Contacts of the helix formed by residues 324 - 336 (chain B) in PDB entry 4XZC
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 324 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319B GLY 4.1 5.6 - - - +
320B ILE* 3.5 17.2 - - + +
321B THR* 2.9 36.2 + - - +
323B VAL* 1.3 81.1 - - - +
325B PHE* 1.3 62.9 + - - +
326B PRO 3.4 1.3 - - - -
327B THR* 2.7 31.3 + - - -
328B LEU* 3.6 3.1 + - - +
354B LEU* 4.3 5.4 - - - +
356B TRP* 3.2 26.7 + - + -
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Residues in contact with PHE 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ASN* 4.4 3.6 - - - -
84B CYS* 4.0 17.3 - - - -
89B VAL* 3.4 47.8 - - + -
93B LEU* 5.2 0.9 - - + -
312B TYR* 4.6 4.7 - + - -
315B ALA* 5.3 1.3 - - + -
320B ILE* 3.7 16.8 - - + -
321B THR 2.9 15.1 + - - +
322B PRO* 4.2 1.6 - - + -
324B THR* 1.3 78.4 - - - +
326B PRO* 1.3 67.5 - - + +
328B LEU* 3.0 31.6 + - + +
329B SER* 2.9 25.2 + - - -
393B PHE* 3.8 41.3 - + + -
398B VAL* 4.1 16.8 - - + -
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Residues in contact with PRO 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET 3.4 11.4 - - - +
2B GLU* 4.7 0.9 - - - -
3B ASN* 3.7 29.8 - - + +
322B PRO 3.7 9.4 - - - +
323B VAL 3.7 12.8 - - - +
324B THR 3.6 3.1 - - - -
325B PHE* 1.3 95.4 - - + +
327B THR* 1.3 57.9 + - + +
329B SER* 3.8 2.0 - - - -
330B GLN* 3.0 25.3 + - - +
398B VAL* 3.5 24.4 + - + +
399B SER* 3.4 26.4 + - - +
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Residues in contact with THR 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET 5.1 12.6 - - - +
323B VAL 5.5 2.0 - - - +
324B THR* 2.7 24.5 + - - +
325B PHE 3.2 0.4 - - - -
326B PRO* 1.3 75.9 - - + +
328B LEU* 1.3 61.3 + - - +
330B GLN* 3.7 7.9 - - + +
331B PHE* 3.0 26.9 + - - +
354B LEU* 3.2 34.8 - - + +
356B TRP* 3.3 7.1 + - - -
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Residues in contact with LEU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B ALA* 4.3 5.8 - - + -
320B ILE* 4.3 17.9 - - + -
324B THR 3.6 1.7 + - - +
325B PHE* 3.0 29.1 + - + +
327B THR* 1.3 79.3 + - - +
329B SER* 1.3 64.9 + - - +
331B PHE* 3.1 1.4 + - - +
332B LEU* 2.9 43.1 + - + +
356B TRP* 3.6 37.2 - - + -
360B ILE* 5.5 2.9 - - + -
386B MET* 5.8 1.8 - - + -
389B MET* 3.7 23.3 - - + -
393B PHE* 3.7 28.7 - - + -
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Residues in contact with SER 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B PHE* 2.9 17.9 + - - -
326B PRO 3.8 2.0 - - - -
328B LEU* 1.3 76.4 - - - +
330B GLN* 1.3 57.8 + - - +
333B PHE* 3.0 29.3 + - - +
393B PHE* 2.9 32.0 + - - +
394B GLY* 3.7 0.2 - - - -
396B VAL 3.8 1.7 + - - -
397B PRO* 3.2 5.0 - - - +
398B VAL* 3.1 46.6 + - - +
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Residues in contact with GLN 330 (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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326B PRO 3.0 18.9 + - - +
327B THR* 3.8 8.7 - - - +
328B LEU 3.1 0.2 - - - -
329B SER* 1.3 78.1 - - - +
331B PHE* 1.3 57.6 + - - +
333B PHE* 3.2 13.5 + - - +
334B GLU* 2.9 66.9 + - + +
397B PRO* 3.7 18.3 - - - +
399B SER* 4.3 10.6 - - - +
400B ASN* 4.2 15.6 + - - +
403B ASP* 5.6 4.4 + - - -
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Residues in contact with PHE 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B THR 3.0 19.9 + - - +
328B LEU 3.1 4.0 + - - +
330B GLN* 1.3 77.3 - - - +
332B LEU* 1.3 70.1 + - + +
334B GLU* 3.5 7.3 + - + +
335B MET* 3.1 30.7 + - + +
345B MET* 3.6 38.1 - - + -
348B ALA* 3.6 26.5 - - + -
349B LEU* 3.6 32.1 - - + -
352B THR* 6.2 2.5 - - - -
356B TRP* 4.3 14.6 - + + -
386B MET* 4.9 2.5 - - + -
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Residues in contact with LEU 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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328B LEU* 2.9 34.6 + - + +
329B SER 4.0 0.2 - - - +
331B PHE* 1.3 87.3 - - + +
333B PHE* 1.3 65.0 + - - +
335B MET* 3.1 32.4 + - + +
386B MET* 4.3 17.9 - - + +
389B MET* 3.4 38.6 - - + +
390B GLY* 3.9 7.6 - - - +
393B PHE* 3.5 18.2 - - + -
394B GLY* 3.6 17.3 - - - +
410B HIS* 3.2 21.7 - - - -
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Residues in contact with PHE 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B SER 3.0 19.9 + - - +
330B GLN* 3.6 12.1 - - - +
332B LEU* 1.3 75.4 - - - +
334B GLU* 1.3 79.2 + - - +
337B GLN* 3.2 35.2 - - - +
394B GLY* 3.3 25.3 - - - +
395B VAL 3.7 8.7 - - - -
397B PRO* 3.5 40.4 - - + -
403B ASP* 3.4 28.0 - - + -
404B ALA* 4.1 3.4 - - - -
406B LEU* 4.0 15.0 - - + -
407B GLY 4.1 11.7 - - - -
408B SER* 2.7 23.1 + - - -
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Residues in contact with GLU 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 GLN* 2.9 48.7 + - + +
331B PHE* 4.0 5.8 - - - +
333B PHE* 1.3 82.9 - - - +
335B MET* 1.3 59.8 + - - +
337B GLN* 3.1 31.9 + - - +
340B ARG* 2.8 38.7 + - - +
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Residues in contact with MET 335 (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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68B VAL* 5.2 0.5 - - - +
331B PHE* 3.1 21.8 + - + +
332B LEU* 3.1 31.5 + - + +
334B GLU* 1.3 78.3 - - - +
336B GLY* 1.3 55.2 + - - +
337B GLN 3.3 0.7 - - - -
338B GLY 3.1 18.7 - - - +
340B ARG* 3.2 15.9 + - + +
341B GLY* 4.0 21.9 + - - +
345B MET* 3.8 32.5 - - + +
386B MET* 4.0 15.5 - - - +
387B SER* 4.9 2.7 - - - +
390B GLY* 3.9 7.4 - - - -
410B HIS* 3.8 24.7 - - + +
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Residues in contact with GLY 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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68B VAL* 3.7 10.1 - - - +
72B LYS* 5.1 1.0 - - - +
332B LEU 3.3 7.9 + - - -
334B GLU 3.3 0.6 - - - -
335B MET* 1.3 78.6 - - - +
337B GLN* 1.3 57.3 + - - -
338B GLY 3.4 2.9 - - - -
408B SER* 3.2 20.6 + - - -
409B GLY* 2.5 44.3 + - - -
410B HIS* 3.9 4.2 - - - -
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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