Contacts of the helix formed by residues 316 - 331 (chain B) in PDB entry 3OP5
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 LEU 316 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305B THR* 5.7 2.4 - - + +
309B LEU* 5.0 1.8 - - - +
314B LYS 3.8 3.5 + - - +
315B PRO* 1.3 72.2 - - - +
317B TYR* 1.3 63.3 + - - +
318B GLU* 3.3 4.3 - - + -
319B ASN* 3.1 41.0 + - + +
320B LEU* 3.3 15.2 + - - +
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Residues in contact with TYR 317 (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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162B LEU* 4.4 10.6 - - + +
165B LEU 4.5 0.4 - - - -
166B GLU* 3.6 63.0 - - + +
169B HIS* 2.7 43.5 + + - +
170B GLU* 4.6 8.7 + - - -
240B ARG* 3.6 2.4 + - - -
244B LEU* 4.6 14.1 - - + -
314B LYS* 4.6 10.8 - - + -
315B PRO* 3.3 55.4 + - + +
316B LEU* 1.3 72.2 - - - +
318B GLU* 1.4 57.0 + - - +
320B LEU* 3.3 11.8 + - + +
321B ARG* 3.0 38.1 + - - +
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Residues in contact with GLU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B LEU* 3.3 2.3 - - + -
317B TYR* 1.4 76.2 - - - +
319B ASN* 1.3 58.8 + - - +
321B ARG* 3.3 34.3 + - - +
322B ASP* 3.0 44.3 + - - +
325B LEU* 5.4 1.9 - - - +
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Residues in contact with ASN 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B THR* 5.5 9.0 - - + +
316B LEU* 3.1 37.8 + - + +
318B GLU* 1.3 80.7 - - - +
320B LEU* 1.4 60.7 + - - +
322B ASP* 3.4 14.1 + - - +
323B ILE* 3.2 29.5 + - + +
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Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LEU* 3.9 18.8 - - + -
244B LEU* 3.7 37.5 - - + -
302B TYR* 3.7 25.8 - - + +
305B THR* 3.9 31.9 - - + -
306B VAL* 4.2 8.3 - - + -
309B LEU* 5.7 1.3 - - + -
315B PRO* 4.6 5.2 - - + -
316B LEU 3.3 13.2 + - - +
317B TYR* 3.3 15.8 + - + +
319B ASN* 1.4 73.8 - - - +
321B ARG* 1.3 63.7 + - - +
323B ILE* 3.4 11.0 + - + +
324B LEU* 3.3 25.8 + - - +
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Residues in contact with ARG 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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103B ARG* 5.3 1.8 - - - +
159B LEU* 3.7 25.1 + - + +
160B ARG* 6.1 1.1 - - - +
162B LEU* 3.5 35.6 + - + +
163B ASP* 3.0 32.1 + - - +
166B GLU* 2.6 32.1 + - - +
317B TYR* 3.0 29.9 + - - +
318B GLU* 3.3 40.4 + - - +
320B LEU* 1.3 73.7 - - - +
322B ASP* 1.4 58.4 + - - +
324B LEU* 3.2 4.2 + - - +
325B LEU* 2.9 39.6 + - + +
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Residues in contact with ASP 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B GLU* 3.0 37.5 + - - +
319B ASN* 3.4 16.3 + - - +
321B ARG* 1.4 70.4 - - - +
323B ILE* 1.3 58.8 + - - +
325B LEU* 3.3 16.4 + - - +
326B GLN* 3.0 30.0 + - - +
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Residues in contact with ILE 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B GLU* 3.3 41.9 - - + +
301B LYS* 3.8 21.1 - - + +
302B TYR* 3.8 15.5 - - + +
305B THR* 3.3 31.6 - - + +
319B ASN* 3.2 19.3 + - + +
320B LEU* 3.5 14.4 - - - +
321B ARG 3.3 0.2 - - - -
322B ASP* 1.3 75.1 - - + +
324B LEU* 1.4 62.0 + - + +
326B GLN* 3.3 18.2 + - - +
327B GLY 3.4 0.3 + - - -
