Contacts of the helix formed by residues 311 - 327 (chain A) in PDB entry 1LWT
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 ASN 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A GLU* 3.1 26.3 + - - -
186A ASN 3.5 1.5 + - - +
187A ASP* 3.5 23.8 + - - +
310A ASP* 1.3 84.9 - - - +
312A ILE* 1.3 53.0 + - - +
313A GLY* 3.1 8.4 + - - +
314A THR* 2.8 42.9 + - - +
315A ARG* 2.7 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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182A ILE 5.2 0.9 - - - +
183A LEU* 4.6 15.9 - - + +
185A GLU* 2.7 28.6 + - + +
310A ASP 3.3 2.6 + - - -
311A ASN* 1.3 69.6 - - - +
313A GLY* 1.3 65.3 + - - +
315A ARG* 2.8 24.7 + - - +
316A GLU* 2.7 35.5 + - - +
357A LEU* 3.4 13.0 - - + -
414A ARG* 3.2 46.7 - - - +
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Residues in contact with GLY 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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185A GLU* 4.4 0.4 + - - -
311A ASN* 3.1 10.0 + - - -
312A ILE* 1.3 79.0 - - - +
314A THR* 1.3 58.8 + - - +
316A GLU* 3.0 17.9 + - - +
317A THR* 2.8 34.1 + - - -
397A LYS* 4.3 2.1 - - - -
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Residues in contact with THR 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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189A PHE* 3.6 41.6 - - + -
205A PRO* 4.1 12.9 + - - +
206A LYS* 6.3 0.2 - - - +
209A ALA* 3.9 13.4 - - + +
307A LEU* 4.4 15.0 - - + -
310A ASP* 4.9 1.8 - - - +
311A ASN* 2.8 26.1 + - - +
313A GLY* 1.3 75.0 - - - +
315A ARG* 1.3 64.6 + - - +
316A GLU 3.1 0.2 + - - -
317A THR* 3.7 7.0 - - - -
318A PHE* 2.9 24.8 + - + +
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Residues in contact with ARG 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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182A ILE* 2.8 28.4 + - - +
183A LEU 4.5 0.2 - - - -
184A TYR 2.8 28.7 + - - -
185A GLU* 4.6 0.6 - - - +
307A LEU* 3.3 27.8 - - + +
308A SER 2.9 24.6 + - - -
309A THR 3.6 3.4 - - - -
310A ASP 2.9 21.0 + - - +
311A ASN 2.7 20.4 + - - +
312A ILE* 2.8 19.9 + - - +
314A THR* 1.3 73.7 - - - +
316A GLU* 1.3 65.4 + - - +
318A PHE* 3.5 4.6 + - - +
319A LEU* 3.4 15.6 + - - +
353A LEU* 4.0 17.7 - - + +
356A SER* 3.0 35.1 + - - -
357A LEU* 4.5 15.4 - - + +
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Residues in contact with GLU 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* 2.7 40.7 + - + +
313A GLY* 3.1 15.9 + - - +
315A ARG* 1.3 69.1 - - - +
317A THR* 1.3 69.5 + - - +
319A LEU* 2.8 19.1 + - - +
320A ALA* 3.0 9.9 + - - +
357A LEU* 4.1 9.8 - - + +
390A VAL 5.0 0.5 - - - +
393A ASN* 3.0 27.8 + - - +
394A VAL* 4.0 23.7 - - + +
397A LYS* 3.1 32.7 + - + -
414A ARG* 3.1 17.5 + - - -
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Residues in contact with THR 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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206A LYS* 3.3 43.5 - - + +
209A ALA* 4.0 5.6 - - - -
210A TYR* 3.6 21.3 - - + +
238A ARG* 5.5 1.6 - - - +
242A TYR* 5.2 0.4 - - + -
313A GLY 2.8 19.9 + - - -
314A THR* 3.7 5.0 - - - -
316A GLU* 1.3 73.9 - - - +
318A PHE* 1.3 64.0 + - - +
320A ALA* 2.8 25.1 - - + +
321A GLY 3.0 5.2 + - - -
397A LYS* 3.7 19.5 - - + +
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Residues in contact with PHE 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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209A ALA* 3.5 18.3 + - + +
212A LEU* 3.2 16.2 - - + -
213A GLY* 3.1 35.4 - - - -
216A ILE* 3.7 26.0 - - + -
295A PHE* 3.6 22.0 - + - -
303A ILE* 4.4 24.9 - - + -
307A LEU* 3.9 22.4 - - + -
314A THR* 2.9 18.6 + - + +
315A ARG 3.7 4.0 - - - +
316A GLU 2.9 1.8 + - - -
317A THR* 1.3 74.6 - - - +
319A LEU* 1.3 67.9 + - + +
321A GLY 3.0 2.8 + - - -
322A LEU* 2.9 30.3 + - + -
350A LEU* 6.6 0.2 - - + -
353A LEU* 4.1 10.3 - - + -
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Residues in contact with LEU 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 ARG 3.4 7.2 + - - +
316A GLU* 2.8 12.8 + - - +
318A PHE* 1.3 77.3 - - + +
320A ALA* 1.3 68.1 + - - +
322A LEU* 2.8 25.4 + - + -
