Contacts of the helix formed by residues 320 - 334 (chain B) in PDB entry 4R0C
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 SER 320 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.8 27.9 - - - +
27A TRP* 5.4 7.5 + - - -
312B ARG* 4.1 13.9 + - - +
319B ASN* 1.3 75.2 - - - +
321B GLY* 1.3 54.6 + - - +
323B VAL* 2.8 36.9 + - - +
324B ILE* 3.4 7.1 + - - +
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Residues in contact with GLY 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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19A PRO 5.5 2.9 - - - -
20A HIS* 5.1 10.9 - - - -
23A LEU* 4.1 10.3 - - - +
319B ASN* 3.2 15.7 - - - +
320B SER* 1.3 79.3 - - - +
322B ALA* 1.3 58.9 + - - +
323B VAL 3.2 0.2 - - - -
324B ILE* 3.3 15.1 - - - +
325B THR* 3.1 23.5 + - - -
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Residues in contact with ALA 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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316B GLN 4.9 1.3 - - - +
317B PHE* 3.8 32.2 - - + -
318B ARG* 3.9 4.0 - - + +
319B ASN* 3.0 28.3 + - - +
320B SER 3.0 0.4 + - - -
321B GLY* 1.3 78.9 - - - +
323B VAL* 1.3 56.0 + - - +
325B THR* 3.4 9.6 + - - -
326B ALA* 3.1 23.7 + - - +
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Residues in contact with VAL 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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95B VAL* 4.3 26.7 - - + -
304B GLY 5.7 0.2 - - - +
308B ALA* 4.6 15.5 - - + -
312B ARG* 4.4 12.6 - - + -
317B PHE* 3.3 31.9 - - + -
319B ASN 4.2 3.1 - - - +
320B SER* 2.8 14.3 + - - +
322B ALA* 1.3 74.1 - - - +
324B ILE* 1.3 69.4 + - + +
325B THR 3.2 0.4 - - - -
326B ALA* 3.4 6.7 + - - +
327B MET* 3.2 27.6 + - + +
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Residues in contact with ILE 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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20A HIS* 3.9 19.1 - - + +
22A THR* 4.0 19.1 - - + -
23A LEU* 3.8 40.4 - - + -
26A VAL* 4.1 13.5 - - + -
339A VAL* 5.3 0.7 - - + -
320B SER 4.0 6.5 - - - +
321B GLY* 3.3 11.9 - - - +
323B VAL* 1.3 79.5 - - + +
325B THR* 1.3 57.5 + - - +
327B MET* 3.3 29.1 + - + +
328B GLU* 3.1 45.3 + - + +
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Residues in contact with THR 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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20A HIS* 5.6 2.9 - - - -
321B GLY 3.1 13.3 + - - -
322B ALA* 3.6 12.1 - - - -
323B VAL 3.2 0.6 - - - -
324B ILE* 1.3 77.6 - - - +
326B ALA* 1.3 60.0 + - - +
328B GLU* 3.2 15.0 + - + +
329B VAL* 2.8 41.1 + - + +
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Residues in contact with ALA 326 (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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94B GLY 4.5 0.7 - - - +
95B VAL* 4.2 12.6 - - + -
98B GLN* 3.8 32.8 - - + +
317B PHE* 4.0 15.7 - - + -
322B ALA 3.1 13.6 + - - +
323B VAL 3.5 10.5 - - - +
325B THR* 1.3 76.2 - - - +
327B MET* 1.3 58.0 + - - +
329B VAL* 3.3 4.8 + - - +
330B THR* 2.8 32.9 + - - -
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Residues in contact with MET 327 (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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339A VAL* 3.5 24.0 - - + -
343A PHE* 3.4 38.8 - - + -
91B LEU* 4.0 27.6 - - + +
95B VAL* 3.5 19.1 - - + -
