Contacts of the helix formed by residues 323 - 338 (chain B) in PDB entry 1F0K
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 323 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184B VAL* 5.6 1.1 - - - -
321B GLY 3.7 4.4 + - - -
322B TRP* 1.3 74.9 - - - +
324B ARG* 1.3 60.6 + - - +
325B GLU* 3.4 8.8 + - - +
326B THR* 3.1 27.5 + - - -
327B LEU* 2.9 28.8 + - - +
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Residues in contact with ARG 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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177B LEU* 5.7 3.0 - - - +
180B ARG* 3.3 42.3 + - - +
181B GLU* 3.7 15.2 + - - +
182B GLY 3.1 29.0 + - - +
183B PRO 3.2 11.1 + - - -
184B VAL* 4.0 12.4 - - + +
185B ARG* 4.8 1.8 - - - +
256B ASP* 2.9 42.9 + - - -
323B SER* 1.3 73.8 - - - +
325B GLU* 1.3 57.7 + - - +
327B LEU* 3.4 10.8 + - + +
328B LEU* 3.0 29.1 + - - +
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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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323B SER* 3.2 8.1 + - - +
324B ARG* 1.3 75.3 - - - +
326B THR* 1.3 66.1 + - - +
328B LEU* 3.3 9.4 + - + +
329B THR* 3.1 25.5 + - - +
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Residues in contact with THR 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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321B GLY 4.8 3.4 + - - +
322B TRP* 4.0 19.1 - - + -
323B SER* 3.1 25.1 + - - -
325B GLU* 1.3 80.0 - - - +
327B LEU* 1.3 58.4 + - - +
329B THR* 3.2 8.4 + - + -
330B MET* 2.9 47.3 + - + +
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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
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177B LEU* 4.8 4.7 - - + +
184B VAL* 3.8 34.1 - - + -
256B ASP* 4.1 21.5 - - + +
257B VAL* 4.2 5.8 - - + -
276B PRO* 3.2 34.3 - - + +
322B TRP* 3.9 39.5 - - + +
323B SER 2.9 22.4 + - - +
324B ARG* 3.7 10.1 - - + +
326B THR* 1.3 73.8 - - - +
328B LEU* 1.3 59.5 + - - +
330B MET* 4.3 2.9 - - - -
331B ALA* 2.8 27.2 + - - +
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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
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173B PRO* 4.2 0.7 - - + -
174B GLN* 3.9 37.5 - - + +
177B LEU* 3.7 31.4 - - + +
324B ARG 3.0 17.0 + - - +
325B GLU* 3.6 8.5 - - + +
326B THR 3.3 0.2 - - - -
327B LEU* 1.3 75.0 - - - +
329B THR* 1.3 63.5 + - - +
331B ALA* 3.2 1.4 + - - +
332B GLU* 3.0 45.2 + - + +
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Residues in contact with THR 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* 3.1 16.5 + - - +
326B THR* 3.5 11.0 - - + +
328B LEU* 1.3 77.8 - - - +
330B MET* 1.3 62.7 + - + +
332B GLU* 3.3 14.0 + - - +
333B ARG* 3.0 63.2 + - + +
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Residues in contact with MET 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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276B PRO* 3.6 20.6 - - + -
277B ALA 4.7 0.2 - - - +
300B GLY 3.6 20.4 - - - +
301B ALA* 3.5 35.1 - - - +
302B ALA* 3.9 7.4 - - - +
322B TRP* 3.5 52.9 - - + +
326B THR* 2.9 36.6 + - + +
327B LEU* 3.6 5.6 - - - +
329B THR* 1.3 75.7 - - + +
331B ALA* 1.3 62.9 + - - +
333B ARG* 3.3 5.1 + - - +
334B ALA* 2.9 20.6 + - - +
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Residues in contact with ALA 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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173B PRO* 3.7 15.2 - - + +
176B ARG* 5.3 0.2 - - - +
