Contacts of the helix formed by residues 590 - 594 (chain C) in PDB entry 6DV9
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 590 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446C LEU* 3.8 25.9 - - + +
450C THR* 4.0 2.9 + - - +
487C GLU* 3.3 29.2 - - - +
588C SER* 3.5 2.8 + - - -
589C VAL* 1.3 78.0 - - - +
591C THR* 1.3 63.5 + - - +
593C MET* 3.2 17.4 + - - +
594C ILE* 4.2 0.2 - - - +
609C ALA* 4.1 14.4 - - + +
612C GLN* 3.1 23.4 + - - -
613C ARG* 4.8 0.4 - - - -
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Residues in contact with THR 591 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484C CYS* 3.2 16.8 - - - -
486C ILE* 3.6 32.5 - - + -
487C GLU* 3.5 17.0 + - - +
587C VAL* 3.9 8.3 - - + -
588C SER* 3.4 15.4 + - - -
589C VAL 3.3 0.4 - - - -
590C ALA* 1.3 77.9 - - - +
592C ALA* 1.3 58.8 + - - +
593C MET 3.0 5.0 + - - -
594C ILE* 3.3 15.6 + - + +
597C LEU* 3.6 34.4 - - + +
609C ALA* 4.0 8.4 - - + +
976C VAL* 4.1 0.3 - - - +
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Residues in contact with ALA 592 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502C VAL* 4.6 2.5 - - + -
584C ARG* 4.9 7.8 + - + -
587C VAL* 3.7 13.9 - - + +
588C SER 2.8 19.5 + - - +
589C VAL 3.7 6.5 - - - +
590C ALA 3.3 0.6 - - - -
591C THR* 1.3 75.1 - - - +
593C MET* 1.3 56.3 + - - +
594C ILE 3.4 0.7 - - - -
628C THR* 2.9 26.9 + - - +
630C MET* 4.0 24.9 - - + +
976C VAL* 3.5 18.4 - - + +
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Residues in contact with MET 593 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C LEU* 3.5 35.9 - - + -
589C VAL* 3.2 25.4 + - + +
590C ALA* 3.2 11.1 + - - +
591C THR 3.0 1.8 - - - -
592C ALA* 1.3 76.4 - - - +
594C ILE* 1.3 59.4 + - - +
595C PRO* 3.2 12.5 - - - +
612C GLN* 3.6 17.3 - - - +
628C THR* 3.5 19.8 - - + +
630C MET* 4.2 8.3 - - + -
631C GLU* 4.1 14.3 - - + +
634C ALA* 4.0 17.3 - - + -
713C MET* 4.2 28.7 - - - -
715C LEU* 5.1 1.1 - - - -
888C ARG* 3.7 14.4 + - - -
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Residues in contact with ILE 594 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591C THR* 3.3 16.6 + - + +
592C ALA 3.4 0.4 - - - -
593C MET* 1.3 76.7 - - - +
595C PRO* 1.3 67.4 - - + +
597C LEU* 3.3 34.9 + - + +
600C ASP* 3.9 7.6 - - - +
605C ALA* 3.7 14.6 - - - +
608C GLY* 4.1 0.2 - - - -
609C ALA* 3.7 29.2 - - + +
612C GLN* 3.8 16.6 - - - +
628C THR* 5.1 0.7 - - - -
888C ARG* 3.2 31.6 - - + +
889C HIS* 3.7 22.7 - - + +
976C VAL* 3.7 9.7 - - - +
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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