Contacts of the helix formed by residues 305 - 321 (chain A) in PDB entry 4LBD
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 GLY 305 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ARG* 4.6 1.0 + - - -
221A GLN 5.4 1.8 - - - -
300A HIS* 3.1 37.7 + - - -
303A GLY 3.0 4.4 + - - -
304A PHE* 1.3 74.7 - - - +
306A PRO* 1.3 67.9 - - - +
307A LEU 3.1 2.6 + - - -
308A THR* 2.7 24.1 + - - -
396A ARG* 3.8 11.2 - - - -
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Residues in contact with PRO 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ARG* 5.9 2.2 - - - +
300A HIS* 4.6 2.2 - - + +
305A GLY* 1.3 81.6 - - - +
307A LEU* 1.3 57.1 + - - +
308A THR 3.5 0.4 - - - -
309A ASP* 4.8 4.6 + - - +
310A LEU* 5.3 4.5 + - - +
396A ARG* 3.9 27.4 - - - +
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Residues in contact with LEU 307 (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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1A 961 3.7 18.8 - - + -
272A MET* 4.2 9.9 - - + -
304A PHE* 3.0 11.7 + - + +
306A PRO* 1.3 79.1 - - + +
308A THR* 1.3 65.2 + - - +
309A ASP 3.4 2.5 - - - -
310A LEU* 3.2 26.6 + - + +
311A VAL* 3.1 26.1 + - + +
389A ILE* 3.9 11.0 - - + +
392A LYS* 3.7 28.3 - - + +
393A GLY* 3.7 31.2 - - - +
396A ARG* 4.3 8.5 - - + -
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Residues in contact with THR 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ARG* 4.3 7.9 - - - +
296A ARG* 3.6 41.5 - - + +
299A MET* 4.3 2.7 - - + -
300A HIS* 3.2 28.3 - - + +
304A PHE* 3.4 17.5 + - + +
305A GLY 2.7 21.3 + - - -
306A PRO 3.5 0.2 - - - -
307A LEU* 1.3 77.5 - - - +
309A ASP* 1.3 60.5 - - - +
311A VAL* 3.3 1.7 + - - +
312A PHE* 3.0 43.6 + - + -
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Residues in contact with ASP 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ARG* 2.8 39.1 + - - -
296A ARG* 3.0 28.6 + - - +
306A PRO 4.8 4.1 + - - +
307A LEU 3.4 0.6 - - - -
308A THR* 1.3 79.4 - - - +
310A LEU* 1.3 57.3 + - - +
312A PHE* 3.4 2.4 + - - +
313A ALA* 2.9 28.9 + - - +
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Residues in contact with LEU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PRO 5.3 3.1 + - - +
307A LEU* 3.2 20.5 + - + +
309A ASP* 1.3 75.0 - - - +
311A VAL* 1.3 56.4 + - - +
313A ALA* 3.1 9.4 + - + +
314A PHE* 2.8 35.2 + - - +
389A ILE* 3.7 14.8 - - + +
392A LYS* 3.6 40.2 - - + +
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Residues in contact with VAL 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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272A MET* 4.4 8.7 - - - -
275A ILE* 4.8 5.2 - - + -
276A CYS* 3.9 12.9 - - - -
286A MET* 4.0 22.0 - - + -
299A MET* 5.6 0.2 - - + -
304A PHE* 3.8 35.0 - - + -
307A LEU* 3.1 28.1 + - + +
308A THR 3.5 8.1 - - - +
310A LEU* 1.3 75.8 - - - +
312A PHE* 1.3 63.5 + - + +
314A PHE* 2.9 22.2 + - - +
315A ALA* 2.9 11.3 + - - +
389A ILE* 4.1 17.7 - - + -
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Residues in contact with PHE 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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279A TYR* 3.6 25.8 + + - -
284A ASP* 3.6 27.8 - - - -
285A THR 4.7 0.7 - - - -
286A MET* 3.8 29.2 - - + -
295A ASN 4.5 0.9 - - - -
296A ARG* 3.5 64.1 + - + +
299A MET* 3.8 25.1 - - + -
304A PHE* 6.1 0.7 - + - -
308A THR* 3.0 46.5 + - + +
309A ASP 3.7 0.7 - - - +
311A VAL* 1.3 80.7 - - + +
313A ALA* 1.3 55.3 + - - +
315A ALA* 3.5 2.4 + - - +
316A GLY* 3.0 22.5 + - - -
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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
----------------------------------------------------------
296A ARG* 5.3 0.2 - - - +
