Contacts of the helix formed by residues 442 - 454 (chain C) 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 GLY 442 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438C ILE 3.5 3.3 + - - -
439C LYS 3.1 14.9 + - - -
440C LEU 3.6 1.2 - - - -
441C GLU* 1.3 75.1 - - - +
443C LYS* 1.3 57.9 + - - +
444C VAL 3.5 1.6 - - - -
445C PRO* 3.4 27.1 - - - +
446C MET* 3.8 13.9 - - - +
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Residues in contact with LYS 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C ASP* 5.5 2.5 - - - +
262C ILE* 3.6 18.6 - - + +
438C ILE 4.6 2.8 + - - +
441C GLU* 2.8 14.1 + - + +
442C GLY* 1.3 72.6 - - - +
444C VAL* 1.3 64.4 + - + +
445C PRO 3.5 0.7 - - - -
446C MET* 3.7 11.0 + - + +
447C HIS* 3.4 17.7 + - - +
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Residues in contact with VAL 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C ILE* 3.8 32.9 - - + +
265C LEU* 5.2 10.1 - - + -
266C THR* 4.2 11.2 - - + +
438C ILE* 4.7 24.9 - - + +
439C LYS* 6.3 0.7 - - - -
442C GLY* 4.4 0.2 - - - -
443C LYS* 1.3 77.1 - - + +
445C PRO* 1.3 73.5 - - + +
446C MET 3.5 0.2 + - - -
447C HIS* 3.5 5.4 + - - +
448C LYS* 3.4 32.0 + - - +
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Residues in contact with PRO 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442C GLY* 3.4 28.7 - - - +
444C VAL* 1.3 92.7 - - + +
446C MET* 1.3 66.4 + - + +
448C LYS* 2.8 30.3 + - + +
449C LEU* 3.2 5.1 + - - +
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Residues in contact with MET 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442C GLY 3.8 16.8 - - - +
443C LYS* 3.7 10.9 + - - +
444C VAL 3.3 0.6 - - - -
445C PRO* 1.3 77.1 - - + +
447C HIS* 1.3 56.7 + - - +
449C LEU* 2.7 37.9 + - + +
450C PHE* 2.9 57.3 + - + -
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Residues in contact with HIS 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C VAL* 4.4 14.8 - - + +
258C PRO* 4.9 3.6 - - + -
260C SER* 3.5 26.7 + - - -
262C ILE* 3.4 49.1 - - + +
263C LYS* 4.6 3.1 + - - -
266C THR* 5.3 1.5 + - - -
443C LYS 3.4 3.5 + - - +
444C VAL 3.6 6.3 - - - +
446C MET* 1.3 77.3 - - - +
448C LYS* 1.3 69.0 + - + +
450C PHE* 3.8 10.6 - - - +
451C LEU* 3.0 43.1 + - + +
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Residues in contact with LYS 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C ILE* 6.0 0.2 - - - -
266C THR* 5.0 14.4 - - - +
444C VAL* 3.4 33.0 - - - +
445C PRO* 2.8 16.6 + - + +
446C MET 2.8 4.0 + - - -
447C HIS* 1.3 78.5 - - + +
449C LEU* 1.3 63.0 + - - +
451C LEU* 4.1 3.1 - - - +
452C GLU* 3.1 42.1 + - - +
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Residues in contact with LEU 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445C PRO 3.2 4.2 + - - +
446C MET* 2.7 22.0 + - + +
448C LYS* 1.3 73.0 - - - +
450C PHE* 1.3 74.5 + - + +
452C GLU* 3.3 14.4 + - - +
453C MET* 2.8 53.8 + - + +
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Residues in contact with PHE 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446C MET* 2.9 53.6 + - + -
447C HIS* 3.8 13.9 - - - +
449C LEU* 1.3 87.7 - - + +
451C LEU* 1.3 64.1 + - - +
453C MET* 3.0 6.4 + - - +
454C LEU* 3.0 38.3 + - + +
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Residues in contact with LEU 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C VAL* 3.9 38.4 - - + -
258C PRO* 4.2 22.0 - - + -
447C HIS* 3.0 31.1 + - + +
448C LYS* 4.1 2.9 - - - +
450C PHE* 1.3 79.8 - - - +
452C GLU* 1.3 65.1 + - + +
454C LEU* 3.6 11.0 + - + +
455C GLU* 3.1 47.3 - - + +
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Residues in contact with GLU 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448C LYS* 3.1 37.0 + - - +
449C LEU* 3.4 19.7 - - - +
451C LEU* 1.3 80.9 - - + +
453C MET* 1.3 62.9 + - + +
455C GLU* 3.4 21.0 + - - +
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Residues in contact with MET 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449C LEU* 2.8 44.6 - - + +
450C PHE* 3.0 4.8 + - - +
452C GLU* 1.3 76.1 - - + +
454C LEU* 1.3 60.9 + - - +
455C GLU 3.1 10.9 + - - +
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Residues in contact with LEU 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450C PHE* 3.0 29.6 + - + +
451C LEU* 3.6 10.7 + - + +
452C GLU 3.4 0.6 - - - -
453C MET* 1.3 76.9 - - + +
455C GLU* 1.3 61.1 + - + +
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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