Contacts of the helix formed by residues 365 - 373 (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 365 (chain B).
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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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Residues in contact with LEU 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B THR* 3.2 30.7 - - + +
362B ILE* 3.7 26.2 - - + +
365B LEU* 1.3 69.3 - - - +
367B PRO* 1.3 63.8 - - + +
368B LEU 2.6 0.9 + - - -
369B PHE* 2.8 17.4 + - + -
370B LEU* 2.5 40.4 + - + +
391B VAL* 5.8 0.7 - - + -
395B ILE* 4.1 21.1 - - + -
403B SER* 3.3 31.4 - - - +
404B LEU* 3.7 23.3 - - + -
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Residues in contact with PRO 367 (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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362B ILE 4.2 8.5 - - - +
363B GLU 3.9 15.0 - - - +
364B HIS 4.0 4.9 - - - +
365B LEU 3.2 12.1 - - - +
366B LEU* 1.3 95.9 - - + +
368B LEU* 1.3 57.9 + - + +
370B LEU* 3.4 9.4 - - + +
371B ALA* 3.1 24.6 + - - +
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Residues in contact with LEU 368 (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* 4.5 9.9 - - + -
330B ILE* 4.8 4.3 - - + -
331B LYS* 4.1 32.3 - - + -
334B VAL* 4.2 20.4 - - + -
349B ILE* 4.3 21.1 - - + -
364B HIS 3.1 24.5 - - - +
365B LEU* 2.5 41.2 + - + +
367B PRO* 1.3 70.5 - - + +
369B PHE* 1.3 66.0 + - + +
370B LEU 2.9 1.3 - - - -
371B ALA* 2.8 16.8 + - - +
372B GLN* 2.8 19.4 + - - +
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Residues in contact with PHE 369 (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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349B ILE* 4.1 18.6 - - + -
350B MET* 3.6 50.5 - - + -
353B SER* 3.8 16.8 - - - -
361B THR* 4.3 6.3 - - + -
365B LEU* 3.7 34.5 - - + -
366B LEU* 2.8 28.0 + - + +
368B LEU* 1.3 78.0 - - + +
370B LEU* 1.3 53.7 + - - +
372B GLN* 3.0 1.5 + - - +
373B LEU* 2.5 46.5 + - + +
384B ILE* 4.2 12.2 - - + +
391B VAL* 3.9 19.5 - - + -
404B LEU* 4.9 10.8 - - + -
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Residues in contact with LEU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B LEU* 2.5 22.8 + - + +
367B PRO* 3.4 11.0 - - + +
369B PHE* 1.3 74.1 - - - +
371B ALA* 1.3 61.6 + - - +
373B LEU* 3.4 4.6 + - + +
374B LYS* 3.1 53.8 + - + +
403B SER* 3.2 29.2 - - - +
404B LEU* 3.6 21.1 - - + -
407B ALA* 4.3 13.7 - - + -
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Residues in contact with ALA 371 (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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334B VAL* 4.8 11.7 - - + -
367B PRO 3.1 10.8 + - - +
368B LEU* 2.8 12.6 + - - +
370B LEU* 1.3 73.9 - - - +
372B GLN* 1.3 61.4 + - - +
374B LYS* 3.3 6.9 + - - +
375B ASP* 3.0 24.6 + - - +
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Residues in contact with GLN 372 (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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334B VAL* 3.8 29.3 + - + +
342B LYS* 4.1 11.7 + - - +
345B LEU* 4.2 8.7 - - - +
346B ALA* 3.8 21.7 - - - +
349B ILE* 3.4 38.1 - - - +
368B LEU 2.8 19.4 + - - +
369B PHE 3.5 1.8 - - - +
371B ALA* 1.3 74.1 - - - +
373B LEU* 1.3 54.3 + - - +
374B LYS 2.5 15.9 + - - -
375B ASP* 2.7 24.5 + - - +
380B VAL* 4.2 11.1 - - + +
381B ARG* 4.0 9.0 - - - +
384B ILE* 3.4 23.4 - - + +
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Residues in contact with LEU 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B PHE* 2.5 28.3 + - + +
370B LEU* 3.4 14.6 - - + +
372B GLN* 1.3 71.2 - - - +
374B LYS* 1.3 59.2 + - - +
381B ARG* 3.6 17.8 - - - +
384B ILE* 3.1 35.6 - - + +
385B ILE* 4.1 14.6 - - + -
388B LEU* 3.9 21.5 - - + -
404B LEU* 4.9 9.9 - - + -
407B ALA* 4.4 12.8 - - + +
408B ILE* 5.8 2.5 - - + -
411B LEU* 3.2 43.5 - - + +
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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