323B VAL* 3.2 14.1 - - + +
324B ILE* 3.4 35.7 - - + +
326B ALA* 1.3 75.4 - - - +
328B GLU* 1.3 63.6 + - - +
330B THR* 3.0 10.6 + - - -
331B MET* 2.9 23.4 + - - +
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Residues in contact with GLU 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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20A HIS* 3.5 26.9 + - - -
22A THR* 4.4 2.4 + - - -
335A ALA* 3.5 18.1 - - + +
336A GLY* 4.1 21.3 - - - +
339A VAL* 4.0 22.0 - - + +
324B ILE* 3.1 24.1 + - + +
325B THR* 3.5 16.1 + - + +
327B MET* 1.3 75.3 - - - +
329B VAL* 1.3 62.8 + - + +
331B MET 3.2 1.1 + - - +
332B ALA* 3.0 20.6 + - - +
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Residues in contact with VAL 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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98B GLN* 3.3 32.8 - - - +
325B THR* 2.8 35.6 + - + +
326B ALA* 3.7 4.7 - - - +
327B MET 3.2 0.2 - - - -
328B GLU* 1.3 74.1 - - + +
330B THR* 1.3 63.6 + - - +
332B ALA* 3.4 7.3 + - - +
333B SER* 3.1 26.9 + - - +
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Residues in contact with THR 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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90B MET* 3.5 50.3 - - + +
91B LEU* 5.5 0.4 - - - -
94B GLY* 3.3 29.4 + - - -
98B GLN* 5.2 2.3 + - - -
326B ALA 2.8 15.6 + - - -
327B MET* 3.0 9.9 + - - -
329B VAL* 1.3 75.8 - - - +
331B MET* 1.3 67.2 + - + +
333B SER* 3.0 22.8 + - - -
334B MET* 3.3 8.3 - - - +
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Residues in contact with MET 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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77A PHE* 5.9 2.5 - - - -
331A MET 5.3 2.1 - - - +
335A ALA* 4.3 16.6 - - + +
338A LEU* 4.6 24.5 - - + +
339A VAL* 3.8 14.1 - - + -
87B LEU* 3.6 34.3 - - + +
90B MET* 3.9 12.6 - - + -
91B LEU* 3.4 37.7 - - + +
327B MET 2.9 12.6 + - - +
328B GLU 3.8 6.1 - - - +
330B THR* 1.3 78.0 - - + +
332B ALA* 1.3 63.6 + - - +
334B MET* 3.1 36.4 + - + +
335B ALA* 3.8 2.8 + - - -
338B LEU* 5.2 4.9 - - - +
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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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331A MET 5.3 0.2 - - - -
332A ALA* 3.7 36.8 - - + +
335A ALA* 4.0 3.8 - - + +
328B GLU 3.0 16.1 + - - +
329B VAL* 3.7 7.9 - - - +
330B THR 3.2 0.4 - - - -
331B MET* 1.3 77.5 - - - +
333B SER* 1.3 62.0 + - - +
335B ALA* 3.2 20.8 + - - +
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Residues in contact with SER 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 VAL* 3.1 16.8 + - - +
330B THR* 3.0 16.6 + - - -
332B ALA* 1.3 80.4 - - - +
334B MET* 1.3 58.0 + - - +
335B ALA* 3.1 5.3 + - - +
336B GLY 4.3 4.0 + - - -
337B TYR 5.4 0.2 + - - -
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Residues in contact with MET 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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86B VAL* 3.7 29.8 - - + -
87B LEU* 3.9 16.8 - - + -
90B MET* 3.7 28.7 - - + -
330B THR* 3.3 17.0 - - - +
331B MET* 3.1 29.6 + - + +
333B SER* 1.3 78.0 - - - +
335B ALA* 1.3 63.5 + - - +
336B GLY 3.3 1.1 - - - -
337B TYR* 3.0 29.3 + - + +
338B LEU* 3.0 25.3 + - + +
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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