Contacts of the helix formed by residues 305 - 319 (chain A) in PDB entry 4I6J
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 PHE 305 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A TYR* 3.4 75.6 - + + -
287A LEU* 3.7 25.4 - - + -
288A TRP* 4.4 12.1 - + - -
300A PRO* 4.1 19.3 - - + -
301A PRO 4.3 3.8 - - - -
302A LEU* 3.0 24.2 + - + +
304A LEU* 1.3 96.9 - - + +
306A GLY* 1.3 66.2 + - - +
307A GLN* 3.2 3.4 - - - -
308A LEU* 2.8 22.5 + - + +
309A LEU* 3.0 21.9 + - + -
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Residues in contact with GLY 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TYR* 3.9 15.9 - - - -
302A LEU 3.3 4.4 + - - -
303A SER* 2.8 20.1 + - - -
304A LEU 3.3 0.4 - - - -
305A PHE* 1.3 76.7 - - - +
307A GLN* 1.3 62.2 + - - +
310A TRP* 3.1 37.4 + - - -
427B THR* 4.6 2.0 - - - -
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Residues in contact with GLN 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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242A HIS* 5.2 6.6 + - - -
269A LEU* 4.9 4.8 - - - +
270A SER* 4.0 31.5 - - - +
273A LEU* 4.3 10.6 - - + +
283A PHE* 3.9 27.5 - - + -
304A LEU 5.1 1.0 + - - +
305A PHE 3.0 1.8 + - - -
306A GLY* 1.3 75.9 - - - +
308A LEU* 1.3 60.9 + - + +
311A ARG* 3.7 5.7 + - - +
427B THR* 4.0 16.8 + - - +
428B TRP* 3.1 39.7 + - + +
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LEU* 3.9 15.3 - - + -
273A LEU* 4.1 15.9 - - + -
280A CYS* 3.7 37.2 - - + +
283A PHE* 3.7 38.8 - - + -
284A TYR* 3.9 27.1 - - + +
287A LEU* 5.5 1.8 - - + -
305A PHE* 2.8 20.2 + - + +
307A GLN* 1.3 72.9 - - + +
309A LEU* 1.3 61.9 + - - +
311A ARG* 3.2 14.7 + - - +
312A GLU* 3.1 29.2 + - - +
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Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LEU* 4.2 20.2 - - + -
151A TYR* 5.0 4.5 - - + -
168A TYR* 3.4 24.0 - - + +
171A PHE* 3.5 19.5 - - + -
172A GLN* 4.7 4.5 - - + -
175A ILE* 4.7 14.6 - - + -
284A TYR* 5.4 3.6 - - + -
302A LEU* 3.7 52.7 - - + +
305A PHE* 3.0 21.9 + - + +
308A LEU* 1.3 75.5 - - - +
310A TRP* 1.3 56.2 + - - +
312A GLU* 3.2 4.6 + - + +
313A PHE* 2.8 34.5 + - - +
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Residues in contact with TRP 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TYR* 3.4 52.7 + + + -
306A GLY* 3.1 30.2 + - - +
309A LEU* 1.3 72.9 - - - +
311A ARG* 1.3 66.3 + - - +
313A PHE* 3.2 8.4 + + - +
314A PHE* 3.0 42.2 + + + -
417A TRP* 3.6 44.0 - + - -
424B MET* 3.9 14.0 - - + +
425B MET 3.6 19.5 + - - -
426B PRO* 3.6 33.7 - - + -
427B THR* 3.8 15.7 - - + +
428B TRP* 4.1 17.3 - - + -
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Residues in contact with ARG 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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148A HIS* 2.9 56.9 + - - -
149A THR* 4.3 5.7 - - - +
150A LEU* 6.3 0.2 - - - +
273A LEU* 3.3 27.9 + - - +
274A ARG* 5.0 2.0 - - - +
278A LEU 5.8 0.4 + - - -
280A CYS* 3.4 27.1 - - - +
307A GLN 3.7 11.0 + - - +
308A LEU* 3.2 19.3 + - - +
310A TRP* 1.3 81.4 - - - +
312A GLU* 1.3 66.2 + - - +
314A PHE* 3.3 1.8 + - - +
315A TYR* 3.0 50.4 + - + -
