Contacts of the helix formed by residues 316 - 330 (chain B) in PDB entry 1L6O
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 316 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B ASN* 4.6 6.7 - - - +
314B ASN 4.2 0.2 + - - -
315B MSE 1.3 75.5 - - - +
317B ASN* 1.3 65.7 + - - +
318B ASP* 3.4 11.6 + - - +
319B ASP* 3.1 35.8 + - - +
320B ALA* 3.0 19.3 + - - +
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Residues in contact with ASN 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A HIS* 5.7 0.4 - - - +
271B GLY* 4.4 2.9 - - - -
272B GLN 2.8 22.8 + - - +
273B SER* 4.2 2.8 - - - +
274B ASN* 2.8 27.1 + - - +
280B GLY* 3.1 33.2 + - - +
281B ILE* 3.3 16.7 - - + +
315B MSE 3.8 1.1 + - - +
316B SER* 1.3 72.2 - - - +
318B ASP* 1.3 63.9 + - - +
320B ALA* 3.1 5.1 + - - +
321B VAL* 2.8 35.3 + - - +
3E LYS* 4.7 4.2 - - - +
5E MET* 4.3 14.5 - - + +
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Residues in contact with ASP 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A HIS* 3.6 34.4 - - - +
316B SER* 3.5 11.1 + - - +
317B ASN* 1.3 78.2 + - - +
319B ASP* 1.4 58.9 + - - +
321B VAL* 2.9 8.5 + - - +
322B ARG* 2.7 46.3 + - - +
5E MET* 5.4 1.7 - - - +
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Residues in contact with ASP 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B MSE 3.9 21.3 - - + +
316B SER* 3.1 25.1 + - - +
318B ASP* 1.4 79.3 - - - +
320B ALA* 1.4 61.9 + - - +
321B VAL 3.1 0.3 + - - -
322B ARG* 2.6 28.5 + - - +
323B VAL* 2.9 26.5 + - + +
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Residues in contact with ALA 320 (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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281B ILE* 3.9 20.4 - - + -
312B PHE* 3.6 40.0 - - + +
315B MSE 4.2 9.3 - - + +
316B SER 3.0 13.5 + - - +
317B ASN* 3.1 8.7 + - - +
319B ASP* 1.4 77.6 - - - +
321B VAL* 1.4 58.0 + - - +
323B VAL* 3.1 5.5 + - - +
324B LEU* 3.0 24.1 + - - +
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Residues in contact with VAL 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ILE* 4.5 13.9 - - + -
281B ILE* 4.7 7.4 - - + -
317B ASN 2.8 17.9 + - - +
318B ASP* 2.9 10.1 + - - +
320B ALA* 1.4 77.7 - - - +
322B ARG* 1.3 57.0 + - - +
324B LEU* 2.8 30.7 + - + +
325B ARG* 2.9 26.1 + - + +
5E MET* 3.6 30.5 - - + -
6E THR* 3.7 33.9 - - + +
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Residues in contact with ARG 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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318B ASP* 2.7 20.2 + - - +
319B ASP* 2.6 39.7 + - - +
321B VAL* 1.3 71.7 - - - +
323B VAL* 1.4 69.8 + - + +
324B LEU 3.1 0.2 + - - -
325B ARG* 3.2 7.3 + - - +
326B ASP* 3.0 40.3 + - - +
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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
----------------------------------------------------------
307B VAL* 5.5 0.9 - - + +
310B ILE* 4.3 18.6 - - + -
312B PHE* 4.2 17.7 - - + -
315B MSE 4.3 16.6 - - + -
319B ASP* 2.9 20.6 + - - +
320B ALA 3.4 8.1 - - - +
322B ARG* 1.4 79.8 - - + +
324B LEU* 1.4 64.6 + - - +
326B ASP* 3.6 4.0 + - - +
327B ILE* 3.2 40.4 + - + +
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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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265B LEU* 3.8 28.0 - - + -
267B ILE* 5.7 0.7 - - + -
269B ILE* 4.2 29.2 - - + -
281B ILE* 4.9 9.0 - - + -
304B LEU* 4.6 9.6 - - + -
307B VAL* 4.1 26.2 - - + -
312B PHE* 4.8 8.3 - - + -
320B ALA 3.0 12.4 + - - +
321B VAL* 2.8 13.6 + - + +
323B VAL* 1.4 77.5 - - - +
325B ARG* 1.3 55.1 + - + +
327B ILE* 3.7 4.2 - - - +
328B VAL* 2.6 49.7 + - + +
334B ILE* 5.7 0.9 - - + -
336B LEU* 4.2 8.3 - - + -
8E VAL* 4.5 10.8 - - + -
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Residues in contact with ARG 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B VAL* 2.9 21.5 + - + +
322B ARG* 3.2 5.8 + - - +
324B LEU* 1.3 78.2 - - + +
326B ASP* 1.3 59.0 + - - +
328B VAL* 2.7 23.6 + - - +
329B HIS* 2.8 49.1 + - + +
261C LYS* 4.3 18.3 - - - +
6E THR* 3.9 34.9 - - - +
7E THR 5.3 0.4 + - - -
8E VAL* 4.8 17.0 - - + +
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Residues in contact with ASP 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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322B ARG* 3.0 27.9 + - - +
323B VAL* 3.9 4.9 - - - +
325B ARG* 1.3 77.7 - - - +
327B ILE* 1.3 64.5 - - + +
328B VAL 3.0 0.7 + - - -
329B HIS* 3.1 18.3 + - - +
330B LYS* 3.2 20.2 + - + +
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Residues in contact with ILE 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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307B VAL* 3.7 26.7 - - + +
308B ASN* 3.4 41.5 - - + +
310B ILE* 4.6 7.0 - - + -
323B VAL* 3.2 32.7 + - + +
324B LEU* 3.8 6.1 - - - +
326B ASP* 1.3 78.1 - - + +
328B VAL* 1.3 67.6 + - + +
330B LYS* 3.5 18.0 + - - +
331B PRO 5.1 0.2 - - - +
334B ILE* 4.4 16.8 - - + +
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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
----------------------------------------------------------
259B MSE 5.0 6.9 - - + +
263B ASN 5.3 2.0 - - - +
264B PHE* 4.6 8.7 - - + -
265B LEU* 4.0 23.3 - - + +
324B LEU* 2.6 45.4 + - + +
325B ARG* 2.7 10.8 + - - +
327B ILE* 1.3 85.1 - - + +
329B HIS* 1.3 67.7 + - + +
330B LYS 3.3 5.5 + - - +
334B ILE* 4.3 13.1 - - + +
8E VAL* 3.8 27.8 - - + +
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Residues in contact with HIS 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ARG* 2.8 52.7 + - + +
326B ASP* 3.1 9.6 + - - +
328B VAL* 1.3 86.1 - - + +
330B LYS* 1.3 66.0 + - + +
331B PRO* 3.8 4.2 - - - +
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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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259B MSE 5.7 2.3 - - - +
326B ASP* 3.2 16.7 + - + +
327B ILE* 3.5 17.3 - - - +
328B VAL 3.3 5.6 - - - +
329B HIS* 1.3 84.2 - - + +
331B PRO* 1.3 81.8 - - + +
332B GLY 4.4 2.6 - - - +
334B ILE* 5.9 0.3 - - - +
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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