Contacts of the helix formed by residues 308 - 325 (chain A) in PDB entry 1LD8
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 308 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A PRO 4.2 7.4 + - - -
272A HIS* 3.8 22.4 - - - -
277A TRP* 4.5 1.9 - - - -
306A HIS 4.2 1.8 + - - -
307A SER* 1.3 86.3 + - - +
309A PRO* 1.3 76.7 - - - +
310A TYR* 3.4 12.8 + - - +
311A LEU* 3.3 18.4 + - - +
312A ILE* 3.1 26.1 + - - +
348A LYS* 5.1 4.9 - - - +
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Residues in contact with PRO 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A HIS* 4.8 5.8 - - + +
308A SER* 1.3 89.5 - - - +
310A TYR* 1.3 69.9 + - + +
312A ILE* 3.9 2.1 - - + +
313A ALA* 2.8 33.1 + - - +
344A LEU* 4.0 9.6 - - + +
348A LYS* 3.4 30.5 - - + +
349A ASP* 4.2 13.6 - - + +
536B GLN* 6.1 0.7 - - - +
783B ARG* 3.3 30.7 - - - +
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Residues in contact with TYR 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PRO 4.0 10.5 - - - -
272A HIS* 3.6 42.5 + + + +
274A GLU* 3.8 39.0 + - + +
277A TRP* 3.5 34.2 - + + +
308A SER* 3.1 14.5 - - - +
309A PRO* 1.3 85.2 - - + +
311A LEU* 1.3 56.7 + - - +
313A ALA* 3.8 4.7 - - - +
314A PHE* 3.0 28.9 + - - +
352A ARG* 5.9 1.3 - - - -
783B ARG* 4.1 29.3 + - - -
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Residues in contact with LEU 311 (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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277A TRP* 3.6 28.6 - - + -
299A LEU* 3.5 51.1 - - + +
302A LEU* 4.0 9.4 - - + -
303A GLN* 3.7 26.7 - - + +
306A HIS* 3.8 18.6 - - + +
307A SER* 4.2 1.3 - - - -
308A SER* 3.3 18.2 + - - +
310A TYR* 1.3 75.6 - - - +
312A ILE* 1.3 61.3 + - + +
314A PHE* 3.1 1.7 + - - +
315A LEU* 3.0 31.9 + - + +
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Residues in contact with ILE 312 (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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303A GLN* 3.1 41.3 - - + +
307A SER* 4.2 7.2 - - - +
308A SER 3.1 17.4 + - - +
309A PRO 3.9 3.4 - - - +
311A LEU* 1.3 76.9 - - + +
313A ALA* 1.3 62.7 + - - +
315A LEU* 3.2 10.5 + - + +
316A VAL* 3.1 21.5 + - - +
340A LEU* 4.1 24.0 - - + +
343A ILE* 5.1 6.3 - - + -
344A LEU* 3.6 30.1 - - + -
348A LYS* 4.1 21.3 - - + -
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Residues in contact with ALA 313 (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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309A PRO 2.8 20.2 + - - +
310A TYR* 3.8 6.1 - - - +
312A ILE* 1.3 75.0 - - - +
314A PHE* 1.3 64.8 + - - +
316A VAL* 3.2 4.0 + - - +
317A ASP* 3.0 31.7 + - - +
344A LEU* 4.1 4.5 - - + +
349A ASP* 5.7 1.1 - - - +
356A TRP* 3.7 33.3 - - + -
775B GLN* 5.0 3.6 - - - +
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Residues in contact with PHE 314 (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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277A TRP* 3.8 27.4 - + + -
280A LEU* 3.9 24.9 - - + -
281A LYS* 3.7 35.4 - - + -
289A LEU* 4.1 22.2 - - + -
295A LEU* 3.8 23.1 - - + -
299A LEU* 3.4 20.9 - - + -
310A TYR 3.0 19.1 + - - +
311A LEU 3.1 5.8 + - - +
313A ALA* 1.3 77.5 - - - +
315A LEU* 1.3 61.8 + - - +
317A ASP* 3.1 12.2 + - - +
318A ILE* 2.9 35.1 + - + +
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Residues in contact with LEU 315 (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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296A LEU* 3.6 17.5 - - + -
299A LEU* 4.2 19.5 - - + +
300A LEU* 3.5 26.7 - - + +
303A GLN* 3.6 37.5 - - + +
311A LEU* 3.0 23.9 + - + +
312A ILE* 3.2 13.9 + - + +
314A PHE* 1.3 77.0 - - - +
316A VAL* 1.3 57.2 + - - +
318A ILE* 3.1 8.6 + - + +
319A TYR* 2.9 39.0 + - + +
340A LEU* 3.8 18.6 - - + -
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Residues in contact with VAL 316 (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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312A ILE 3.1 15.7 + - - +
313A ALA 3.2 6.7 + - - +
315A LEU* 1.3 76.0 - - - +
317A ASP* 1.3 57.1 + - - +
319A TYR* 3.3 8.5 + - - +
320A GLU* 2.8 49.0 + - + +
337A ALA* 4.4 7.9 - - + +
340A LEU* 3.5 27.8 - - + -
341A CYS* 4.0 16.8 - - - +
344A LEU* 3.9 15.3 - - + -
356A TRP* 3.9 17.3 - - + -
359A ILE* 4.2 1.6 - - + -
363A LEU* 4.9 3.4 - - + -
