Contacts of the helix formed by residues 474 - 481 (chain B) in PDB entry 2PKG
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 474 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470B VAL* 2.7 22.0 + - - +
471B GLU 4.7 1.2 + - - -
472B LYS 3.8 0.2 - - - -
473B PHE* 1.3 72.1 - - - +
475B LYS* 1.3 52.4 + - - -
476B GLU* 2.7 12.2 + - - +
477B TRP* 2.6 39.9 + - - +
478B ALA 3.2 2.4 + - - -
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Residues in contact with LYS 475 (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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470B VAL* 3.9 9.6 - - + +
474B GLY* 1.3 64.1 - - - -
476B GLU* 1.3 88.5 + - - +
478B ALA* 3.4 15.6 - - + +
479B HIS* 2.8 23.0 + - - +
511B VAL 4.1 10.2 + - - +
512B CYS* 3.4 44.2 + - + +
513B GLY* 5.0 4.0 - - - -
516B ILE* 4.4 10.7 - - + +
100C TRP* 4.5 4.7 - - + +
153C CYS* 5.9 0.7 - - - -
154C GLU* 2.4 53.3 + - - +
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Residues in contact with GLU 476 (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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473B PHE 5.9 0.4 - - - +
474B GLY* 2.7 8.5 + - - +
475B LYS* 1.3 107.5 + - - +
477B TRP* 1.3 55.0 - - - +
479B HIS* 2.7 33.4 + - - +
480B ALA* 3.1 9.1 + - - +
100C TRP* 2.8 37.3 + - - -
101C PRO* 5.0 8.0 - - + +
105C LYS* 5.3 7.8 + - - +
152C LEU* 3.2 39.1 - - + +
153C CYS* 4.1 10.2 - - + +
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Residues in contact with TRP 477 (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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436B VAL* 3.9 17.2 - - + +
439B PHE* 3.7 15.5 - + - -
440B ASP* 2.8 28.0 + - - -
469B LEU* 3.7 38.6 - - + -
470B VAL* 3.9 11.7 - - + -
473B PHE* 3.4 45.1 - + + +
474B GLY 2.6 19.0 + - - +
476B GLU* 1.3 75.0 - - - +
478B ALA* 1.3 72.4 + - - -
480B ALA* 3.3 4.9 + - - +
481B THR* 3.1 37.1 + - + +
482B ILE* 3.5 36.6 - - + -
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Residues in contact with ALA 478 (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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470B VAL* 4.1 24.7 - - + -
474B GLY 3.2 4.8 + - - -
475B LYS* 3.4 21.1 - - - +
476B GLU 3.1 0.6 - - - -
477B TRP* 1.3 84.2 - - + +
479B HIS* 1.3 61.2 + - - +
482B ILE* 3.2 13.9 + - + -
483B ILE* 2.9 32.3 + - + +
508B LEU* 5.2 1.3 - - + -
512B CYS* 4.2 16.6 - - - -
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Residues in contact with HIS 479 (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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475B LYS 2.8 13.3 + - - +
476B GLU* 2.7 16.2 + - - +
478B ALA* 1.3 77.8 - - - +
480B ALA* 1.3 64.4 + - + +
483B ILE* 4.0 12.1 - - + +
484B PRO* 3.5 18.9 - - - +
516B ILE* 3.5 29.1 - - + +
520B HIS* 3.6 23.4 + + - -
101C PRO* 3.8 12.2 - - + +
102C GLU* 2.7 32.7 + - + -
105C LYS* 5.3 6.7 + - + +
107C MET* 4.5 20.4 - - + -
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Residues in contact with ALA 480 (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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476B GLU 3.1 11.0 + - - +
477B TRP* 3.3 4.9 + - - +
479B HIS* 1.3 85.1 - - + +
481B THR* 1.3 62.5 + - - +
484B PRO* 4.2 7.6 - - - +
105C LYS* 4.4 17.0 - - - +
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Residues in contact with THR 481 (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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440B ASP* 4.0 12.9 + - - +
444B ASN* 3.3 18.0 - - - +
477B TRP* 3.1 29.9 + - + +
479B HIS 3.5 2.0 + - - -
480B ALA* 1.3 82.5 + - - +
482B ILE* 1.3 93.2 + - + +
484B PRO* 3.6 7.8 - - - +
485B LYS* 3.7 22.7 + - - +
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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