323A ILE* 2.6 59.2 + - + +
339A ILE* 4.4 4.5 - - + -
350A LEU* 4.3 13.9 - - + -
353A LEU* 5.3 9.0 - - + -
354A ALA* 5.7 1.1 - - - -
357A LEU* 5.5 4.9 - - + -
359A LEU* 5.2 3.4 - - + -
385A MSE 3.5 30.5 - - + -
391A LEU* 5.4 2.2 - - + -
394A VAL* 4.1 16.2 - - + -
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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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210A TYR* 4.0 7.0 - - + -
316A GLU 3.0 6.1 + - - +
317A THR* 2.8 26.9 + - - +
319A LEU* 1.3 74.9 - - - +
321A GLY* 1.3 49.2 + - - +
323A ILE* 3.3 2.5 + - - +
324A ASP* 2.7 33.8 + - - +
394A VAL* 3.9 9.7 - - - +
397A LYS* 3.4 34.8 - - + +
398A CYS* 3.6 16.5 - - - -
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Residues in contact with GLY 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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210A TYR* 3.5 37.1 - - - -
213A GLY 3.5 6.5 - - - -
214A LEU* 3.5 12.0 - - - +
317A THR 3.0 10.7 + - - -
318A PHE 3.0 3.5 + - - -
320A ALA* 1.3 74.6 - - - +
322A LEU* 1.3 68.0 + - - +
324A ASP 3.0 11.3 + - - -
325A SER 3.4 6.6 + - - -
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Residues in contact with LEU 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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213A GLY* 3.2 15.8 + - - +
214A LEU* 4.8 0.2 - - - +
216A ILE* 4.1 12.8 - - + -
217A GLY* 3.8 24.7 - - - +
303A ILE* 4.5 12.6 - - + -
318A PHE* 2.9 18.5 + - + +
319A LEU* 2.8 24.8 + - + +
321A GLY* 1.3 72.8 - - - +
323A ILE* 1.3 64.0 + - - +
325A SER* 3.3 1.0 + - - -
326A ASP* 3.1 24.4 + - + -
339A ILE* 4.2 20.2 - - + -
346A VAL* 5.5 2.9 - - + -
350A LEU* 3.9 29.8 - - + -
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Residues in contact with ILE 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 LEU* 2.6 55.0 + - + +
320A ALA* 3.6 3.8 - - - +
322A LEU* 1.3 66.3 - - - +
324A ASP* 1.3 54.2 + - - +
325A SER 2.4 20.2 + - - -
327A GLY* 3.0 22.0 + - - -
329A VAL* 4.1 20.0 - - + -
337A ALA* 4.6 14.8 - - + -
339A ILE* 3.8 12.8 - - + -
385A MSE 5.5 0.2 - - - -
391A LEU* 4.9 5.8 - - + -
394A VAL* 4.0 15.3 - - + -
395A LEU* 4.9 7.0 - - + -
398A CYS* 4.6 8.1 - - - -
403A LYS* 2.8 27.7 - - + -
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Residues in contact with ASP 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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210A TYR* 2.3 37.4 + - - +
214A LEU* 3.8 4.0 - - + -
235A LEU* 3.4 30.3 - - + +
320A ALA 2.7 20.1 + - - +
321A GLY 3.0 5.5 + - - +
323A ILE* 1.3 71.2 - - - +
325A SER* 1.3 53.0 + - - +
398A CYS* 3.6 8.4 - - - +
399A ALA 2.7 23.0 + - - -
400A GLY* 2.8 23.8 + - - -
403A LYS* 2.7 31.1 + - - +
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Residues in contact with SER 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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214A LEU* 3.5 28.5 - - - -
217A GLY* 3.3 1.4 - - - -
218A ASP* 2.9 33.5 + - - +
235A LEU* 5.5 0.9 - - - -
321A GLY 3.4 2.3 + - - -
322A LEU 3.3 6.2 + - - -
323A ILE 2.4 13.5 + - - -
324A ASP* 1.3 70.6 - - - +
326A ASP* 1.3 94.1 + - - +
327A GLY 3.2 6.4 + - - -
403A LYS* 4.3 5.2 + - - -
16B G 4.7 5.0 + - - -
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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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217A GLY* 2.7 28.7 - - - +
218A ASP* 2.9 11.7 - - - +
322A LEU* 3.1 14.5 + - + +
325A SER* 1.3 96.1 + - - +
327A GLY* 1.3 56.4 + - - +
338A THR 4.8 0.4 - - - -
339A ILE* 3.1 30.3 - - + +
340A LYS 4.1 14.8 + - - +
15B C 3.9 23.8 + - - +
16B G 3.1 27.6 + - - -
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Residues in contact with GLY 327 (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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323A ILE* 3.0 27.1 + - - +
325A SER 3.2 4.0 + - - -
326A ASP* 1.3 80.8 - - - +
328A TYR* 1.3 60.9 + - - -
329A VAL 3.9 0.9 + - - -
338A THR 3.9 4.7 - - - -
339A ILE* 4.3 4.9 - - - -
403A LYS* 2.6 31.2 - - - +
16B G 5.5 1.9 + - - -
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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