Contacts of the helix formed by residues 357 - 365 (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 357 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353B SER 2.6 18.9 + - - -
354B PRO* 4.7 4.5 - - - -
355B ILE 3.1 3.6 - - - -
356B LEU* 1.3 74.4 - - - +
358B LYS* 1.3 55.2 + - - -
360B ASN* 4.2 2.0 - - - -
361B THR* 2.7 43.5 + - - -
394B VAL* 3.7 5.8 - - - -
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Residues in contact with LYS 358 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357B GLY* 1.3 65.6 - - - -
359B ASP* 1.3 77.7 + - - +
360B ASN 3.0 0.2 - - - -
361B THR* 2.8 14.6 + - - -
362B ILE* 2.8 36.3 + - + +
394B VAL* 3.6 30.7 - - - +
395B ILE* 4.0 1.8 - - - -
396B GLY* 3.6 30.2 - - - +
399B GLN* 4.6 7.6 - - - +
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Residues in contact with ASP 359 (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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358B LYS* 1.3 87.5 - - - +
360B ASN* 1.3 59.2 + - - +
362B ILE* 3.1 13.3 + - - +
363B GLU* 2.9 32.9 + - - +
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Residues in contact with ASN 360 (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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319B GLU* 2.9 21.5 + - - -
323B MET* 2.8 32.7 - - + +
356B LEU* 2.9 42.6 + - + +
357B GLY* 3.5 1.5 - - - +
358B LYS 3.0 0.4 - - - -
359B ASP* 1.3 79.4 - - - +
361B THR* 1.3 63.2 + - - +
363B GLU* 3.3 1.7 + - - -
364B HIS* 3.0 38.3 + - - +
365B LEU* 4.6 0.3 - - - +
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Residues in contact with THR 361 (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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353B SER* 3.1 45.9 + - - +
356B LEU* 4.2 0.2 - - - +
357B GLY 2.7 28.7 + - - -
358B LYS 2.8 3.1 + - - -
360B ASN* 1.3 72.8 - - - +
362B ILE* 1.3 57.9 + - - +
365B LEU* 2.9 49.1 + - + +
366B LEU* 3.1 21.5 + - + +
369B PHE* 4.3 3.1 - - + -
391B VAL* 5.1 1.8 - - + -
394B VAL* 3.8 3.8 - - - +
395B ILE* 3.8 13.5 - - + -
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Residues in contact with ILE 362 (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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358B LYS* 2.8 55.2 + - + +
359B ASP* 3.5 12.8 - - - +
361B THR* 1.3 77.8 - - - +
363B GLU* 1.3 59.8 + - - +
366B LEU* 3.7 18.0 - - + +
367B PRO* 4.2 11.4 - - - +
395B ILE* 3.7 15.0 - - + -
399B GLN* 4.1 35.2 - - + +
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Residues in contact with GLU 363 (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 ASP 2.9 15.5 + - - +
360B ASN* 4.2 3.1 - - - +
362B ILE* 1.3 79.5 - - - +
364B HIS* 1.3 90.8 + - + +
367B PRO* 3.9 13.6 - - - +
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Residues in contact with HIS 364 (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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323B MET* 3.8 30.8 - - + +
327B LEU* 3.8 27.4 - - + +
356B LEU* 5.5 0.9 - - + -
360B ASN* 3.0 21.7 + - - +
363B GLU* 1.3 114.9 + - + +
365B LEU* 1.3 61.8 + - + +
367B PRO* 4.0 6.3 - - - +
368B LEU* 3.1 23.2 - - - +
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Residues in contact with LEU 365 (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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327B LEU* 4.2 10.1 - - + -
330B ILE* 6.1 0.4 - - + -
349B ILE* 5.1 1.6 - - + -
352B LEU* 4.1 16.6 - - + -
353B SER* 4.0 19.1 - - - +
356B LEU* 3.5 34.3 - - + -
361B THR* 2.9 41.1 + - + +
364B HIS* 1.3 76.2 - - - +
366B LEU* 1.3 52.9 + - - +
367B PRO* 3.2 2.5 - - - -
368B LEU* 2.5 58.8 + - + +
369B PHE* 3.1 24.4 + - + -
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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