Contacts of the helix formed by residues 325 - 337 (chain B) in PDB entry 2P1N
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 ILE 325 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B SER* 3.0 15.6 + - - +
306B LEU* 3.5 27.9 - - + +
307B VAL* 5.8 0.2 - - + -
310B LEU* 4.4 16.2 - - + -
319B LEU* 5.3 2.2 - - + -
321B VAL* 4.3 13.9 - - + -
322B LEU 3.0 16.1 + - - +
323B ASP 2.8 3.0 + - - -
324B TYR* 1.3 75.3 - - - +
326B GLU* 1.3 74.3 + - - +
329B GLY* 3.1 49.5 - - - +
330B LEU* 3.3 34.5 - - + +
333B LEU* 4.9 0.9 - - + -
345B VAL* 4.7 3.1 - - + -
359B LEU* 4.2 9.4 - - + -
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Residues in contact with GLU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B GLN* 5.9 1.4 + - - -
303B SER* 3.9 13.6 + - - +
323B ASP 3.1 11.0 + - - +
324B TYR* 3.3 19.1 - - - +
325B ILE* 1.3 87.4 - - - +
327B ASP* 1.3 69.9 + - - +
328B ALA* 4.3 7.1 - - + +
329B GLY 4.6 0.2 - - - +
330B LEU* 3.2 18.9 + - - +
357B VAL* 4.0 10.6 - - + +
358B ALA* 3.2 44.7 + - + +
359B LEU* 3.9 9.1 - - - +
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Residues in contact with ASP 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B GLU* 1.3 76.5 - - - +
328B ALA* 1.3 58.4 + - + +
330B LEU* 3.4 2.6 + - - +
331B GLU* 3.0 26.2 + - - +
358B ALA* 3.1 13.5 + - - +
359B LEU* 3.4 1.0 - - - -
360B THR* 2.7 49.9 + - - +
362B GLN* 3.5 12.9 - - + +
363B GLY* 3.2 27.5 + - - +
366B SER* 4.7 1.6 + - - -
379B TYR* 4.5 0.9 + - - -
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Residues in contact with ALA 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B SER* 5.4 2.7 - - - +
307B VAL* 5.1 1.1 - - - -
326B GLU* 3.2 5.9 - - + +
327B ASP* 1.3 77.6 - - - +
329B GLY* 1.3 64.8 - - - +
331B GLU* 3.5 10.4 + - - +
332B VAL* 3.3 26.7 + - - +
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Residues in contact with GLY 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B SER* 4.0 3.5 + - - -
307B VAL* 3.7 25.1 - - - +
310B LEU* 4.7 3.5 - - - +
325B ILE* 3.1 38.3 + - - +
328B ALA* 1.3 81.0 - - - +
330B LEU* 1.3 54.4 + - - +
332B VAL* 3.6 4.4 + - - +
333B LEU* 3.1 20.3 + - - +
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Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 5.5 0.7 - - + -
325B ILE* 3.3 24.0 - - + +
326B GLU 3.2 17.8 + - - +
327B ASP 3.7 4.7 - - - +
329B GLY* 1.3 74.4 - - - +
331B GLU* 1.3 67.3 + - - +
332B VAL 3.2 0.4 - - - -
333B LEU* 3.2 29.3 - - + +
334B ALA* 2.9 18.0 + - - +
343B LEU* 4.1 19.3 - - + -
345B VAL* 4.5 2.0 - - + -
359B LEU* 4.1 9.6 - - + -
363B GLY* 3.6 35.7 - - - +
366B SER* 4.5 0.7 - - - -
367B VAL* 3.5 11.3 - - + +
379B TYR* 3.8 26.0 - - + +
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Residues in contact with GLU 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ASP 3.0 16.6 + - - +
328B ALA* 3.6 12.1 - - - +
330B LEU* 1.3 80.4 - - - +
332B VAL* 1.3 59.7 + - + +
334B ALA* 2.9 19.7 + - + +
335B SER* 3.2 13.1 + - - -
362B GLN* 5.5 2.3 + - - -
366B SER* 4.0 23.3 + - - +
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Residues in contact with VAL 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B VAL* 4.2 22.4 - - + +
310B LEU* 5.5 2.7 - - + -
311B CYS* 3.8 29.6 - - - +
328B ALA 3.3 15.0 + - - +
329B GLY 3.6 7.4 - - - +
330B LEU 3.2 0.2 - - - -
331B GLU* 1.3 76.0 - - + +
333B LEU* 1.3 66.6 + - - +
335B SER* 3.0 18.1 + - - +
336B THR* 3.0 23.3 + - + +
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B LEU* 3.9 18.5 - - + +
316B LEU* 4.8 3.1 - - + -
319B LEU* 3.7 29.6 - - + -
329B GLY 3.1 16.1 + - - +
330B LEU* 3.2 37.5 - - + +
332B VAL* 1.3 77.0 - - - +
334B ALA* 1.3 60.1 + - - +
335B SER 2.9 1.2 + - - -
336B THR* 3.2 11.0 + - - -
337B CYS* 3.3 37.0 + - + +
340B LEU* 4.0 26.7 - - + -
343B LEU* 4.3 5.6 - - + -
367B VAL* 4.0 9.6 - - + -
371B CYS* 4.6 0.7 - - - -
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Residues in contact with ALA 334 (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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330B LEU 2.9 15.4 + - - +
331B GLU* 2.9 13.0 + - + +
333B LEU* 1.3 71.2 - - - +
335B SER* 1.3 57.3 + - - +
337B CYS 4.7 0.8 + - - -
338B LYS* 2.7 26.2 + - - +
366B SER* 3.6 32.8 - - - +
367B VAL* 4.0 3.3 - - - +
370B GLY* 3.3 13.4 - - - +
371B CYS* 4.0 14.1 - - - -
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Residues in contact with SER 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B GLU* 3.2 8.7 + - - -
332B VAL* 3.5 13.1 + - - +
333B LEU 2.9 1.0 - - - -
334B ALA* 1.3 82.0 - - - +
336B THR* 1.3 66.0 + - - +
338B LYS* 2.8 24.1 + - - +
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Residues in contact with THR 336 (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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310B LEU* 4.3 11.9 + - - +
311B CYS* 4.4 29.1 - - - +
313B CYS 5.7 0.2 - - - -
314B PRO* 3.8 21.4 - - - +
332B VAL* 3.0 23.8 + - + +
333B LEU* 4.2 3.1 + - - -
335B SER* 1.3 87.7 - - - +
337B CYS* 1.3 67.0 + - - +
338B LYS* 3.7 4.5 + - - +
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Residues in contact with CYS 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B LEU* 4.8 6.3 - - - -
313B CYS 3.2 26.2 - - - -
314B PRO 4.3 4.7 - - - -
316B LEU* 3.9 24.9 - - - +
333B LEU* 3.3 36.5 + - + +
334B ALA 5.3 0.2 - - - -
335B SER 3.7 1.2 - - - -
336B THR* 1.3 86.9 - - - +
338B LYS* 1.3 62.4 + - - +
339B ASP 3.0 7.1 + - - -
340B LEU* 3.3 15.8 + - + -
371B CYS* 3.6 17.7 - - - -
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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