Contacts of the helix formed by residues 579 - 588 (chain K) in PDB entry 6R1U
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 TYR 579 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421K VAL* 3.5 22.4 - - + -
423K ASP* 3.2 4.0 + - - -
436K ALA* 3.5 34.2 + - + +
437K GLN* 3.6 21.5 - - - -
438K ILE 2.7 28.9 + - - -
439K VAL* 3.3 18.1 - - + +
447K VAL* 3.9 18.9 - - + +
575K LEU* 3.5 19.7 - - + +
578K GLY* 1.3 70.3 - - - -
580K SER* 1.3 64.3 + - - +
581K VAL 3.1 0.2 - - - -
582K ILE* 3.0 26.7 + - + +
583K ILE* 3.0 13.5 + - + +
805K VAL* 3.6 34.7 - - + +
806K THR* 5.0 2.1 + - - -
901K FAD 3.9 5.7 + - - -
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Residues in contact with SER 580 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421K VAL* 3.7 12.6 - - - +
422K TRP* 5.8 0.2 - - - -
423K ASP* 2.7 34.1 + - - -
425K LYS* 3.0 29.3 + - - -
577K PRO 4.4 1.0 + - - -
579K TYR* 1.3 78.8 - - - +
581K VAL* 1.3 52.3 + - - +
583K ILE* 4.0 2.5 - - - -
584K GLU* 2.6 53.1 + - - +
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Residues in contact with VAL 581 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425K LYS* 4.9 5.4 - - - +
454K LEU* 4.4 4.9 - - + +
456K ILE* 3.3 32.5 - - + -
575K LEU* 5.7 1.6 - - + -
577K PRO* 3.8 28.0 - - + +
578K GLY 3.2 13.2 + - - +
580K SER* 1.3 79.5 + - - +
582K ILE* 1.3 73.0 + - + +
584K GLU* 3.6 8.4 + - - +
585K LYS* 3.2 24.6 + - - +
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Residues in contact with ILE 582 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366K VAL* 4.0 3.1 - - + +
447K VAL* 3.9 31.2 - - + +
450K MET* 3.7 45.5 - - + -
451K CYS* 4.5 5.8 - - - -
454K LEU* 4.0 21.5 - - + -
456K ILE* 5.2 1.3 - - + -
575K LEU* 4.2 14.4 - - + -
579K TYR* 3.0 14.9 + - + +
581K VAL* 1.3 87.2 - - + +
583K ILE* 1.3 69.1 + - + +
585K LYS* 3.2 4.5 + - - +
586K LEU* 2.9 31.3 + - + +
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Residues in contact with ILE 583 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391K GLY 4.8 0.2 - - - -
392K PRO* 4.2 32.5 - - + -
395K LEU* 3.7 26.8 - - + +
417K ILE* 3.9 16.2 - - + -
418K GLY* 4.0 10.8 - - - -
421K VAL* 3.6 24.2 - - + -
579K TYR* 3.0 16.9 + - + +
580K SER* 3.5 9.0 - - - +
582K ILE* 1.3 77.1 - - + +
584K GLU* 1.3 76.9 + - - +
586K LEU* 3.1 14.2 + - + +
587K ALA* 3.1 21.3 + - - +
805K VAL* 5.7 2.7 - - + -
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Residues in contact with GLU 584 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417K ILE* 4.3 16.3 - - - +
425K LYS* 6.3 2.5 - - - -
580K SER* 2.6 48.2 + - - +
581K VAL* 3.8 7.9 - - - +
583K ILE* 1.3 85.7 - - - +
585K LYS* 1.3 59.8 - - + +
587K ALA* 3.3 2.1 + - - +
588K GLU* 3.0 34.2 + - + +
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Residues in contact with LYS 585 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366K VAL* 3.8 31.3 + - + +
368K SER* 5.6 7.7 - - - -
399K ARG* 3.9 7.6 + - - -
454K LEU* 3.7 32.2 - - + +
581K VAL 3.2 15.1 + - - +
582K ILE* 3.2 4.7 + - - +
583K ILE 3.1 0.4 - - - -
584K GLU* 1.3 79.7 - - + +
586K LEU* 1.3 65.3 + - - +
588K GLU* 3.6 22.0 + - + +
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Residues in contact with LEU 586 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365K GLY 3.6 25.8 - - - +
366K VAL* 4.0 12.3 - - + -
392K PRO* 5.0 3.4 - - + +
395K LEU* 4.2 25.1 - - + +
396K ALA* 4.7 3.4 - - - +
399K ARG* 2.7 51.0 + - + +
450K MET* 4.3 3.1 - - + -
582K ILE* 2.9 32.0 + - + +
583K ILE* 3.1 15.7 + - + +
585K LYS* 1.3 76.3 - - - +
587K ALA* 1.3 57.0 + - - +
590K LEU* 3.3 8.8 - - - +
809K TYR* 4.3 25.6 - - + -
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Residues in contact with ALA 587 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395K LEU* 3.9 8.5 - - + -
417K ILE* 3.5 32.5 - - + -
583K ILE 3.1 9.6 + - - +
584K GLU 3.9 2.5 - - - +
586K LEU* 1.3 76.6 - - - +
588K GLU* 1.3 66.4 + - - +
589K GLY 3.0 0.5 + - - -
590K LEU* 3.0 29.4 + - - +
592K ILE* 3.6 20.1 - - + +
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Residues in contact with GLU 588 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368K SER* 5.0 3.1 + - - -
399K ARG* 3.2 21.8 + - - -
584K GLU* 3.0 20.5 + - + +
585K LYS* 3.7 20.0 - - + +
586K LEU 3.3 1.6 - - - -
587K ALA* 1.3 75.2 - - - +
589K GLY* 1.3 63.6 + - - +
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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