Contacts of the helix formed by residues 412 - 419 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B ASP* 3.1 10.2 + - - +
411B PRO* 1.3 97.8 - - + +
413B ARG* 1.3 64.7 + - - +
414B ALA* 3.1 4.2 + - - -
415B GLY 3.1 4.1 + - - +
416B LYS* 2.9 29.0 + - - +
390E LYS* 6.1 0.2 - - - +
393E ASP* 3.0 31.4 + - - -
396E HIS* 3.4 21.6 - - + +
397E GLU* 3.0 64.4 + - - +
400E GLN* 4.0 18.1 - - + +
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Residues in contact with ARG 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B MET* 2.8 42.9 + - + +
360B LYS* 3.3 11.9 + - - +
362B GLU* 4.2 0.2 + - - -
365B GLU* 2.9 36.1 + - - +
403B GLU* 3.3 22.7 - - + +
407B HIS* 3.2 42.0 + - + -
409B GLU* 4.7 1.4 + - - -
410B ASP* 3.1 39.3 + - - +
411B PRO 3.6 0.4 - - - -
412B ARG* 1.3 76.3 - - - +
414B ALA* 1.3 56.5 + - - +
416B LYS* 3.3 6.8 + - - +
417B MET* 2.9 36.4 + - + +
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Residues in contact with ALA 414 (chain B).
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* 5.6 0.7 - - - +
399B LEU* 4.1 9.7 - - + +
400B GLN* 3.8 38.8 - - + +
403B GLU* 3.7 27.5 - - + +
411B PRO 5.3 1.7 + - - +
412B ARG 3.1 1.6 + - - -
413B ARG* 1.3 77.1 - - - +
415B GLY* 1.3 59.3 + - - +
417B MET* 3.2 9.7 - - - +
418B LEU* 3.0 33.2 + - + +
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Residues in contact with GLY 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400B GLN* 5.3 1.2 - - - +
412B ARG* 3.1 4.0 + - - +
414B ALA* 1.3 77.2 - - - +
416B LYS* 1.3 53.0 + - - +
418B LEU* 3.0 10.6 + - - +
419B MET* 2.8 39.7 + - - +
396E HIS* 3.5 25.1 - - - -
400E GLN* 5.9 1.4 - - - +
415E GLY* 5.8 0.7 - - - -
418E LEU* 3.8 11.4 - - - -
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Residues in contact with LYS 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B MET* 3.5 23.4 - - + +
410B ASP* 3.1 39.6 + - - +
412B ARG* 2.9 16.9 + - - +
413B ARG* 3.4 7.6 - - - +
415B GLY* 1.3 74.6 - - - +
417B MET* 1.3 64.1 + - - +
419B MET* 3.1 23.4 + - - +
420B THR* 3.5 11.1 + - - +
389E GLN* 4.5 15.2 - - - +
393E ASP* 3.0 31.9 + - - +
396E HIS* 3.6 9.5 - - - +
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Residues in contact with MET 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B TYR* 4.5 6.7 - - - -
359B MET* 3.6 28.9 - - + -
361B LEU* 3.4 32.1 - - + -
365B GLU* 3.1 30.1 - - + +
369B LEU* 3.9 27.0 - - + +
399B LEU* 4.4 11.7 - - + -
403B GLU* 4.4 7.4 - - - +
413B ARG* 2.9 31.6 + - + +
414B ALA* 3.2 10.8 - - - +
416B LYS* 1.3 76.5 - - - +
418B LEU* 1.3 61.2 + - - +
420B THR* 2.8 27.1 + - - -
421B LEU* 4.2 0.9 + - - +
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Residues in contact with LEU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B LEU* 5.0 2.2 - - + -
372B ILE* 4.4 19.5 - - + -
396B HIS* 3.6 30.3 - - + +
399B LEU* 4.5 7.0 - - + -
414B ALA* 3.0 17.9 + - + +
415B GLY* 3.0 14.3 + - - +
417B MET* 1.3 77.7 - - - +
419B MET* 1.3 56.4 + - - +
420B THR 3.2 4.3 + - - -
421B LEU* 3.3 35.2 + - + +
422B PRO* 3.9 3.3 - - - +
415E GLY* 3.7 25.6 - - - +
418E LEU* 4.5 18.1 - - + +
419E MET* 3.7 28.7 - - + +
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Residues in contact with MET 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B LYS* 3.4 6.4 + - - +
415B GLY 2.8 14.7 + - - +
416B LYS* 3.1 15.6 + - - +
418B LEU* 1.3 76.1 - - - +
420B THR* 1.3 56.9 + - - +
421B LEU 3.5 0.7 - - - -
422B PRO* 3.7 5.1 - - - +
372E ILE* 4.3 11.9 - - + -
376E ASN* 2.8 65.9 + - + +
378E ASP* 4.9 0.3 - - - +
392E GLN* 3.4 26.7 - - + +
396E HIS* 4.2 29.4 - - - -
418E LEU* 3.9 29.2 - - + -
421E LEU* 5.3 3.1 - - + -
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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