Contacts of the helix formed by residues 565 - 570 (chain A) in PDB entry 2VGL
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 SER 565 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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561A ASP 3.4 20.6 + - - -
562A VAL* 3.7 13.7 - - - -
563A LEU 3.3 2.2 - - - +
564A ARG* 1.3 83.5 - - - +
566A ASP* 1.3 70.9 + - - +
567A SER* 3.4 17.5 + - - -
568A GLN* 3.5 3.9 + - - -
569A LEU* 3.4 17.7 + - - +
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Residues in contact with ASP 566 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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564A ARG 4.7 1.7 - - - +
565A SER* 1.3 80.5 + - - +
567A SER* 1.3 58.2 + - - +
569A LEU* 5.4 0.4 - - - -
570A LYS* 2.9 62.4 + - + +
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Residues in contact with SER 567 (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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531A HIS* 4.1 21.6 + - - -
565A SER* 3.4 9.1 + - - -
566A ASP* 1.3 76.9 - - - +
568A GLN* 1.3 75.2 + - - +
570A LYS 5.3 1.1 - - - -
571A ASN* 2.5 37.9 + - - +
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Residues in contact with GLN 568 (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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527A HIS* 5.0 0.2 + - - -
530A PHE* 3.7 25.6 - - + -
531A HIS* 4.2 8.0 + - - -
538A ARG* 6.0 0.6 - - - +
542A LEU* 3.7 28.8 - - + +
562A VAL* 2.9 50.3 - - + +
563A LEU 3.7 5.2 - - - +
565A SER* 3.5 3.2 + - - +
566A ASP 3.2 0.6 - - - -
567A SER* 1.3 102.7 + - - +
569A LEU* 1.3 62.4 + - - +
571A ASN* 3.5 13.2 - - - +
576A LEU* 3.1 26.0 - - - +
577A GLN* 3.5 0.2 - - - -
580A ALA* 3.1 13.5 - - + +
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Residues in contact with LEU 569 (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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563A LEU 3.1 20.9 - - - +
564A ARG* 3.1 29.6 - - + +
565A SER 3.4 6.5 + - - +
566A ASP* 5.4 0.4 - - - -
568A GLN* 1.3 73.4 - - - +
570A LYS* 1.3 61.2 + - + +
571A ASN 2.8 14.9 + - - -
577A GLN* 3.0 28.5 - - - +
580A ALA* 3.3 17.5 - - - +
581A VAL* 3.2 32.8 - - + +
584A LEU* 5.1 6.5 - - + -
546B PRO* 3.9 28.9 - - + +
548B ILE* 4.9 0.7 - - - +
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Residues in contact with LYS 570 (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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566A ASP* 2.9 46.2 + - + +
567A SER* 5.4 0.7 - - - -
569A LEU* 1.3 72.1 - - + +
571A ASN* 1.3 59.7 + - - +
546B PRO* 4.1 17.9 - - + +
547B LEU 3.7 23.2 + - - +
548B ILE* 3.2 35.8 - - + +
549B SER* 4.2 19.7 - - - +
551B GLU* 3.5 17.5 - - + +
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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