Contacts of the helix formed by residues 316 - 329 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277A GLY 6.1 0.2 - - - -
278A ASP* 6.3 2.2 - - - +
314A ASN 4.1 0.2 + - - -
315A MSE 1.3 77.2 - - - +
317A ASN* 1.3 65.9 + - - +
318A ASP* 3.5 7.3 + - - +
319A ASP* 3.1 35.0 + - - +
320A ALA* 3.2 16.6 + - - +
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Residues in contact with ASN 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A GLY 3.7 4.2 - - - -
272A GLN 2.8 39.8 + - - +
273A SER* 3.9 6.5 - - - -
277A GLY 3.8 11.3 + - - +
278A ASP* 4.8 1.4 - - - +
280A GLY* 3.3 32.2 + - - +
281A ILE* 3.9 14.3 - - + +
315A MSE 5.0 1.6 - - - +
316A SER* 1.3 75.0 - - - +
318A ASP* 1.3 63.8 + - - +
320A ALA* 3.4 3.1 + - - +
321A VAL* 3.2 25.3 + - - +
3D LYS* 6.1 2.0 - - - +
5D MET* 4.1 15.0 - - + +
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Residues in contact with ASP 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A SER* 3.1 8.1 + - - +
317A ASN* 1.3 73.9 - - - +
319A ASP* 1.4 61.5 + - - +
321A VAL* 3.4 5.8 + - - +
322A ARG* 2.8 57.8 + - - +
3D LYS* 5.2 7.3 + - - -
5D MET* 3.7 21.1 - - - +
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Residues in contact with ASP 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A MSE 3.3 26.1 - - + +
316A SER* 3.1 21.9 + - - +
318A ASP* 1.4 75.9 - - - +
320A ALA* 1.3 68.2 + - - +
322A ARG* 3.0 30.8 + - - +
323A VAL* 3.1 21.3 + - - +
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A ILE* 4.0 15.3 - - + -
312A PHE* 3.8 40.7 - - + +
315A MSE 3.4 13.5 - - + +
316A SER 3.2 17.6 + - - +
317A ASN* 3.8 5.8 - - - +
319A ASP* 1.3 77.6 - - - +
321A VAL* 1.3 64.3 + - - +
323A VAL* 3.3 3.2 + - - +
324A LEU* 2.9 22.7 + - - +
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Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A ILE* 3.9 28.7 - - + -
281A ILE* 4.3 9.4 - - + -
317A ASN 3.2 16.1 + - - +
318A ASP* 3.8 6.1 - - - +
319A ASP 3.1 0.4 - - - -
320A ALA* 1.3 79.6 - - - +
322A ARG* 1.3 68.0 + - + +
324A LEU* 3.7 9.3 - - + +
325A ARG* 3.0 42.1 + - + +
5D MET* 3.9 21.8 - - + +
6D THR* 4.1 16.4 - - + +
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Residues in contact with ARG 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A ASP* 2.8 45.6 + - - +
319A ASP* 3.0 31.7 + - - +
321A VAL* 1.3 80.1 - - + +
323A VAL* 1.3 63.2 + - + +
325A ARG* 3.5 9.0 + - - +
326A ASP* 3.0 30.7 + - - +
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Residues in contact with VAL 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ILE* 4.1 21.5 - - + -
312A PHE* 3.8 21.8 - - + -
315A MSE 4.5 14.4 - - + -
319A ASP 3.1 12.9 + - - +
320A ALA 3.6 6.1 - - - +
322A ARG* 1.3 76.7 - - + +
324A LEU* 1.3 66.7 + - - +
326A ASP* 3.1 14.9 + - - +
327A ILE* 3.2 31.9 + - + +
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Residues in contact with LEU 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A LEU* 4.3 21.1 - - + -
267A ILE* 5.3 0.2 - - + -
269A ILE* 3.6 28.0 - - + -
281A ILE* 4.8 6.1 - - + -
304A LEU* 3.4 27.1 - - + -
307A VAL* 3.8 28.0 - - + -
312A PHE* 4.4 7.2 - - + -
320A ALA 2.9 16.4 + - - +
321A VAL* 3.2 8.7 + - + +
323A VAL* 1.3 73.8 - - - +
325A ARG* 1.3 68.4 + - + +
327A ILE* 2.9 15.6 + - + +
328A VAL* 3.1 19.4 + - + +
334A ILE* 6.0 0.7 - - + -
336A LEU* 4.5 1.6 - - + -
6D THR* 6.1 0.2 - - - +
8D VAL* 4.3 15.7 - - + -
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Residues in contact with ARG 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A VAL* 3.0 30.4 + - + +
322A ARG* 3.7 8.5 - - - +
324A LEU* 1.3 77.1 - - + +
326A ASP* 1.3 68.2 + - - +
327A ILE 3.0 0.3 + - - -
328A VAL* 3.4 1.2 + - - +
329A HIS* 3.1 42.3 + - + +
6D THR* 2.9 33.3 - - - +
8D VAL* 4.3 23.6 - - + -
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Residues in contact with ASP 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A ARG* 3.0 24.2 + - - +
323A VAL* 3.1 7.6 + - - +
324A LEU 3.0 1.0 - - - -
325A ARG* 1.3 81.4 - - - +
327A ILE* 1.3 66.0 + - + +
329A HIS* 3.2 6.6 + - - +
330A LYS* 3.2 28.4 - - + +
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Residues in contact with ILE 327 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307A VAL* 3.9 31.9 - - + +
308A ASN* 3.9 23.8 - - + +
310A ILE* 4.3 15.3 - - + -
323A VAL* 3.2 28.0 + - + +
324A LEU* 2.9 9.0 + - + +
326A ASP* 1.3 80.8 - - + +
328A VAL* 1.3 63.1 - - + +
329A HIS 2.9 5.4 + - - -
330A LYS* 3.1 20.0 + - - +
334A ILE* 4.7 14.4 - - + +
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A MSE 5.3 3.5 - - + +
263A ASN 5.2 3.5 - - - +
264A PHE* 5.0 10.8 - - + -
265A LEU* 4.0 25.8 - - + -
324A LEU* 3.1 18.8 + - + +
325A ARG 4.2 2.5 - - - +
327A ILE* 1.3 77.4 - - + +
329A HIS* 1.3 66.0 + - + +
330A LYS 3.1 10.5 + - - +
334A ILE* 3.8 27.7 - - + +
8D VAL* 4.4 27.4 - - + +
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Residues in contact with HIS 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A ARG* 3.1 40.8 + - + +
326A ASP* 3.7 7.9 - - - +
327A ILE 2.9 2.4 - - - -
328A VAL* 1.3 88.5 - - + +
330A LYS* 1.3 77.8 + - + +
331A PRO* 4.5 0.3 - - - +
8D VAL* 6.1 4.0 - - + -
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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
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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