Contacts of the helix formed by residues 592 - 604 (chain C) in PDB entry 6VVT
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 ASP 592 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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590C HIS 3.9 1.0 + - - -
591C ASP* 1.3 74.9 - - - +
593C ALA* 1.3 68.5 + - - +
594C ASN* 3.7 25.2 + - - +
595C ARG* 3.0 17.7 + - + +
596C ALA* 2.8 26.5 + - - +
916C ARG 5.6 5.6 - - - +
918C ASN* 6.0 1.2 - - - +
839D PHE* 3.9 24.2 - - + -
848D TYR* 3.2 0.7 - - - -
851D ASN* 3.7 19.6 + - - -
855D ALA* 5.1 2.3 - - - +
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Residues in contact with ALA 593 (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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477C ILE* 4.1 7.4 - - + +
592C ASP* 1.3 78.1 + - - +
594C ASN* 1.3 56.3 + - - +
596C ALA* 3.7 2.4 - - - +
597C LEU* 2.8 33.5 + - - +
848D TYR* 3.1 19.5 + - + +
851D ASN* 4.8 4.9 - - + +
852D THR* 4.3 24.5 - - + -
855D ALA* 4.2 21.5 - - + -
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Residues in contact with ASN 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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592C ASP* 3.1 17.2 + - - +
593C ALA* 1.3 77.8 - - - +
595C ARG* 1.3 67.5 + - - +
597C LEU* 3.4 4.7 + - - +
598C MET* 2.8 32.7 + - - +
855D ALA* 3.7 23.8 - - - +
859D LEU* 3.6 35.1 - - + +
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Residues in contact with ARG 595 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591C ASP* 4.6 8.3 - - + -
592C ASP* 3.0 22.1 + - + +
594C ASN* 1.3 80.1 - - - +
596C ALA* 1.3 54.9 + - - +
598C MET* 3.2 25.9 + - - +
599C GLY* 2.5 34.5 + - - -
880C HIS 3.1 26.9 + - - +
881C GLY 3.9 14.1 + - - -
882C ASN* 4.3 4.4 - - - +
883C LYS 5.2 0.8 - - - +
911C HIS* 3.1 36.4 + - - -
916C ARG 5.5 4.9 - - - +
918C ASN* 4.0 26.5 - - + +
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Residues in contact with ALA 596 (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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477C ILE* 3.5 19.0 - - + +
585C ILE* 3.5 13.6 - - - +
588C LEU* 3.5 31.6 - - + -
591C ASP* 4.6 7.0 - - + +
592C ASP 2.8 16.3 + - - +
593C ALA 3.7 0.7 - - - +
595C ARG* 1.3 77.1 - - - +
597C LEU* 1.3 62.7 + - - +
599C GLY 3.1 0.7 + - - +
600C ALA* 2.9 23.2 + - - +
880C HIS* 5.4 0.9 - - - +
848D TYR* 3.6 7.2 - - - +
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Residues in contact with LEU 597 (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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476C PRO 5.5 0.7 - - - +
477C ILE* 2.9 26.1 + - + +
478C GLU* 4.1 1.1 - - - -
479C THR* 2.8 57.0 - - + +
480C PRO 4.8 3.1 - - - +
481C GLU* 5.2 6.5 - - + -
593C ALA 2.8 20.8 + - - +
594C ASN* 3.6 4.9 - - - +
596C ALA* 1.3 73.4 - - - +
598C MET* 1.3 63.9 + - - +
600C ALA* 3.3 1.8 + - - +
601C ASN* 3.0 36.3 + - - +
859D LEU* 4.7 19.7 - - + -
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Residues in contact with MET 598 (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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481C GLU* 3.1 39.4 - - + +
594C ASN* 2.8 20.0 + - - +
595C ARG* 3.4 32.5 - - - +
597C LEU* 1.3 73.3 - - - +
599C GLY* 1.3 62.0 + - - +
601C ASN* 3.3 1.7 + - - +
