Contacts of the helix formed by residues 352 - 357 (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 LEU 352 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B VAL* 4.4 5.4 - - + -
307B LYS* 4.6 12.3 - - - -
310B CYS* 3.9 33.7 - - + -
322B ILE* 4.6 11.9 - - + -
327B LEU* 5.7 1.1 - - + -
330B ILE* 3.6 30.5 - - + -
348B VAL 4.8 3.4 - - - +
349B ILE* 3.0 27.9 + - + +
350B MET 2.8 0.6 - - - -
351B GLY* 1.3 79.9 - - - +
353B SER* 1.3 64.7 + - - +
354B PRO 3.6 0.2 - - - -
355B ILE* 2.9 15.7 + - + +
356B LEU* 2.9 27.9 + - + +
365B LEU* 4.1 21.1 - - + -
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Residues in contact with SER 353 (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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350B MET 3.1 13.4 + - - -
352B LEU* 1.3 72.5 - - - +
354B PRO* 1.3 61.3 - - - +
355B ILE 2.7 8.2 + - - -
357B GLY* 2.6 34.1 + - - -
361B THR* 3.1 32.6 + - - +
365B LEU* 4.0 1.4 - - - +
369B PHE* 3.8 13.5 - - - -
390B CYS* 5.6 0.2 - - - -
391B VAL* 3.9 11.7 - - - +
394B VAL* 3.5 20.0 - - - -
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Residues in contact with PRO 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ARG* 5.9 0.2 + - - -
350B MET 4.1 1.6 - - - +
351B GLY* 3.3 21.5 - - - +
353B SER* 1.3 92.2 - - - +
355B ILE* 1.3 64.2 + - + +
357B GLY* 4.2 5.0 + - - +
390B CYS* 5.3 7.4 - - - -
394B VAL* 3.3 20.1 - - + -
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Residues in contact with ILE 355 (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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307B LYS* 4.7 1.6 - - + +
310B CYS* 4.1 7.6 - - + +
311B GLU* 3.3 51.4 - - + +
318B ARG* 4.1 28.0 + - - +
319B GLU* 5.4 1.6 - - - +
322B ILE* 3.3 31.0 - - + -
351B GLY 4.4 11.9 - - - +
352B LEU* 2.9 17.2 + - + +
353B SER 2.7 2.2 + - - -
354B PRO* 1.3 85.2 - - + +
356B LEU* 1.3 72.9 + - + +
357B GLY* 3.1 2.0 + - - -
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Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B GLU* 3.6 14.2 - - - +
322B ILE* 3.5 43.1 - - + -
323B MET* 4.0 29.2 - - + -
327B LEU* 4.9 7.2 - - + -
352B LEU* 2.9 22.4 + - + +
355B ILE* 1.3 77.8 - - + +
357B GLY* 1.3 59.7 + - - +
360B ASN* 2.9 40.8 + - + +
361B THR* 4.2 4.9 - - - +
364B HIS* 5.5 0.9 - - + -
365B LEU* 3.5 36.3 - - + -
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Residues in contact with GLY 357 (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 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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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