Contacts of the helix formed by residues 412 - 419 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393C ASP* 4.4 11.9 + - - +
396C HIS* 3.4 33.0 - - + +
397C GLU* 3.8 54.2 + - - +
400C GLN* 4.8 16.0 - - + +
410F ASP* 2.9 12.2 + - - +
411F PRO* 1.3 106.4 - - - +
413F ARG* 1.3 64.2 + - - +
414F ALA 3.3 2.7 - - - -
415F GLY 3.1 4.9 + - - +
416F LYS* 2.9 34.1 + - - +
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Residues in contact with ARG 413 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359F MET* 2.7 43.1 + - + +
360F LYS* 3.3 10.5 + - - +
365F GLU* 3.0 36.4 + - - +
403F GLU* 3.2 24.6 + - + +
407F HIS* 3.5 35.8 + - + -
409F GLU* 4.7 4.6 + - - -
410F ASP* 3.1 33.5 + - - +
411F PRO 3.6 0.4 - - - -
412F ARG* 1.3 75.6 - - - +
414F ALA* 1.3 52.9 + - - +
416F LYS* 3.0 9.2 + - + +
417F MET* 2.8 44.7 + - + +
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Residues in contact with ALA 414 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399F LEU* 4.0 9.0 - - + +
400F GLN* 3.4 43.3 - - - +
403F GLU* 3.9 24.6 - - + +
411F PRO 5.1 1.7 + - - +
412F ARG 5.1 0.2 - - - -
413F ARG* 1.3 77.8 - - - +
415F GLY* 1.3 62.7 + - - +
417F MET* 3.0 9.5 + - - +
418F LEU* 3.0 27.5 + - + +
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Residues in contact with GLY 415 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396C HIS* 3.5 26.4 - - - -
400C GLN* 6.0 1.3 - - - +
415C GLY* 6.0 0.4 - - - -
418C LEU* 3.9 12.1 - - - +
412F ARG* 3.1 5.5 + - - +
414F ALA* 1.3 77.8 - - - +
416F LYS* 1.3 62.0 + - - +
417F MET 3.1 0.2 + - - -
418F LEU* 3.1 9.4 + - - +
419F MET* 2.9 27.7 + - - +
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Residues in contact with LYS 416 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389C GLN* 4.6 9.4 - - - +
393C ASP* 3.5 32.5 + - - +
396C HIS* 3.8 8.7 - - - +
359F MET* 3.4 22.5 - - + +
410F ASP* 2.2 46.7 + - - +
412F ARG* 2.9 27.3 + - - +
413F ARG* 3.0 9.4 + - + +
415F GLY* 1.3 76.6 - - - +
417F MET* 1.3 62.7 + - - +
419F MET* 3.5 15.6 + - - +
420F THR* 3.4 18.0 + - - +
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Residues in contact with MET 417 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356F TYR* 4.8 2.5 - - - -
359F MET* 3.5 32.1 - - + +
361F LEU* 3.6 30.5 - - + -
365F GLU* 3.1 29.6 - - + +
369F LEU* 4.1 22.5 - - + +
399F LEU* 4.1 19.3 - - + -
403F GLU* 4.2 9.2 - - - +
413F ARG* 2.8 32.9 + - + +
414F ALA 3.0 8.9 + - - +
416F LYS* 1.3 73.9 - - - +
418F LEU* 1.3 62.6 + - - +
420F THR* 2.5 28.9 + - - -
421F LEU 4.2 0.2 + - - -
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Residues in contact with LEU 418 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415C GLY* 3.7 31.4 - - - +
418C LEU* 4.6 17.3 - - + +
419C MET* 3.7 28.8 - - + -
422C PRO* 5.4 0.3 - - - +
369F LEU* 4.9 1.1 - - + -
372F ILE* 4.4 12.3 - - + -
396F HIS* 3.7 16.8 - - + +
399F LEU* 4.1 17.5 - - + -
400F GLN* 5.0 1.3 - - - +
414F ALA 3.0 22.9 + - - +
415F GLY* 3.7 9.6 - - - +
417F MET* 1.3 77.2 - - - +
419F MET* 1.3 56.1 + - - +
420F THR 3.2 0.7 - - - -
421F LEU* 3.2 40.8 + - + +
422F PRO* 3.8 3.6 - - - +
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Residues in contact with MET 419 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C ILE* 3.6 30.1 - - + -
376C ASN* 3.2 45.2 + - + +
378C ASP* 4.8 1.0 - - - +
392C GLN* 4.5 22.9 - - + +
396C HIS* 4.3 28.9 - - + -
418C LEU* 3.9 24.9 - - + -
421C LEU* 4.4 4.0 - - + -
355F LYS* 4.2 4.4 + - - -
415F GLY 2.9 20.1 + - - +
416F LYS* 3.8 11.4 - - - +
417F MET 3.1 0.6 + - - -
418F LEU* 1.3 74.1 - - - +
420F THR* 1.3 57.3 + - - +
421F LEU 3.1 5.2 - - - -
422F PRO* 3.3 11.7 - - - +
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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