Contacts of the helix formed by residues 365 - 374 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327A LEU* 4.0 18.4 - - + -
330A ILE* 5.8 0.9 - - + -
349A ILE* 4.9 6.7 - - + +
352A LEU* 2.9 40.4 - - + +
353A SER* 4.1 4.9 - - - +
356A LEU* 4.0 11.9 - - + -
361A THR* 2.6 38.5 + - + +
364A HIS* 1.3 75.7 - - + +
366A LEU* 1.3 58.8 + - - +
367A PRO* 3.2 2.2 - - - -
368A LEU* 2.8 30.2 + - + +
369A PHE* 2.8 52.9 + - + -
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Residues in contact with LEU 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A THR* 3.2 30.0 + - + +
362A ILE* 3.4 22.9 - - + +
365A LEU* 1.3 73.0 - - - +
367A PRO* 1.3 60.9 - - + +
369A PHE* 3.5 13.6 - - + +
370A LEU* 2.6 43.1 + - + +
391A VAL* 6.4 0.4 - - + -
395A ILE* 4.1 19.1 - - + -
399A GLN* 3.9 12.8 - - - +
403A SER* 3.5 33.4 - - - +
404A LEU* 4.1 15.9 - - + -
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Residues in contact with PRO 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A LYS* 6.0 5.8 - - - -
362A ILE 4.0 4.5 - - - +
363A GLU 3.9 17.9 - - - +
364A HIS 4.1 2.0 - - - +
365A LEU 3.3 11.7 - - - +
366A LEU* 1.3 94.1 - - + +
368A LEU* 1.3 54.6 + - + +
370A LEU* 3.5 6.8 - - + +
371A ALA* 2.7 36.2 + - - +
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Residues in contact with LEU 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A LEU* 4.9 5.4 - - + -
330A ILE* 4.4 9.4 - - + -
331A LYS* 3.9 31.2 - - + +
334A VAL* 3.3 29.4 - - + -
349A ILE* 4.3 17.5 - - + -
364A HIS 3.1 24.7 - - - +
365A LEU* 2.8 26.8 + - + +
367A PRO* 1.3 78.1 - - + +
369A PHE* 1.3 69.7 + - + +
371A ALA* 2.7 20.5 + - + +
372A GLN* 3.0 17.3 + - - +
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Residues in contact with PHE 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A ILE* 4.0 28.5 - - + -
350A MET* 3.8 35.9 - - + -
353A SER* 4.5 2.0 - - - -
361A THR* 4.5 7.9 - - + -
365A LEU* 2.8 51.1 + - + -
366A LEU* 3.5 17.0 - - + +
368A LEU* 1.3 74.3 - - + +
370A LEU* 1.3 51.7 + - - +
372A GLN* 3.0 5.8 + - - +
373A LEU* 2.5 51.0 + - + +
384A ILE* 4.1 16.4 - - + -
391A VAL* 3.8 25.4 - - + -
404A LEU* 5.0 13.7 - - + -
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Residues in contact with LEU 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A LEU* 2.6 25.1 + - + +
367A PRO* 3.5 7.2 - - + +
369A PHE* 1.3 71.3 - - - +
371A ALA* 1.3 65.6 + - - +
372A GLN 3.2 0.2 + - - -
373A LEU* 3.3 11.7 + - + +
374A LYS* 3.4 41.4 + - - +
403A SER* 3.6 18.4 - - - +
404A LEU* 3.2 37.9 - - + -
407A ALA* 4.0 18.8 - - + -
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Residues in contact with ALA 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A VAL* 3.9 19.3 - - + -
367A PRO 2.7 17.9 + - - +
368A LEU* 2.7 14.5 + - + +
370A LEU* 1.3 73.0 - - - +
372A GLN* 1.3 59.8 + - - +
374A LYS* 3.5 6.6 + - - +
375A ASP* 3.4 16.5 + - - +
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Residues in contact with GLN 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A VAL* 3.7 32.3 + - + +
342A LYS* 4.2 8.3 + - - +
345A LEU* 4.8 4.6 - - - +
346A ALA* 3.4 27.9 - - - +
349A ILE* 3.5 23.2 - - - +
368A LEU 3.2 14.1 - - - +
369A PHE* 3.0 6.8 + - - +
371A ALA* 1.3 74.4 - - - +
373A LEU* 1.3 53.9 + - - +
374A LYS 2.4 18.6 + - - -
375A ASP* 2.6 20.3 + - - +
380A VAL* 3.9 17.5 - - + +
381A ARG* 4.1 2.8 - - - +
384A ILE* 3.1 34.7 - - + +
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Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A PHE* 2.5 47.7 + - + +
370A LEU* 3.3 12.8 + - + +
372A GLN* 1.3 69.9 - - - +
374A LYS* 1.3 58.8 + - + +
381A ARG* 3.5 19.3 - - - +
384A ILE* 3.1 33.1 - - + +
385A ILE* 4.2 15.3 - - + -
388A LEU* 4.9 11.4 - - + -
404A LEU* 4.9 13.5 - - + -
407A ALA* 4.2 24.7 - - + -
408A ILE* 5.6 3.4 - - + -
411A LEU* 3.7 34.2 - - + +
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Residues in contact with LYS 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A LEU* 3.4 36.2 + - - +
371A ALA* 3.8 6.5 - - - +
372A GLN 2.4 12.3 + - - -
373A LEU* 1.3 77.9 - - + +
375A ASP* 1.3 68.3 + - - +
376A GLU* 3.5 4.2 + - - +
381A ARG* 4.6 1.6 - - - +
407A ALA* 5.0 9.6 - - + +
410A GLU* 5.2 13.5 - - - +
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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