Contacts of the helix formed by residues 601 - 607 (chain A) in PDB entry 2VF8
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 ASN 601 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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594A ILE* 4.2 5.4 - - - -
598A PRO 4.7 1.3 - - - +
599A ARG 4.6 0.9 - - - +
600A SER* 1.3 79.1 + - - +
602A MET* 1.3 65.0 + - - +
603A ALA* 2.9 14.6 + - - +
604A THR* 3.1 32.8 + - - +
605A TYR* 3.1 21.9 + - - +
609A PHE* 5.7 0.8 - - - -
634A PHE* 3.6 22.6 - - - -
671A ARG* 5.1 0.7 - - - +
690A LEU* 4.4 1.4 - - - +
724A LEU 2.3 30.0 - - - +
725A GLY* 3.3 18.0 - - - +
726A GLN 3.3 18.2 - - - +
727A PRO* 3.9 1.6 - - + -
728A ALA* 3.9 8.7 - - - +
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Residues in contact with MET 602 (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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594A ILE* 4.2 11.2 - - + +
601A ASN* 1.3 77.1 + - - +
603A ALA* 1.3 60.7 + - - +
605A TYR* 3.7 1.1 + - - +
606A THR* 3.1 27.9 + - + +
608A LEU* 4.4 4.9 - - + -
694A VAL* 4.1 8.3 - - + -
714A LEU* 4.0 31.0 - - + -
719A LEU* 5.4 0.7 - - - -
722A LEU* 4.5 15.5 - - - -
723A ARG 4.2 11.7 - - - +
724A LEU* 3.5 43.9 + - + +
726A GLN 3.7 7.0 + - - +
731A LEU* 5.0 6.3 - - + -
739A ILE* 3.3 33.0 - - + -
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Residues in contact with ALA 603 (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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601A ASN* 2.9 13.1 + - - +
602A MET* 1.3 74.8 - - - +
604A THR* 1.3 66.4 + - - +
605A TYR 2.9 2.3 + - - -
606A THR* 3.2 10.2 + - - -
608A LEU* 3.3 27.3 + - + -
609A PHE* 3.4 30.4 + - + +
690A LEU* 4.5 3.8 - - + -
724A LEU* 3.1 27.4 + - + +
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Residues in contact with THR 604 (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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599A ARG 4.2 0.7 + - - -
600A SER* 4.1 22.4 - - - -
601A ASN* 3.1 32.1 + - - +
603A ALA* 1.3 77.9 - - - +
605A TYR* 1.3 68.8 + - + +
606A THR 3.5 0.2 + - - -
607A GLY* 3.6 7.6 + - - -
609A PHE* 3.9 15.9 - - - +
610A ASP* 4.6 5.8 - - - +
634A PHE* 4.1 10.0 - - - -
635A ASN* 4.3 7.4 + - - +
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Residues in contact with TYR 605 (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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594A ILE* 3.6 48.9 - - + -
600A SER* 5.8 1.1 - - - +
601A ASN 3.1 13.4 + - - +
602A MET 4.1 4.0 - - - +
603A ALA 2.9 0.8 + - - -
604A THR* 1.3 87.5 - - + +
606A THR* 1.3 65.2 + - - +
607A GLY 3.4 0.7 + - - -
739A ILE* 3.4 30.5 - - + -
740A LYS* 3.3 34.4 - - + +
743A THR* 4.4 7.7 + - + -
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Residues in contact with THR 606 (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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602A MET* 3.1 19.5 - - + +
603A ALA 3.2 1.0 + - - -
605A TYR* 1.3 80.9 - - - +
607A GLY* 1.3 56.4 + - - +
608A LEU* 3.0 31.0 + - + +
710A ALA* 5.4 5.2 - - - +
714A LEU* 4.1 26.1 - - + +
739A ILE* 4.2 18.6 - - + +
742A ALA* 5.9 0.7 - - + -
743A THR* 4.6 18.2 + - - +
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Residues in contact with GLY 607 (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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603A ALA 3.6 1.8 + - - -
604A THR 3.6 3.5 + - - -
605A TYR 3.2 4.6 + - - -
606A THR* 1.3 77.5 - - - +
608A LEU* 1.3 65.0 + - - +
609A PHE 3.1 3.2 + - - -
610A ASP* 3.4 24.7 + - - +
611A GLN* 3.5 22.8 + - - -
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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