309A ASP 2.9 17.7 + - - +
310A LEU* 3.7 11.7 - - + +
312A PHE* 1.3 74.3 - - - +
314A PHE* 1.3 64.9 + - - +
316A GLY* 4.3 1.1 - - - +
317A GLN* 3.1 34.9 + - - +
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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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272A MET 4.9 0.9 - - - -
273A LEU* 5.0 3.8 - - + -
276A CYS* 3.6 28.0 - - + -
310A LEU 2.8 12.0 + - - +
311A VAL* 2.9 11.4 + - - +
313A ALA* 1.3 78.8 - - - +
315A ALA* 1.3 61.5 + - - +
317A GLN* 3.5 5.8 + - - +
318A LEU* 3.2 30.9 + - + +
382A LYS* 4.5 22.2 + - + -
385A ASP* 3.5 35.2 - - + -
386A LEU* 3.8 40.2 - - + -
389A ILE* 4.7 19.3 - - + -
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Residues in contact with ALA 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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276A CYS* 3.6 34.2 - - + +
279A TYR* 3.9 10.9 - - + -
286A MET* 3.6 31.9 - - + -
311A VAL 2.9 5.2 + - - +
312A PHE 3.8 3.8 - - - +
314A PHE* 1.3 75.5 - - - +
316A GLY* 1.3 68.1 + - - +
318A LEU* 3.1 16.3 + - - +
319A LEU* 3.3 10.6 + - - +
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Residues in contact with GLY 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TYR* 4.0 7.6 - - - -
312A PHE 3.0 16.5 + - - -
313A ALA* 3.5 2.4 + - - -
314A PHE 3.2 0.8 - - - -
315A ALA* 1.3 75.8 - - - +
317A GLN* 1.3 64.2 + - - +
319A LEU* 2.8 44.6 + - - +
320A PRO* 3.2 4.2 - - - +
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Residues in contact with GLN 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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313A ALA* 3.1 25.0 + - - +
314A PHE* 3.8 5.4 - - + +
315A ALA 3.4 0.2 - - - -
316A GLY* 1.3 77.8 + - - +
318A LEU* 1.3 58.9 + - - +
319A LEU 3.5 0.4 - - - -
320A PRO* 3.7 17.9 - - - +
321A LEU* 3.6 11.4 - - - +
382A LYS* 3.4 22.7 + - - +
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Residues in contact with LEU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LEU* 4.3 18.6 - - + -
276A CYS* 4.0 32.5 - - + +
277A THR* 4.1 23.6 - - + -
314A PHE* 3.2 18.6 + - + +
315A ALA 3.1 9.8 + - - +
316A GLY 2.8 0.6 + - - -
317A GLN* 1.3 76.3 - - - +
319A LEU* 1.3 68.6 + - - +
320A PRO* 3.4 0.7 - - - -
321A LEU* 3.2 23.5 + - + +
322A GLU 3.9 1.7 + - - -
323A MET* 4.5 20.3 + - + +
382A LYS* 4.4 24.5 - - + +
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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
----------------------------------------------------------
276A CYS 5.9 1.1 - - - +
279A TYR* 3.9 37.0 - - + +
281A PRO* 4.0 32.5 - - + -
315A ALA 3.7 7.0 - - - +
316A GLY* 2.8 19.2 + - - +
318A LEU* 1.3 77.6 - - - +
320A PRO* 1.4 54.2 - - + +
322A GLU* 2.7 36.6 + - - +
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Residues in contact with PRO 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 GLY 3.2 12.8 - - - +
317A GLN* 3.7 20.6 - - - +
318A LEU 3.6 3.6 - - - -
319A LEU* 1.4 90.2 - - + +
321A LEU* 1.3 65.9 + - + +
322A GLU* 3.4 11.9 + - + +
369A ARG* 5.0 0.5 + - - -
375A MET* 4.5 9.4 - - - +
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Residues in contact with LEU 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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317A GLN 3.6 22.9 - - - +
318A LEU* 3.5 12.3 - - + +
319A LEU 2.9 1.2 + - - -
320A PRO* 1.3 82.3 - - + +
322A GLU* 1.3 66.5 + - - +
323A MET* 3.0 27.7 + - + +
369A ARG* 2.8 25.3 + - - -
375A MET* 3.9 19.8 - - + +
378A ARG* 4.4 22.4 - - + +
379A MET* 4.4 9.4 - - + -
382A LYS* 3.8 36.8 - - + -
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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