177B LEU* 4.1 12.3 - - + -
274B GLY* 3.1 30.4 - - - +
276B PRO* 3.6 14.7 - - + +
327B LEU 2.8 17.3 + - - +
328B LEU 3.5 4.9 - - - +
330B MET* 1.3 77.1 - - - +
332B GLU* 1.3 57.1 + - - +
334B ALA* 3.1 4.7 + - - +
335B ARG 3.0 23.6 + - - -
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Residues in contact with GLU 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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173B PRO* 4.1 20.2 - - + -
174B GLN* 4.2 19.3 - - - +
328B LEU* 3.0 30.5 + - + +
329B THR* 3.7 13.8 + - - +
331B ALA* 1.3 71.9 - - - +
333B ARG* 1.3 62.0 + - + +
335B ARG* 3.3 4.5 + - - +
336B ALA* 2.9 29.3 + - - +
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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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299B ALA* 3.2 25.8 + - + +
300B GLY* 3.1 32.0 + - - -
301B ALA* 3.8 7.9 - - + +
329B THR* 3.0 43.2 + - + +
330B MET* 3.6 6.8 - - - +
331B ALA 3.3 0.2 - - - -
332B GLU* 1.3 76.5 - - + +
334B ALA* 1.3 62.3 + - - +
336B ALA* 3.4 8.0 + - - +
337B ALA* 3.0 24.3 + - - +
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Residues in contact with ALA 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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270B ILE* 5.1 1.1 - - + -
271B ALA* 3.2 24.1 - - - +
274B GLY* 4.0 0.7 - - - -
275B LEU 3.6 31.2 - - - +
296B LEU* 4.4 7.6 - - + -
301B ALA* 3.5 13.6 - - + +
330B MET 2.9 12.8 + - - +
331B ALA 3.3 9.6 - - - +
333B ARG* 1.3 74.7 - - - +
335B ARG* 1.3 66.0 + - - +
337B ALA* 3.0 11.3 + - - -
338B SER 3.2 6.4 + - - -
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Residues in contact with ARG 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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168B LEU 4.3 9.2 + - - -
170B LEU* 3.0 24.4 + - - +
171B PRO 3.3 18.0 + - - -
172B LEU* 3.3 39.5 - - + +
173B PRO* 3.9 15.0 - - + +
271B ALA 3.2 7.3 + - - -
272B ALA* 3.2 29.7 + - - +
273B ALA* 3.7 12.3 + - - +
274B GLY* 3.9 4.4 - - - -
331B ALA 3.0 11.9 + - - +
332B GLU* 3.3 8.3 + - - +
334B ALA* 1.3 75.1 - - - +
336B ALA* 1.3 58.9 + - - +
338B SER* 3.0 27.6 + - - +
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Residues in contact with ALA 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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332B GLU 2.9 17.7 + - - +
333B ARG* 3.6 9.2 - - - +
334B ALA 3.2 0.2 - - - -
335B ARG* 1.3 77.9 - - - +
337B ALA* 1.3 59.4 + - - +
338B SER 3.1 6.1 + - - +
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Residues in contact with ALA 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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149B PHE* 6.1 0.7 - - - -
271B ALA* 4.5 3.4 - - - +
295B PRO 5.7 1.1 - - - +
296B LEU* 3.7 23.1 - - + -
299B ALA* 4.7 12.8 - - + -
333B ARG 3.0 16.4 + - - +
334B ALA 3.0 4.9 + - - +
336B ALA* 1.3 76.0 - - - +
338B SER* 1.3 60.6 + - - +
339B ILE* 4.0 7.7 + - - +
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Residues in contact with SER 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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163B VAL* 5.8 0.3 - - - +
268B SER 4.7 0.9 + - - -
271B ALA* 3.4 31.9 - - - -
272B ALA* 3.3 22.1 + - - +
334B ALA 3.2 2.2 + - - -
335B ARG* 3.0 20.6 + - - +
336B ALA 3.9 6.6 - - - +
337B ALA* 1.3 81.2 - - - +
339B ILE* 1.3 70.5 + - - +
340B PRO* 3.8 12.5 - - - +
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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