Contacts of the helix formed by residues 321 - 335 (chain B) in PDB entry 4CZ8
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 321 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B PHE* 3.6 26.1 - - + -
317B VAL* 2.6 31.6 + - - +
318B ILE* 3.4 5.4 - - - -
319B TRP 3.0 0.2 - - - -
320B SER* 1.3 87.3 - - - +
322B LEU* 1.3 62.6 + - - +
323B GLY 3.5 1.8 - - - -
324B LYS* 3.1 26.5 + - - +
325B GLY* 3.0 20.3 + - - -
388B HIS* 5.8 2.0 + - - -
392B ILE* 3.6 27.4 - - + +
395B ALA* 5.7 4.3 - - + -
396B THR* 6.2 0.4 - - + -
399B ILE* 5.6 2.1 - - - +
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Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ILE* 2.9 19.0 + - + +
319B TRP* 3.4 32.1 + - + +
320B SER 3.7 0.2 - - - -
321B ASN* 1.3 77.8 - - - +
323B GLY* 1.3 63.7 + - - +
326B LEU* 2.9 47.6 + - + +
399B ILE* 4.9 14.8 - - + +
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Residues in contact with GLY 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B ASN 3.5 0.2 - - - -
322B LEU* 1.3 85.3 - - - +
324B LYS* 1.3 64.2 + - - +
326B LEU* 3.3 8.7 + - - +
327B LEU* 2.9 35.0 + - - +
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Residues in contact with LYS 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B VAL* 3.6 27.8 - - + +
112B PHE* 3.6 19.7 - - + -
320B SER 2.5 29.8 + - - -
321B ASN* 3.1 25.2 + - - +
322B LEU 3.3 0.2 - - - -
323B GLY* 1.3 77.3 - - - +
325B GLY* 1.3 60.0 + - - +
327B LEU* 3.1 5.5 + - - +
328B VAL* 2.9 31.1 + - - +
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Residues in contact with GLY 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE* 3.7 8.6 - - - -
321B ASN 3.0 13.1 + - - -
322B LEU 3.9 0.4 - - - -
324B LYS* 1.3 78.7 - - - +
326B LEU* 1.3 57.3 + - - +
328B VAL* 3.4 14.7 - - - +
329B ALA* 2.9 26.3 + - - +
396B THR* 4.2 16.9 - - - +
399B ILE* 3.7 12.7 - - - +
400B THR* 5.4 0.2 - - - -
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Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B LEU* 2.9 36.8 + - + +
323B GLY* 3.4 7.9 - - - +
324B LYS 3.1 0.2 - - - -
325B GLY* 1.3 78.3 - - - +
327B LEU* 1.3 66.8 + - + +
329B ALA* 3.0 4.3 + - - +
330B LEU* 2.9 53.1 + - + +
399B ILE* 3.7 9.4 - - + +
403B THR* 3.7 24.2 - - + -
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Residues in contact with LEU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ILE* 4.7 3.0 - - - +
111B VAL* 5.4 6.0 - - + +
323B GLY* 2.9 22.3 + - - +
324B LYS* 3.7 5.2 - - - +
326B LEU* 1.3 84.3 - - + +
328B VAL* 1.3 60.3 + - - +
330B LEU* 4.5 15.9 - - + +
331B GLY* 2.9 25.0 + - - +
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Residues in contact with VAL 328 (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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107B ILE* 4.0 17.4 - - + +
108B PHE* 4.7 11.2 - - + +
111B VAL* 3.7 23.8 - - + -
112B PHE* 3.7 22.0 - - + -
122B PHE* 3.8 33.4 - - + -
324B LYS 2.9 20.2 + - - +
325B GLY* 3.4 9.9 - - - +
327B LEU* 1.3 77.8 - - - +
329B ALA* 1.3 57.7 + - - +
331B GLY* 3.3 0.5 + - - -
332B VAL* 2.9 37.4 + - + +
396B THR* 5.2 1.8 - - - -
400B THR* 6.1 0.2 - - - -
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Residues in contact with ALA 329 (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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325B GLY 2.9 14.5 + - - +
326B LEU* 3.0 10.1 + - - +
328B VAL* 1.3 73.8 - - - +
330B LEU* 1.3 62.8 + - + +
332B VAL* 3.1 8.6 + - - +
333B MSE 2.9 32.7 + - - +
399B ILE* 4.2 3.8 - - + -
400B THR* 3.5 26.9 - - - +
403B THR* 3.4 25.8 - - - +
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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
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326B LEU* 2.9 45.2 + - + +
327B LEU* 4.6 17.3 - - + +
329B ALA* 1.3 77.9 - - + +
331B GLY* 1.3 57.0 + - - +
333B MSE 4.2 16.4 - - + -
334B ILE* 2.9 43.8 + - + +
403B THR* 4.7 9.2 - - + -
407B VAL* 5.9 4.3 - - + -
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Residues in contact with GLY 331 (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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107B ILE* 3.7 14.4 - - - +
327B LEU 2.9 22.7 + - - -
328B VAL 3.5 1.8 - - - -
329B ALA 3.0 0.4 - - - -
330B LEU* 1.3 77.5 - - - +
332B VAL* 1.3 55.4 + - - +
334B ILE* 5.2 0.4 - - - -
335B LEU* 2.8 38.8 + - - +
336B ALA 3.3 0.5 + - - -
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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
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100B THR* 5.9 2.0 - - + -
104B ALA* 3.5 30.1 - - + -
107B ILE* 3.7 12.6 - - + -
122B PHE* 4.6 5.2 - - + -
126B ILE* 5.1 10.1 - - + -
328B VAL* 2.9 29.6 + - + +
329B ALA* 3.1 14.4 - - - +
331B GLY* 1.3 74.4 - - - +
333B MSE 1.3 64.3 + - + +
336B ALA* 3.2 12.6 - - + +
337B ARG* 3.0 31.2 + - - +
362B ARG* 5.3 9.4 + - + +
400B THR* 3.9 20.0 - - - +
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Residues in contact with MSE 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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329B ALA* 2.9 24.3 + - - +
330B LEU* 3.9 14.8 - - + +
332B VAL* 1.3 85.6 - - + +
334B ILE* 1.3 67.7 + - + +
337B ARG* 4.1 7.5 - - - +
338B PRO* 3.6 13.9 - - - +
358B LEU* 4.8 10.4 - - - +
362B ARG* 6.4 0.4 - - + +
400B THR* 4.8 1.6 - - - +
403B THR* 4.0 12.6 - - - -
404B SER* 3.6 42.4 - - - +
407B VAL* 3.6 40.6 - - + -
408B GLU* 4.0 13.9 - - - +
411B TRP* 5.3 6.9 - - + -
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Residues in contact with ILE 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 28.8 + - + +
331B GLY* 4.6 0.4 - - - +
333B MSE 1.3 88.7 - - + +
335B LEU* 1.3 61.3 + - + +
338B PRO* 3.2 22.2 - - - +
358B LEU* 5.3 5.8 - - + +
411B TRP* 4.4 25.8 - - + -
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Residues in contact with LEU 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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103B ILE* 4.8 9.0 - - + -
107B ILE* 4.8 15.5 - - + -
331B GLY* 2.8 22.6 + - - +
334B ILE* 1.3 77.5 - - + +
336B ALA* 1.3 60.9 + - - +
338B PRO* 3.9 0.7 - - - +
339B LEU* 3.1 44.3 + - + +
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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