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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
----------------------------------------------------------
155B LEU* 3.6 29.8 - - + +
158B SER* 3.6 31.4 - - - -
159B LEU* 3.9 16.4 - - + +
162B LEU* 3.7 26.7 - - + -
251B MET* 4.2 20.2 - - + -
298B GLU* 4.5 9.0 - - + +
299B ILE* 5.1 0.9 - - + -
302B TYR* 4.4 20.0 - - + -
320B LEU 3.3 9.1 + - - +
321B ARG 3.2 6.3 + - - +
323B ILE* 1.4 73.4 - - - +
325B LEU* 1.4 63.4 + - - +
327B GLY* 3.1 12.1 + - - -
328B LEU* 3.3 13.5 + - - +
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Residues in contact with LEU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B LEU* 4.0 15.0 - - + -
318B GLU* 5.4 1.8 - - - +
321B ARG* 2.9 30.5 + - + +
322B ASP* 3.3 19.7 + - - +
324B LEU* 1.4 73.0 - - - +
326B GLN* 1.4 64.0 + - - +
328B LEU* 3.3 11.0 + - + +
329B LYS* 3.1 22.0 + - - +
335B ASP* 3.6 35.4 - - + +
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Residues in contact with GLN 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B GLU* 5.6 0.9 - - + -
322B ASP 3.0 13.2 + - - +
323B ILE* 3.4 12.8 - - - +
324B LEU 3.3 0.2 - - - -
325B LEU* 1.4 74.8 - - - +
327B GLY* 1.3 56.4 + - - +
329B LYS* 3.4 11.5 + - - +
330B ALA* 3.0 28.3 + - - +
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Residues in contact with GLY 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ARG* 4.2 1.4 + - - -
155B LEU* 3.6 8.4 - - - +
298B GLU* 3.6 30.9 - - - +
323B ILE 3.4 4.4 + - - -
324B LEU 3.1 10.0 + - - -
326B GLN* 1.3 76.7 - - - +
328B LEU* 1.4 61.3 + - - +
330B ALA* 3.4 7.5 + - - +
331B ILE* 3.3 26.0 + - - +
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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
----------------------------------------------------------
152B LYS* 3.7 28.9 - - + +
155B LEU* 4.0 25.8 - - + -
156B GLN* 3.4 27.1 - - - +
159B LEU* 3.8 25.1 - - + -
324B LEU 3.3 6.9 + - - +
325B LEU* 3.3 14.4 + - + +
327B GLY* 1.4 71.9 - - - +
329B LYS* 1.3 59.8 + - - +
331B ILE* 3.3 12.8 - - + +
333B SER* 2.7 37.1 + - - +
334B LYS* 4.2 11.7 - - - +
335B ASP* 3.9 14.8 - - + +
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Residues in contact with LYS 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 LEU 3.1 12.6 + - - +
326B GLN* 3.6 12.6 - - - +
328B LEU* 1.3 75.8 - - - +
330B ALA* 1.4 61.0 + - - +
332B GLY* 3.1 14.0 + - - -
333B SER 3.8 9.6 + - - +
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Residues in contact with ALA 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ARG* 4.1 18.2 - - - +
326B GLN 3.0 16.6 + - - +
327B GLY* 3.5 9.0 - - - +
329B LYS* 1.4 77.9 - - - +
331B ILE* 1.4 57.1 - - - +
332B GLY 3.3 2.5 + - - -
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Residues in contact with ILE 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ARG* 3.7 46.2 - - + +
152B LYS* 3.8 39.0 - - + +
155B LEU* 4.8 1.3 - - + -
327B GLY 3.3 9.2 + - - +
328B LEU* 3.3 18.4 - - + +
330B ALA* 1.4 74.9 - - - +
332B GLY* 1.3 59.5 + - - +
333B SER* 3.5 16.0 + - - -
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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
------------------------------------------------------------
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