602C MET* 2.8 37.2 + - - +
881C GLY* 3.7 23.8 - - - +
537D ASP* 6.1 0.7 - - - +
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Residues in contact with GLY 599 (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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585C ILE* 4.1 1.8 - - - -
595C ARG 2.5 16.7 + - - -
596C ALA 3.1 1.7 + - - -
598C MET* 1.3 73.8 - - - +
600C ALA* 1.3 61.3 + - - +
602C MET* 3.3 2.4 + - - +
603C GLN* 2.9 28.2 + - - +
878C GLY 4.6 2.2 - - - -
879C ARG* 3.4 27.9 - - - +
881C GLY* 3.4 14.1 - - - -
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Residues in contact with ALA 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478C GLU* 4.4 10.5 - - + +
581C ALA* 4.1 16.8 - - + +
582C THR* 4.1 24.7 - - - +
585C ILE* 3.8 2.7 - - + +
596C ALA 2.9 15.6 + - - +
597C LEU* 3.8 6.3 - - - +
599C GLY* 1.3 75.4 - - - +
601C ASN* 1.3 67.8 + - - +
603C GLN* 3.2 23.4 + - - +
604C ARG* 3.4 16.7 + - - +
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Residues in contact with ASN 601 (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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478C GLU* 4.5 3.3 - - - +
479C THR 3.6 11.0 + - - +
480C PRO* 4.1 7.9 - - - +
481C GLU* 4.0 22.2 + - - +
597C LEU* 3.0 38.0 + - - +
598C MET* 3.7 5.6 - - - +
600C ALA* 1.3 77.1 - - - +
602C MET* 1.3 61.0 + - + +
604C ARG* 2.9 40.8 + - - +
605C GLN* 3.1 29.1 + - - +
1201C SRN 5.7 0.6 + - - -
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Residues in contact with MET 602 (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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481C GLU* 5.6 2.0 - - - +
598C MET* 2.8 32.1 + - + +
599C GLY 3.9 3.1 - - - +
600C ALA 3.2 0.2 - - - -
601C ASN* 1.3 76.3 - - + +
603C GLN* 1.3 64.5 + - - +
605C GLN* 3.0 24.9 + - - +
606C ALA 3.4 9.0 + - - -
875C LYS* 3.8 11.9 - - - +
877C ALA* 3.7 15.5 - - + -
878C GLY 4.7 6.1 - - - +
881C GLY* 3.7 26.9 - - - +
883C LYS* 3.2 23.6 - - + -
1022C LEU* 3.9 9.2 - - + +
1024C LEU* 3.1 41.6 - - + +
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Residues in contact with GLN 603 (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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435C ASN* 3.4 6.2 + - - -
437C LEU* 4.7 8.5 - - + -
581C ALA* 2.8 28.8 - - + +
584C MET* 3.7 30.4 + - - +
585C ILE* 3.8 11.4 - - - +
599C GLY 2.9 14.3 + - - +
600C ALA* 3.4 11.1 - - - +
602C MET* 1.3 78.3 - - - +
604C ARG* 1.3 59.0 + - - +
605C GLN 3.3 0.7 + - - -
606C ALA* 3.4 10.4 + - - +
706C LEU* 3.4 27.9 - - + +
879C ARG* 3.5 40.6 - - + +
1022C LEU* 3.8 12.3 - - + +
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Residues in contact with ARG 604 (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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432C ASP* 4.4 8.9 - - - +
434C ASN* 2.9 12.1 + - - +
435C ASN* 2.8 26.8 + - - +
437C LEU* 4.3 7.1 - - + +
438C SER* 3.5 21.1 - - - +
441C THR* 3.3 10.3 + - - +
445C ARG* 3.2 24.1 - - - +
478C GLU* 2.1 41.2 + - - +
581C ALA* 3.9 10.1 - - - +
600C ALA 3.4 8.5 + - - -
601C ASN* 2.9 56.5 + - - +
603C GLN* 1.3 74.5 - - - +
605C GLN* 1.3 58.9 + - + +
1201C SRN 3.4 23.6 + - - -
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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