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Residues in contact with ASP 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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281A LYS* 3.7 18.0 + - + +
289A LEU* 3.4 22.7 - - + +
313A ALA* 3.0 22.1 + - - +
314A PHE* 3.1 15.6 + - - +
316A VAL* 1.3 75.7 - - - +
318A ILE* 1.3 62.2 + - - +
320A GLU* 3.4 22.8 - - - +
321A ASP* 3.2 21.7 + - - +
356A TRP* 4.9 2.1 - - - -
775B GLN* 3.1 33.9 + - - +
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Residues in contact with ILE 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LEU* 4.1 27.8 - - + +
290A SER* 4.3 1.7 - - - -
292A TYR 5.9 0.7 - - - +
295A LEU* 4.7 4.5 - - + -
296A LEU* 4.0 42.4 - - + +
299A LEU* 4.0 13.5 - - + -
314A PHE* 2.9 45.1 + - + +
315A LEU* 3.1 9.4 + - + +
317A ASP* 1.3 73.2 - - - +
319A TYR* 1.3 61.5 + - + +
321A ASP* 3.1 4.7 + - - +
322A MET* 2.9 51.9 + - + +
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Residues in contact with TYR 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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296A LEU* 4.2 27.4 - - + +
300A LEU* 4.0 23.2 - - - +
315A LEU* 2.9 26.0 + - + +
316A VAL* 3.6 4.9 - - - +
318A ILE* 1.3 75.7 - - + +
320A GLU* 1.3 64.3 + - - +
322A MET* 3.5 11.0 - - - +
323A LEU* 2.9 32.3 + - - +
333A ILE* 3.8 33.2 - - + -
336A LYS* 3.8 26.5 + - + +
337A ALA* 3.8 32.8 - - + -
340A LEU* 3.8 23.1 - - + -
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Residues in contact with GLU 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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316A VAL* 2.8 30.3 + - + +
317A ASP* 3.4 22.0 - - - +
319A TYR* 1.3 78.5 - - - +
321A ASP* 1.3 63.2 + - - +
323A LEU* 3.4 3.5 + - - +
324A GLU* 3.2 24.8 + - - +
355A TYR* 4.9 2.1 + - - -
356A TRP* 4.9 1.2 - - - -
359A ILE* 3.3 35.5 - - - +
363A LEU* 3.7 29.2 - - + -
367A HIS* 4.6 1.6 - - - -
771B LYS* 4.6 16.3 - - - +
775B GLN* 5.5 1.0 - - - +
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Residues in contact with ASP 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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288A GLY* 3.2 18.4 - - - -
289A LEU* 3.7 13.5 - - + +
290A SER* 2.5 36.5 + - - +
291A LYS* 4.9 0.3 - - - +
317A ASP 3.2 8.8 + - - +
318A ILE 3.1 8.5 + - - +
320A GLU* 1.3 76.7 - - - +
322A MET* 1.3 65.4 + - - +
324A GLU* 3.1 15.7 + - - +
325A ASN* 2.8 34.5 + - - -
771B LYS* 5.6 3.1 + - - -
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Residues in contact with MET 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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290A SER* 3.4 22.7 - - - +
296A LEU* 4.0 15.5 - - + -
318A ILE* 2.9 28.6 + - + +
319A TYR* 3.5 31.6 - - - +
321A ASP* 1.3 76.8 - - - +
323A LEU* 1.3 57.9 + - - +
325A ASN* 3.0 19.3 + - - +
327A CYS* 3.4 39.8 + - + +
328A ASP 5.4 0.9 - - - +
333A ILE* 3.8 26.2 - - + -
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Residues in contact with LEU 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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319A TYR 2.9 22.6 + - - +
320A GLU 3.7 1.6 - - - +
322A MET* 1.3 77.2 - - - +
324A GLU* 1.3 61.0 + - - +
325A ASN 3.4 0.5 + - - -
326A GLN* 3.8 1.7 + - - -
327A CYS* 4.2 0.2 - - - -
330A LYS* 3.0 68.5 + - + +
333A ILE* 3.7 17.5 - - + -
334A LEU* 4.0 25.8 - - + +
337A ALA* 4.8 3.8 - - + -
363A LEU* 3.9 18.8 - - + -
367A HIS* 3.2 38.9 + - + +
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Residues in contact with GLU 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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320A GLU 3.2 13.1 + - - +
321A ASP* 3.1 18.8 + - - +
323A LEU* 1.3 76.9 - - - +
325A ASN* 1.3 65.3 + - - +
326A GLN* 3.6 3.5 + - - +
366A LYS* 4.0 18.5 + - - +
367A HIS* 3.7 20.0 + - - -
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Residues in contact with ASN 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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288A GLY* 5.8 0.2 - - - -
290A SER* 3.3 16.8 + - - +
291A LYS* 3.6 27.6 + - - +
321A ASP* 2.8 36.9 + - - +
322A MET* 3.0 5.7 + - - +
324A GLU* 1.3 84.6 - - - +
326A GLN* 1.3 73.4 + - - +
327A CYS* 3.3 3.2 + - - -
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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