Contacts of the helix formed by residues 387 - 395 (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 ASN 387 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B ALA 4.5 1.4 + - - -
347B SER* 3.7 25.3 + - - +
348B VAL* 5.3 0.6 - - - +
350B MET* 3.5 37.4 - - + +
351B GLY 5.4 1.8 - - - +
383B ASN 4.2 9.3 + - - -
384B ILE 3.3 3.8 + - - -
386B SER* 1.3 95.9 + - - +
388B LEU* 1.3 66.4 + - - +
389B ASP* 2.8 6.0 + - - +
390B CYS* 3.3 17.4 + - + +
391B VAL* 3.8 6.6 + - - +
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Residues in contact with LEU 388 (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* 4.1 16.2 - - + -
373B LEU* 3.9 27.1 - - + -
384B ILE 3.8 2.3 + - - +
385B ILE* 3.2 32.7 + - + +
387B ASN* 1.3 77.3 - - - +
389B ASP* 1.3 53.8 + - - +
390B CYS 2.6 14.0 + - - -
391B VAL* 3.3 14.1 + - - +
392B ASN* 3.6 9.5 + - - +
400B LEU* 5.2 3.1 - - + +
404B LEU* 4.2 20.6 - - + -
408B ILE* 3.5 23.3 - - + -
411B LEU* 6.4 0.2 - - + -
423B ILE* 5.2 1.6 - - + -
426B TYR* 3.5 42.9 + - + +
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Residues in contact with ASP 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B ILE 3.8 3.8 - - - +
386B SER 2.8 23.5 - - - +
387B ASN* 4.3 2.9 - - - -
388B LEU* 1.3 75.7 + - - +
390B CYS* 1.3 58.6 + - + +
392B ASN* 4.3 12.4 + - - -
393B GLU* 4.1 9.9 - - - +
426B TYR* 3.6 34.6 + - + +
429B LEU* 4.6 14.4 - - + +
433B GLN* 4.4 6.1 + - - -
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Residues in contact with CYS 390 (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 4.7 11.9 - - - -
351B GLY* 5.6 2.0 - - - -
354B PRO* 5.3 9.9 - - - -
387B ASN* 3.3 19.0 + - + +
388B LEU 2.6 5.9 + - - -
389B ASP* 1.3 79.4 - - + +
391B VAL* 1.3 64.3 + - - +
392B ASN 2.8 6.7 - - - -
393B GLU* 2.7 38.2 + - + +
394B VAL* 3.4 4.7 + - - +
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Residues in contact with VAL 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B MET* 3.7 35.7 - - + -
353B SER* 3.9 20.0 - - - +
361B THR* 5.1 3.6 - - + -
366B LEU* 5.8 0.2 - - + -
369B PHE* 3.9 13.7 - - + -
387B ASN 3.8 3.8 - - - +
388B LEU* 3.3 8.3 + - - +
390B CYS* 1.3 79.0 - - - +
392B ASN* 1.3 57.7 + - - +
393B GLU 2.8 0.7 + - - -
394B VAL* 2.7 16.7 + - + +
395B ILE* 2.7 42.0 + - + +
400B LEU* 4.3 5.2 - - + -
404B LEU* 4.2 24.9 - - + -
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Residues in contact with ASN 392 (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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388B LEU 3.6 10.7 + - - +
389B ASP 4.3 4.5 + - - +
390B CYS 2.8 0.4 - - - -
391B VAL* 1.3 79.1 - - - +
393B GLU* 1.3 64.0 + - - +
394B VAL 3.5 0.2 - - - -
395B ILE* 3.9 13.5 - - - +
397B ILE* 3.3 35.4 + - - +
400B LEU* 3.3 28.4 - - + +
426B TYR* 4.5 0.9 + - - +
433B GLN* 2.5 47.3 + - - +
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Residues in contact with GLU 393 (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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308A GLU* 5.7 1.0 - - - +
389B ASP 4.1 5.7 - - - +
390B CYS* 2.8 29.2 - - + +
392B ASN* 1.3 80.0 - - - +
394B VAL* 1.3 67.6 + - + +
395B ILE 3.8 2.7 - - - -
433B GLN* 4.7 9.4 + - - -
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Residues in contact with VAL 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B SER* 3.5 13.2 - - - +
354B PRO* 3.3 39.0 - - + -
357B GLY* 3.7 9.4 - - - -
358B LYS* 3.6 43.0 + - - +
361B THR* 3.8 15.3 - - - +
390B CYS* 4.1 8.7 - - - +
391B VAL 2.7 6.4 + - - +
393B GLU* 1.3 83.9 - - + +
395B ILE* 1.3 67.0 + - + +
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Residues in contact with ILE 395 (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* 4.0 11.2 - - - +
361B THR* 3.8 24.7 - - + -
362B ILE* 3.7 27.1 - - + -
366B LEU* 4.1 24.9 - - + -
391B VAL* 2.7 29.3 + - + +
392B ASN* 3.9 3.6 - - - +
393B GLU 3.8 7.1 + - - -
394B VAL* 1.3 88.4 + - + +
396B GLY* 1.3 70.4 + - - +
399B GLN* 3.9 10.8 - - + +
400B LEU* 3.8 33.2 - - + +
404B LEU* 4.9 0.2 - - + -
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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
------------------------------------------------------------
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