Contacts of the helix formed by residues 331 - 341 (chain B) in PDB entry 1PJS
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 THR 331 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ILE* 6.4 0.9 - - + -
331A THR* 6.4 2.2 - - + -
334A SER* 5.2 3.8 - - - +
225B PRO* 4.8 0.2 - - - -
303B ASP* 4.1 11.0 - - - +
306B ILE* 3.8 18.3 - - + +
329B GLY 3.1 5.5 + - - +
330B ILE* 1.3 75.5 - - - +
332B ALA* 1.3 61.7 + - - +
333B ALA* 3.9 4.9 - - + +
334B SER* 2.9 32.8 + - - +
335B GLY 2.9 11.4 + - - -
355B LEU* 5.4 2.9 - - + -
381B TYR* 2.6 26.5 + - - +
503B SAH 2.7 25.9 + - - -
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Residues in contact with ALA 332 (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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225B PRO* 4.3 13.8 - - + +
330B ILE 3.8 0.8 + - - -
331B THR* 1.3 72.0 + - - +
333B ALA* 1.3 62.8 + - - +
336B CYS* 3.0 31.2 + - - +
381B TYR* 3.9 6.5 - - + -
438B LEU* 3.4 10.3 - - + -
503B SAH 2.8 61.2 + - + +
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Residues in contact with ALA 333 (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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306A ILE* 6.2 0.7 - - + -
331B THR* 3.1 6.7 - - + -
332B ALA* 1.3 76.1 - - - +
334B SER* 1.3 57.6 + - - +
336B CYS* 4.4 0.7 - - - +
337B SER* 3.0 30.0 + - - -
344B LEU* 3.7 14.7 - - + +
355B LEU* 3.6 26.9 - - + -
379B VAL* 4.1 7.6 - - + -
381B TYR* 2.9 23.6 + - + +
438B LEU* 3.6 10.5 - - - +
440B ILE* 5.7 1.6 - - - +
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Residues in contact with SER 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ASP* 2.8 34.8 + - - +
306A ILE* 3.9 10.4 - - - +
328A PRO* 3.8 5.5 - - - +
329A GLY 4.0 5.5 + - - -
331A THR* 5.1 2.1 - - - -
330B ILE* 3.9 12.8 - - - -
331B THR* 2.9 19.9 + - - +
333B ALA* 1.3 77.6 - - - +
335B GLY* 1.3 66.0 + - - +
337B SER* 3.4 4.9 + - - -
338B ALA* 3.1 24.9 + - - +
344B LEU* 4.5 2.5 - - - -
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Residues in contact with GLY 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A PRO* 4.3 6.3 - - - -
225B PRO* 4.0 3.6 - - - -
330B ILE* 3.6 14.2 - - - +
331B THR 2.9 12.7 + - - -
332B ALA 4.0 0.2 - - - -
334B SER* 1.3 78.0 - - - +
336B CYS* 1.3 56.1 + - - +
338B ALA* 3.3 0.3 + - - +
339B TYR* 3.0 34.3 + - - +
412B THR* 3.5 22.9 - - - -
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Residues in contact with CYS 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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225B PRO* 5.5 0.9 - - - -
332B ALA* 3.0 25.2 + - - +
333B ALA 4.4 0.4 - - - +
335B GLY* 1.3 71.7 - - - +
337B SER* 1.3 59.2 + - - +
339B TYR* 4.7 4.0 - - - -
340B SER* 2.7 38.1 + - - -
408B VAL* 3.4 32.1 - - + -
411B GLY* 3.8 7.0 - - - -
412B THR* 4.1 0.6 - - - +
438B LEU* 3.7 13.9 - - + -
440B ILE* 5.1 5.2 - - + -
503B SAH 3.4 38.6 - - - -
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Residues in contact with SER 337 (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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303A ASP* 5.7 0.4 - - - -
305A PHE* 3.5 24.1 - - - +
333B ALA 3.0 22.4 + - - -
334B SER* 3.6 5.2 - - - -
335B GLY 3.2 0.2 - - - -
336B CYS* 1.3 79.6 - - - +
338B ALA* 1.3 62.5 + - - +
340B SER* 4.0 2.5 - - - -
341B GLY 3.4 1.0 + - - -
342B ILE* 2.7 49.6 + - - +
344B LEU* 3.6 21.0 + - - +
440B ILE* 5.2 4.9 - - - +
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Residues in contact with ALA 338 (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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303A ASP* 5.3 2.5 - - - +
305A PHE* 3.7 15.6 - - + -
326A VAL* 3.6 28.1 - - + +
328A PRO* 3.7 24.9 - - + -
334B SER 3.1 14.3 + - - +
335B GLY 3.7 1.6 - - - +
337B SER* 1.3 81.9 - - - +
339B TYR* 1.3 60.9 + - + +
340B SER 3.6 0.7 + - - -
341B GLY 3.8 3.5 + - - -
453B TRP* 2.8 23.4 + - - -
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Residues in contact with TYR 339 (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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234A LYS* 4.3 12.1 + - - +
326A VAL 4.0 5.2 - - - -
327A VAL* 5.6 0.2 - - - -
328A PRO* 3.6 23.5 - - + +
227B ASP* 2.8 26.6 + - - -
230B LEU* 3.4 27.9 - - + +
335B GLY 3.0 22.4 + - - +
336B CYS* 4.3 1.1 - - - +
338B ALA* 1.3 80.4 - - + +
340B SER* 1.3 59.3 + - - +
412B THR* 3.4 26.9 - - + +
416B GLN* 2.9 33.2 + - - +
452B ASN* 5.0 1.6 - - - +
453B TRP* 4.1 19.7 + + - -
454B PHE* 3.4 50.3 + + - +
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Residues in contact with SER 340 (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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336B CYS 2.7 22.0 + - - -
337B SER* 3.5 0.7 + - - -
339B TYR* 1.3 79.8 - - - +
341B GLY* 1.3 58.2 + - - +
342B ILE* 3.3 28.2 + - - +
408B VAL* 4.0 13.7 - - - +
416B GLN* 4.2 3.1 - - - +
418B VAL* 3.9 24.5 - - - -
440B ILE* 4.9 0.3 - - - +
448B ARG* 2.9 32.0 + - - +
452B ASN* 4.3 7.1 - - - +
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Residues in contact with GLY 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A PHE* 4.7 4.5 - - - -
337B SER 3.4 5.2 + - - -
338B ALA 3.8 6.2 + - - -
339B TYR 3.5 2.4 - - - -
340B SER* 1.3 80.4 - - - +
342B ILE* 1.3 59.7 + - - +
343B PRO* 3.4 12.6 - - - +
448B ARG* 3.3 22.1 + - - -
451B LEU* 3.5 34.0 - - - +
452B ASN* 4.2 1.3 - - - +
453B TRP* 5.0 1.9 - - - +
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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