 1.3 65.0 + - - +
585A LEU* 3.2 3.1 + - - +
586A LEU* 3.0 31.5 + - + +
118C PHE* 3.7 35.0 - - + -
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Residues in contact with GLY 583 (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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579A GLY 3.0 12.8 + - - -
580A LYS 3.2 2.2 + - - -
582A THR* 1.3 78.1 - - - +
584A MET* 1.3 61.2 + - - +
586A LEU* 3.4 14.6 + - - +
587A GLU* 3.8 9.2 + - - +
115C ALA* 3.6 14.1 - - - +
116C ALA 3.2 23.6 - - - +
118C PHE* 3.9 8.7 - - - +
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Residues in contact with MET 584 (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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580A LYS* 2.9 22.6 + - + +
581A ILE* 3.2 18.6 + - - +
583A GLY* 1.3 75.1 - - - +
585A LEU* 1.3 69.7 + - + +
587A GLU* 3.3 18.4 + - - +
588A ILE 4.4 0.9 + - - -
610A ALA* 3.6 27.6 - - + +
613A VAL* 4.1 8.1 - - + -
614A LEU* 4.1 21.1 - - - +
111C LEU* 4.0 26.4 - - + +
112C ASN 3.3 21.1 + - - +
113C PRO* 3.8 30.1 - - + -
115C ALA* 3.6 11.2 - - + -
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Residues in contact with LEU 585 (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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566A LEU* 5.2 4.5 - - + -
570A ILE* 3.8 17.3 - - + -
581A ILE* 3.0 21.4 + - + +
582A THR 3.2 3.6 + - - +
584A MET* 1.3 78.2 - - - +
586A LEU* 1.3 58.0 + - - +
587A GLU 3.1 0.4 - - - -
588A ILE* 3.0 36.9 + - + +
593A LEU* 3.3 14.3 - - + +
596A MET* 4.3 4.9 - - - -
603A LEU* 3.8 30.1 - - + -
606A LYS* 3.9 29.8 - - + +
607A VAL* 3.9 8.5 - - + -
610A ALA* 3.7 27.6 - - + -
111C LEU* 4.3 5.4 - - + -
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Residues in contact with LEU 586 (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 LYS* 2.8 68.0 + - + +
562A LEU* 4.0 12.8 - - + -
563A GLY* 3.6 16.8 - - - +
566A LEU* 4.1 7.4 - - + -
582A THR* 3.0 23.8 + - + +
583A GLY* 3.8 8.7 - - - +
584A MET 3.2 1.0 - - - -
585A LEU* 1.3 75.3 - - - +
587A GLU* 1.3 59.2 + - - +
588A ILE 3.2 1.1 - - - -
593A LEU* 4.0 10.8 - - + -
1B CL 4.0 2.0 - - - +
118C PHE* 3.5 36.3 - - + -
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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