Contacts of the helix formed by residues 589 - 599 (chain K) in PDB entry 6D6Q
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 THR 589 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478K VAL* 4.9 2.2 - - - -
479K ASP* 3.2 11.4 - - - +
480K PRO 4.5 9.2 - - - +
481K PRO* 4.7 13.0 - - + -
587K SER 5.3 1.6 - - - +
588K LEU* 1.3 79.7 - - - +
590K TYR* 1.3 55.2 + - - +
591K ALA* 4.0 4.5 + - - +
592K GLU* 2.9 34.0 + - - +
593K ALA* 2.4 39.8 + - - +
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Residues in contact with TYR 590 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478K VAL* 3.6 19.9 + - + +
479K ASP* 4.0 1.7 + - - -
480K PRO* 3.4 43.1 - - + +
481K PRO* 4.6 5.5 - - + +
589K THR* 1.3 72.8 - - - +
591K ALA* 1.3 58.6 + - - +
593K ALA* 3.3 6.7 + - - +
594K GLN* 2.9 28.9 + - - +
657K ARG* 3.6 20.0 + - + +
659K THR* 3.6 22.5 + - + -
660K ASN* 3.8 40.7 + - + -
663K VAL* 4.5 7.0 - - + +
61O A 3.8 27.6 + - - -
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Residues in contact with ALA 591 (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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589K THR* 3.2 4.3 + - - +
590K TYR* 1.3 76.7 - - - +
592K GLU* 1.3 66.0 + - - +
594K GLN* 3.2 4.4 + - - +
595K LEU* 2.9 31.7 + - + +
657K ARG* 3.0 23.4 - - - +
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Residues in contact with GLU 592 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587K SER 4.8 1.7 - - - +
588K LEU* 3.2 31.9 - - + +
589K THR* 2.9 34.8 + - - +
591K ALA* 1.3 78.0 - - - +
593K ALA* 1.3 57.6 + - - +
595K LEU* 3.2 17.0 - - + +
596K ARG* 2.9 49.4 + - + +
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Residues in contact with ALA 593 (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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478K VAL* 4.7 10.5 - - + -
588K LEU* 4.5 15.9 - - + +
589K THR 2.4 28.0 + - - +
590K TYR* 3.3 9.6 - - - +
592K GLU* 1.3 74.9 - - - +
594K GLN* 1.3 57.7 + - - +
596K ARG* 3.3 2.5 + - - +
597K ILE* 2.9 38.6 + - + +
610K LEU* 5.0 3.8 - - + -
659K THR* 3.8 23.1 - - + +
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Residues in contact with GLN 594 (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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590K TYR 2.9 17.0 + - - +
591K ALA* 3.2 5.2 + - - +
593K ALA* 1.3 75.8 - - - +
595K LEU* 1.3 60.4 + - - +
597K ILE* 3.2 12.1 + - + +
598K ASP* 2.5 72.1 + - - +
657K ARG* 3.8 31.0 + - + +
658K GLU* 5.6 9.2 - - + +
659K THR* 4.2 3.1 + - - +
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Residues in contact with LEU 595 (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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591K ALA* 2.9 22.5 + - + +
592K GLU* 3.2 25.8 - - + +
594K GLN* 1.3 82.5 + - - +
596K ARG* 1.3 79.2 + - + +
598K ASP* 4.1 2.9 - - - -
599K SER* 2.3 50.7 + - - +
601K ASN* 5.4 1.6 - - - +
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Residues in contact with ARG 596 (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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588K LEU* 3.7 30.8 - - - +
592K GLU* 2.9 32.4 + - + +
593K ALA 3.7 3.4 - - - +
595K LEU* 1.3 85.8 - - + +
597K ILE* 1.3 57.9 + - - +
601K ASN* 2.6 38.1 - - - +
603K ASN* 3.6 23.4 - - - +
606K ILE* 3.3 42.1 - - - +
607K THR* 3.0 19.4 + - - +
610K LEU* 4.1 8.7 - - + -
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Residues in contact with ILE 597 (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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593K ALA* 2.9 33.8 + - + +
594K GLN* 3.4 10.5 - - + +
595K LEU 3.1 0.2 - - - -
596K ARG* 1.3 75.5 - - - +
598K ASP* 1.3 67.2 + - + +
607K THR* 4.3 4.5 - - - -
610K LEU* 3.6 22.4 - - + -
611K ARG* 2.4 56.5 + - + -
614K ASN* 2.9 41.7 - - + +
658K GLU* 5.4 8.7 - - + +
659K THR* 3.8 15.5 - - + +
662K MET* 5.8 0.4 - - + -
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Residues in contact with ASP 598 (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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594K GLN* 2.5 55.0 + - - +
595K LEU* 4.1 1.6 - - - -
597K ILE* 1.3 83.3 - - + +
599K SER* 1.3 54.6 + - - +
600K ALA 3.3 7.1 + - - +
611K ARG* 4.4 2.7 - - - +
658K GLU* 5.4 5.1 - - - +
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Residues in contact with SER 599 (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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595K LEU* 2.3 38.4 + - - +
597K ILE 3.6 1.2 - - - -
598K ASP* 1.3 77.0 - - - +
600K ALA* 1.3 62.3 + - - +
601K ASN* 3.1 28.0 + - - +
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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