Contacts of the helix formed by residues 397 - 404 (chain A) in PDB entry 2VQO
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 397 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A ARG* 5.0 1.3 - - - -
361A LEU 3.6 4.6 + - - -
362A GLN* 3.3 26.9 + - - -
363A GLN 3.2 26.2 - - - -
364A ARG* 3.9 3.2 - - - +
365A PRO* 4.5 0.2 - - - -
395A GLY 3.9 1.2 + - - -
396A ARG* 1.3 77.1 - - - +
398A LEU* 1.3 65.4 + - - +
399A ILE* 3.8 1.2 + - - +
400A GLU* 3.1 35.8 + - - +
401A ALA* 3.0 20.7 + - - +
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Residues in contact with LEU 398 (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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264A LEU* 3.6 49.1 - - + +
265A ALA* 5.7 0.7 - - - +
268A ARG* 4.2 24.2 - - + +
315A GLN* 6.3 1.3 - - - +
356A LEU* 5.2 1.3 - - + -
360A VAL 5.3 1.7 + - - +
361A LEU* 3.3 35.6 + - + +
363A GLN 4.6 1.0 + - - -
397A SER* 1.3 73.7 - - - +
399A ILE* 1.3 63.9 + - + +
401A ALA* 3.2 6.1 + - - +
402A GLN* 3.0 23.8 + - - +
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Residues in contact with ILE 399 (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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358A GLU* 4.4 8.7 - - - +
361A LEU* 3.3 29.2 + - + +
362A GLN* 3.4 41.7 - - + +
397A SER* 4.4 2.7 - - - +
398A LEU* 1.3 75.5 - - + +
400A GLU* 1.3 61.9 + - + +
402A GLN* 3.3 19.1 + - - +
403A THR* 2.8 43.9 + - - +
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Residues in contact with GLU 400 (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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362A GLN 5.7 0.7 - - - -
364A ARG* 3.1 43.7 + - - +
396A ARG* 3.5 20.5 - - + +
397A SER* 3.1 33.6 + - - +
398A LEU 3.3 0.2 - - - -
399A ILE* 1.3 79.1 - - + +
401A ALA* 1.3 58.1 + - - +
403A THR* 3.4 5.9 + - - -
404A CYS* 2.9 38.5 + - - -
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Residues in contact with ALA 401 (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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268A ARG* 3.5 43.5 - - - +
393A THR* 6.2 0.2 - - - -
396A ARG* 4.0 11.8 - - + +
397A SER 3.0 17.7 + - - +
398A LEU* 3.5 4.9 - - + +
400A GLU* 1.3 76.0 - - - +
402A GLN* 1.3 61.5 + - - +
404A CYS* 3.4 18.7 - - - +
405A GLU* 3.7 5.4 - - - +
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Residues in contact with GLN 402 (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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398A LEU 3.0 12.6 + - - +
399A ILE* 3.6 25.1 + - - +
401A ALA* 1.3 75.5 - - - +
403A THR* 1.3 69.2 + - - +
405A GLU* 3.2 24.6 - - - +
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Residues in contact with THR 403 (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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399A ILE* 2.8 35.8 + - - +
400A GLU* 3.7 7.4 - - - -
402A GLN* 1.3 77.1 + - - +
404A CYS* 1.3 62.7 + - - +
405A GLU 3.1 10.6 + - - +
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Residues in contact with CYS 404 (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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396A ARG* 3.7 38.7 + - - +
400A GLU* 2.9 24.2 + - - +
401A ALA 3.4 7.1 - - - +
402A GLN 3.2 0.2 - - - +
403A THR* 1.3 79.1 - - - +
405A GLU* 1.3 62.1 + - - +
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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