Contacts of the helix formed by residues 315 - 325 (chain B) in PDB entry 3PII
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 LYS 315 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311B GLN* 3.7 32.5 - - + +
312B PRO* 2.9 28.7 + - + +
314B GLU* 1.3 81.2 - - + +
316B ILE* 1.3 65.3 + - - +
317B ASN* 3.3 2.7 - - - -
318B GLU* 2.9 51.4 + - + +
319B VAL* 3.1 13.2 + - + +
334B LEU* 5.3 0.7 - - - -
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Residues in contact with ILE 316 (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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4B ALA* 4.0 21.1 - - + -
13B LEU* 4.5 6.7 - - + -
15B ILE* 4.2 9.2 - - + -
37B VAL* 4.3 7.9 - - + -
120B TYR* 3.7 30.1 - - + +
312B PRO 4.1 0.6 + - - -
313B LEU 3.0 19.5 + - - +
314B GLU 3.3 0.6 - - - -
315B LYS* 1.3 75.1 - - - +
317B ASN* 1.3 71.1 + - - +
319B VAL* 3.0 13.0 + - + +
320B PHE* 2.9 60.3 + - + -
334B LEU* 4.1 20.2 - - + -
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Residues in contact with ASN 317 (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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12B PRO* 3.4 17.2 - - + +
13B LEU* 3.1 59.0 + - - +
15B ILE* 4.3 9.3 - - - +
314B GLU 4.9 1.9 + - - +
315B LYS 3.3 0.6 - - - -
316B ILE* 1.3 84.6 - - - +
318B GLU* 1.3 60.7 + - - +
320B PHE* 3.2 10.5 + - - +
321B ASP* 3.1 28.7 + - - +
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Residues in contact with GLU 318 (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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311B GLN* 5.3 1.7 - - - +
315B LYS* 2.9 50.2 + - + +
317B ASN* 1.3 77.3 - - - +
319B VAL* 1.3 63.1 + - + +
321B ASP* 3.4 11.1 + - + +
322B ARG* 3.2 50.0 + - + +
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Residues in contact with VAL 319 (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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37B VAL* 4.5 16.2 - - + -
311B GLN* 3.9 29.4 - - + -
315B LYS* 3.1 15.0 + - + +
316B ILE* 3.0 15.6 + - + +
318B GLU* 1.3 77.5 - - + +
320B PHE* 1.3 58.8 + - + +
322B ARG* 3.5 15.2 + - - +
323B MET* 3.0 25.8 + - + +
328B ILE* 3.5 20.3 - - + +
332B VAL* 3.9 24.5 - - + -
334B LEU* 5.1 1.6 - - + -
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Residues in contact with PHE 320 (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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13B LEU* 4.0 31.6 - - + -
37B VAL* 3.7 20.2 - - + -
41B ASP* 4.2 11.2 - - + -
42B LEU* 3.9 33.0 - - + +
45B ALA* 4.1 17.0 - - + -
46B HIS* 6.1 2.2 - + - +
59B PRO* 5.8 1.3 - - + -
120B TYR* 3.9 13.2 - + - -
316B ILE* 2.9 40.7 + - + +
317B ASN* 3.2 11.4 + - - +
319B VAL* 1.3 76.6 - - - +
321B ASP* 1.3 58.4 + - - +
323B MET* 3.2 10.8 + - - +
324B LEU* 2.9 38.7 + - + +
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Residues in contact with ASP 321 (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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317B ASN* 3.1 16.8 + - - +
318B GLU* 3.6 13.5 - - + +
320B PHE* 1.3 75.3 - - - +
322B ARG* 1.3 60.3 + - + +
324B LEU* 3.2 14.2 + - - +
325B LYS* 2.9 51.8 + - - +
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Residues in contact with ARG 322 (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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309B GLU* 2.8 42.0 + - - -
311B GLN* 4.5 4.9 + - - +
318B GLU* 3.2 36.9 + - + +
319B VAL* 3.9 21.3 - - - +
320B PHE 3.4 0.2 - - - -
321B ASP* 1.3 77.2 - - + +
323B MET* 1.3 57.7 + - - +
325B LYS* 3.8 3.5 + - - +
326B GLY 3.2 2.4 + - - -
327B GLN* 2.7 64.7 + - + +
328B ILE* 3.9 23.8 + - + +
332B VAL* 4.9 1.4 - - - +
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Residues in contact with MET 323 (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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37B VAL* 3.6 29.6 - - + +
38B CYS* 4.0 15.9 - - - +
39B HIS* 3.9 47.1 + - + +
42B LEU* 4.0 21.1 - - + -
319B VAL* 3.0 14.6 + - + +
320B PHE* 3.3 19.3 - - - +
322B ARG* 1.3 74.4 - - - +
324B LEU* 1.3 61.6 + - - +
326B GLY* 2.8 22.4 + - - -
327B GLN 4.9 0.2 - - - +
328B ILE* 3.7 28.7 - - + +
331B ARG* 6.2 1.6 - - - -
332B VAL* 5.7 1.8 - - + +
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Residues in contact with LEU 324 (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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42B LEU* 4.3 13.9 - - + +
46B HIS* 3.8 34.3 - - + +
320B PHE* 2.9 35.8 + - + +
321B ASP* 3.8 15.3 - - - +
323B MET* 1.3 72.7 - - - +
325B LYS* 1.3 61.8 + - + +
326B GLY* 3.1 5.5 + - - -
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Residues in contact with LYS 325 (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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321B ASP* 2.9 45.2 + - - +
322B ARG* 4.1 1.3 - - - +
324B LEU* 1.3 78.1 - - + +
326B GLY* 1.3 61.0 + - - +
327B GLN* 3.4 37.2 + - + +
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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
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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