Contacts of the helix formed by residues 412 - 419 (chain E) in PDB entry 2GPV
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 ARG 412 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B ASP* 4.1 10.8 + - - +
396B HIS* 3.3 34.2 - - + +
397B GLU* 3.5 61.9 + - - +
400B GLN* 4.4 14.7 - - + +
410E ASP* 2.9 11.4 + - - +
411E PRO* 1.3 104.4 - - + +
413E ARG* 1.3 65.9 + - - +
414E ALA 3.3 2.9 - - - -
415E GLY 3.2 4.7 + - - +
416E LYS* 2.9 30.0 + - - +
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Residues in contact with ARG 413 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359E MET* 2.9 38.8 + - + +
360E LYS* 3.2 10.9 + - - +
365E GLU* 2.8 36.0 + - - +
403E GLU* 3.1 23.2 + - + +
407E HIS* 3.6 33.2 + - + -
409E GLU* 5.0 0.2 - - - -
410E ASP* 3.0 38.2 + - - +
411E PRO 3.6 0.4 - - - -
412E ARG* 1.3 77.7 - - - +
414E ALA* 1.3 63.5 + - - +
416E LYS* 3.2 10.8 + - + +
417E MET* 3.0 37.0 + - + +
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Residues in contact with ALA 414 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396E HIS* 5.9 1.1 - - + +
399E LEU* 3.9 18.2 - - + +
400E GLN* 3.6 24.0 - - - +
403E GLU* 3.7 29.4 - - + +
411E PRO 5.4 0.2 + - - -
412E ARG* 3.3 0.8 - - - -
413E ARG* 1.3 77.3 - - - +
415E GLY* 1.3 63.4 + - - +
417E MET* 3.0 15.1 + - - +
418E LEU* 3.1 20.4 + - + +
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Residues in contact with GLY 415 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396B HIS* 3.4 24.0 - - - -
415B GLY* 5.8 0.9 - - - -
418B LEU* 3.7 15.0 - - - +
412E ARG* 3.2 5.3 + - - +
414E ALA* 1.3 79.0 - - - +
416E LYS* 1.3 61.7 + - - +
417E MET 3.2 0.5 + - - -
418E LEU* 3.3 9.7 + - - +
419E MET* 3.2 25.4 + - - +
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Residues in contact with LYS 416 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389B GLN* 3.7 17.7 - - - +
393B ASP* 3.2 33.9 + - - +
396B HIS* 3.8 8.0 - - - +
359E MET* 3.3 32.0 - - + +
410E ASP* 2.9 37.4 + - - +
412E ARG* 2.9 19.3 + - - +
413E ARG* 3.3 12.1 - - + +
415E GLY* 1.3 74.5 - - - +
417E MET* 1.3 63.2 + - - +
419E MET* 3.2 23.3 + - + +
420E THR* 3.5 5.7 - - - +
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Residues in contact with MET 417 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356E TYR* 4.7 1.6 - - - -
359E MET* 3.8 31.2 - - + +
361E LEU* 3.3 31.6 - - + -
365E GLU* 3.6 11.0 - - - +
369E LEU* 3.9 22.7 - - + +
399E LEU* 4.3 15.0 - - + -
403E GLU* 4.2 14.6 - - - +
413E ARG* 3.0 50.5 + - + +
414E ALA* 3.0 9.4 + - - +
416E LYS* 1.3 75.4 - - - +
418E LEU* 1.3 62.1 + - - +
419E MET 3.0 1.1 + - - -
420E THR* 2.9 27.2 + - - -
421E LEU 4.1 0.3 + - - -
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Residues in contact with LEU 418 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415B GLY* 3.8 25.1 - - - +
418B LEU* 4.5 18.5 - - + +
419B MET* 3.9 21.7 - - + -
422B PRO* 5.3 0.7 - - - +
369E LEU* 4.6 1.8 - - + -
372E ILE* 4.1 16.6 - - + -
396E HIS* 3.7 26.9 - - + +
399E LEU* 3.8 19.7 - - + -
414E ALA* 3.1 15.6 + - + +
415E GLY* 3.3 12.5 + - - +
417E MET* 1.3 78.7 - - - +
419E MET* 1.3 59.2 - - - +
420E THR 3.3 0.2 - - - -
421E LEU* 3.5 35.2 + - + +
422E PRO* 3.9 3.6 - - - +
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Residues in contact with MET 419 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B ILE* 4.1 11.9 - - + -
376B ASN* 3.3 53.6 + - + +
378B ASP* 4.6 0.3 - - - +
392B GLN* 4.0 30.1 - - + +
396B HIS* 4.5 17.5 - - + -
418B LEU* 3.7 35.2 - - + -
421B LEU* 4.7 5.4 - - + -
355E LYS* 3.6 5.9 + - - -
415E GLY 3.2 13.2 + - - +
416E LYS* 3.2 15.9 + - + +
417E MET 3.0 1.4 - - - -
418E LEU* 1.3 74.9 - - - +
420E THR* 1.3 60.7 + - - +
421E LEU 3.2 2.5 - - - -
422E PRO* 3.2 16.1 - - - +
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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