Contacts of the helix formed by residues 320 - 333 (chain B) in PDB entry 1O2D
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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319B VAL* 1.3 79.3 - - - +
321B SER* 1.3 64.3 + - - +
322B GLU* 3.5 9.6 + - - +
323B GLU* 3.0 37.6 + - - +
324B LEU* 3.0 19.6 + - - +
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Residues in contact with SER 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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320B SER* 1.3 71.9 - - - +
322B GLU* 1.3 56.7 + - - +
324B LEU* 3.3 10.2 + - - +
325B GLU* 2.9 43.8 + - - +
354B ARG* 5.6 6.6 + - - +
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Residues in contact with GLU 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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320B SER* 3.2 9.3 - - - +
321B SER* 1.3 79.3 - - - +
323B GLU* 1.3 64.0 + - + +
325B GLU* 3.6 4.2 + - - +
326B LYS* 3.2 24.0 + - + +
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Residues in contact with GLU 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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265B GLU* 4.6 11.4 - - - +
266B LYS* 2.7 42.0 + - - -
318B ALA 4.4 0.2 - - - -
319B VAL* 3.5 3.7 - - + -
320B SER* 3.0 40.4 + - - +
322B GLU* 1.3 75.0 - - + +
324B LEU* 1.3 67.1 + - - +
326B LYS* 3.2 13.5 + - - +
327B TRP* 2.9 46.0 + - + -
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Residues in contact with LEU 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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319B VAL* 4.1 10.3 - - + +
320B SER 3.0 15.5 + - - +
321B SER* 3.6 9.9 - - - +
323B GLU* 1.3 76.6 - - - +
325B GLU* 1.3 66.5 + - - +
327B TRP* 3.2 13.7 + - + +
328B VAL* 2.9 38.1 + - + +
350B ARG* 4.0 15.9 - - + +
353B TYR* 3.5 37.5 - - + -
354B ARG* 3.8 42.6 - - + +
357B LEU* 5.8 0.4 - - + -
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Residues in contact with GLU 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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321B SER* 2.9 31.1 + - - +
322B GLU* 4.2 4.5 - - - +
324B LEU* 1.3 83.5 - - - +
326B LYS* 1.3 57.2 + - - +
328B VAL* 3.3 7.9 + - - +
329B GLU* 3.0 30.0 + - - +
350B ARG* 2.8 48.0 + - - -
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Residues in contact with LYS 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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265B GLU* 2.7 40.0 + - - -
322B GLU* 3.2 14.7 + - + +
323B GLU* 3.2 16.0 + - - +
325B GLU* 1.3 76.4 - - - +
327B TRP* 1.3 70.1 + - + +
329B GLU* 3.2 6.1 + - - +
330B LYS* 2.9 54.4 + - - +
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Residues in contact with TRP 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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261B PRO* 3.6 27.7 - - + +
262B LEU* 3.5 26.7 - - + -
265B GLU* 3.1 27.2 + - + -
266B LYS* 3.9 36.8 - - + -
319B VAL* 3.7 25.8 - - + -
323B GLU* 2.9 31.1 + - + -
324B LEU* 3.7 11.2 - - + +
326B LYS* 1.3 85.6 - - + +
328B VAL* 1.3 61.0 + - - +
330B LYS* 4.0 8.8 - - + +
331B GLY* 2.9 27.2 + - - -
353B TYR* 3.6 44.6 + + + +
357B LEU* 3.7 10.1 - - + -
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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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324B LEU* 2.9 32.0 + - + +
325B GLU* 3.7 9.9 - - - +
326B LYS 3.3 0.2 - - - -
327B TRP* 1.3 75.8 - - - +
329B GLU* 1.3 59.4 + - - +
331B GLY* 3.9 0.7 - - - -
332B SER* 3.1 28.4 + - - +
346B PRO* 3.8 35.0 - - + +
349B ILE* 4.1 14.5 - - + +
350B ARG* 3.7 44.9 - - + +
353B TYR* 4.4 2.0 - - + -
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Residues in contact with GLU 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 GLU 3.0 16.5 + - - +
326B LYS* 3.7 5.1 - - - +
328B VAL* 1.3 77.9 - - + +
330B LYS* 1.3 64.8 + - - +
332B SER* 3.2 20.5 + - - -
333B ARG* 3.4 41.8 + - - +
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Residues in contact with LYS 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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154B GLU 5.7 0.8 + - - -
156B ASN* 3.0 33.3 + - - +
261B PRO* 6.1 6.1 - - + -
265B GLU* 4.3 12.1 + - - +
326B LYS* 2.9 51.4 + - + +
327B TRP* 4.0 9.0 - - + +
329B GLU* 1.3 73.2 + - - +
331B GLY* 1.3 61.0 + - - +
333B ARG* 3.3 38.3 + - - +
334B ALA* 3.5 10.7 + - - +
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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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254B LEU* 3.8 7.1 - - - +
257B ALA* 5.9 1.1 - - - -
258B LEU* 3.9 21.5 - - - -
327B TRP 2.9 17.5 + - - -
328B VAL 3.9 1.3 - - - -
330B LYS* 1.3 73.9 - - - +
332B SER* 1.3 62.6 + - - +
333B ARG 3.1 3.2 + - - -
334B ALA* 3.3 19.2 + - - +
337B LEU* 3.5 10.0 - - - +
349B ILE* 4.1 7.9 - - - +
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Residues in contact with SER 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 VAL* 3.1 17.4 + - - +
329B GLU* 3.2 16.8 + - - -
331B GLY* 1.3 75.2 - - - +
333B ARG* 1.3 60.2 + - - +
337B LEU* 3.2 19.9 - - - +
344B PHE 5.1 2.2 + - - -
346B PRO* 4.4 20.8 - - - +
349B ILE* 4.1 13.0 - - - +
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Residues in contact with ARG 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 GLU* 3.4 38.0 + - - +
330B LYS* 3.3 34.8 + - - +
331B GLY 3.1 0.6 - - - -
332B SER* 1.3 80.0 - - - +
334B ALA* 1.3 63.3 + - - +
335B LYS* 3.4 5.2 + - - +
337B LEU* 4.9 0.2 - - - -
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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