Contacts of the helix formed by residues 412 - 419 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A ASP* 4.0 10.1 + - - +
396A HIS* 3.4 30.9 - - + +
397A GLU* 3.5 61.4 + - - +
400A GLN* 4.8 12.6 - - + +
410D ASP* 3.0 12.7 + - - +
411D PRO* 1.3 106.4 - - - +
413D ARG* 1.3 66.4 + - - +
414D ALA* 3.3 2.7 - - - -
415D GLY 4.0 2.7 - - - +
416D LYS* 3.0 32.6 + - - +
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Residues in contact with ARG 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359D MET* 2.8 37.7 + - + +
360D LYS* 3.3 11.1 + - - +
362D GLU* 4.2 5.1 + - - -
365D GLU* 3.0 33.9 + - - -
403D GLU* 3.1 25.5 + - + +
407D HIS* 3.4 30.8 - - + -
410D ASP* 3.3 34.0 + - - +
411D PRO 3.6 0.8 - - - -
412D ARG* 1.3 77.6 - - - +
414D ALA* 1.3 63.5 + - - +
416D LYS* 3.2 9.5 + - + +
417D MET* 3.0 39.7 + - + +
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Residues in contact with ALA 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399D LEU* 4.0 13.4 - - + +
400D GLN* 4.0 32.5 - - - +
403D GLU* 3.7 27.9 - - + +
411D PRO 5.4 0.8 + - - +
412D ARG* 3.3 0.6 - - - +
413D ARG* 1.3 78.3 - - - +
415D GLY* 1.3 64.1 + - - +
417D MET* 2.8 18.8 + - - +
418D LEU* 3.0 19.5 + - + +
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Residues in contact with GLY 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A HIS* 3.5 25.3 - - - -
415A GLY* 5.9 0.4 - - - -
418A LEU* 3.7 12.5 - - - +
400D GLN* 5.6 1.0 - - - +
412D ARG* 3.4 4.8 + - - +
413D ARG 3.3 0.2 - - - -
414D ALA* 1.3 77.3 - - - +
416D LYS* 1.3 63.4 + - - +
418D LEU* 3.1 10.7 + - - +
419D MET* 2.9 26.6 + - - +
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Residues in contact with LYS 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A GLN* 4.3 10.8 - - - +
393A ASP* 2.9 39.6 + - - +
396A HIS* 3.7 8.9 - - - +
359D MET* 3.4 23.4 - - + +
410D ASP* 3.2 34.5 + - - +
412D ARG* 3.0 26.6 + - - +
413D ARG* 3.3 10.3 - - + +
415D GLY* 1.3 75.5 - - - +
417D MET* 1.3 61.0 + - - +
419D MET* 3.1 20.7 + - - +
420D THR* 3.4 16.1 - - - +
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Residues in contact with MET 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D TYR* 4.8 1.6 - - - -
359D MET* 4.1 26.5 - - + +
361D LEU* 3.6 30.5 - - + -
365D GLU* 3.8 9.9 - - - +
369D LEU* 3.8 22.3 - - + +
399D LEU* 4.1 17.7 - - + -
403D GLU* 4.2 11.2 - - - +
413D ARG* 3.0 58.6 + - + +
414D ALA* 2.8 11.4 + - - +
416D LYS* 1.3 76.3 - - - +
418D LEU* 1.3 58.6 + - - +
420D THR* 2.7 27.6 + - - -
421D LEU* 4.3 1.2 + - - +
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Residues in contact with LEU 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A GLY* 3.8 33.7 - - - +
418A LEU* 4.6 17.6 - - + +
419A MET* 4.1 21.0 - - + -
422A PRO* 5.5 0.5 - - - +
369D LEU* 4.7 1.6 - - + -
372D ILE* 3.8 35.0 - - + -
396D HIS* 3.9 16.6 - - + +
399D LEU* 3.8 10.3 - - + -
400D GLN* 5.5 0.9 - - - +
414D ALA* 3.0 20.1 + - + +
415D GLY* 3.7 11.9 - - - +
417D MET* 1.3 76.7 - - - +
419D MET* 1.3 58.6 + - - +
420D THR 3.1 4.3 + - - -
421D LEU* 3.4 27.8 + - + +
422D PRO* 3.8 3.5 - - - +
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Residues in contact with MET 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A ILE* 3.6 20.0 - - + -
376A ASN* 3.1 55.6 + - + +
378A ASP* 5.2 1.4 - - - +
392A GLN* 3.9 27.4 - - + +
396A HIS* 4.3 24.0 - - - -
418A LEU* 3.7 29.6 - - + -
421A LEU* 4.5 3.8 - - + -
355D LYS* 4.6 2.9 + - - -
415D GLY 2.9 15.6 + - - +
416D LYS* 3.1 15.8 + - - +
418D LEU* 1.3 76.4 - - - +
420D THR* 1.3 58.8 + - - +
421D LEU 3.4 0.9 - - - -
422D PRO* 3.5 8.0 - - - +
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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