407A ASP* 5.3 1.0 + - - -
410A VAL* 4.0 15.7 - - + +
428B TRP* 3.8 28.3 - - + +
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Residues in contact with GLU 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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149A THR* 3.0 15.5 - - - +
150A LEU* 2.3 52.3 + - + +
151A TYR* 3.6 17.1 + - + +
153A LEU* 3.4 21.1 - - - +
156A ILE* 4.4 1.9 - - - +
171A PHE* 3.6 15.7 - - + -
308A LEU 3.1 19.5 + - - +
309A LEU* 3.5 10.8 - - + +
311A ARG* 1.3 80.5 + - + +
313A PHE* 1.3 52.7 + - - +
315A TYR* 3.3 4.7 + - - +
316A THR* 2.7 42.4 + - - -
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Residues in contact with PHE 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A PRO 3.2 24.5 - - - -
166A LEU 4.2 0.4 - - - -
167A THR* 3.8 15.7 - - - -
168A TYR* 3.9 18.6 - + + -
171A PHE* 3.6 39.9 - + + -
309A LEU 2.8 17.9 + - - +
310A TRP* 3.2 17.9 + + - +
312A GLU* 1.3 77.9 - - - +
314A PHE* 1.3 88.1 + + - +
316A THR* 3.9 1.4 - - - -
317A ALA* 3.1 25.6 + - + +
417A TRP* 4.2 15.0 - + - -
423A PHE* 3.8 26.5 - + - -
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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
----------------------------------------------------------
310A TRP* 3.0 53.7 + + + +
311A ARG 4.0 2.2 - - - +
313A PHE* 1.3 86.3 - + - +
315A TYR* 1.3 66.8 + - - +
317A ALA* 3.2 3.5 + - - +
318A ALA* 3.0 25.6 + - - +
324A PHE* 4.1 3.3 - + - -
409A SER* 3.5 18.1 - - - +
410A VAL* 3.9 23.6 - - + -
413A GLY* 3.4 37.7 - - - -
414A SER* 3.8 13.9 - - - -
417A TRP* 4.5 6.1 - + + -
423A PHE* 3.6 23.1 - + - -
426B PRO* 4.0 15.0 - - + -
428B TRP* 5.3 2.5 - + + -
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Residues in contact with TYR 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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29A LYS* 3.7 2.8 + - - -
120A SER* 3.4 22.1 + - - -
121A GLU* 3.4 21.3 - - + -
148A HIS* 2.9 33.2 + + - -
149A THR* 3.9 15.9 - - + -
153A LEU* 3.9 15.1 - - + +
311A ARG* 3.0 55.8 + - + +
312A GLU 3.6 4.3 - - - +
314A PHE* 1.3 75.7 - - - +
316A THR* 1.3 64.6 + - - +
318A ALA* 2.9 13.0 + - - +
319A THR* 3.1 14.0 + - - -
407A ASP* 2.2 36.6 + - - -
409A SER* 3.3 11.8 - - - -
410A VAL* 3.8 9.4 - - + -
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Residues in contact with THR 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU* 3.8 23.9 - - - +
156A ILE* 3.8 26.3 - - + +
157A ILE* 3.6 36.5 - - + +
164A PRO* 3.7 1.5 - - + +
165A PRO* 4.4 12.3 - - + -
171A PHE* 3.8 12.8 - - - -
312A GLU 2.7 29.1 + - - -
313A PHE 3.9 4.5 - - - -
315A TYR* 1.3 73.3 - - - +
317A ALA* 1.3 61.9 + - - +
319A THR* 3.4 12.2 + - - -
320A ASN 5.1 0.9 + - - -
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Residues in contact with ALA 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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164A PRO* 3.9 19.9 - - + +
165A PRO 4.7 4.7 - - - +
166A LEU* 4.6 11.6 - - + +
313A PHE* 3.1 19.3 + - + +
314A PHE* 3.7 5.6 - - - +
315A TYR 3.1 0.4 - - - -
316A THR* 1.3 79.0 - - - +
318A ALA* 1.3 60.1 + - - +
319A THR 4.0 0.2 + - - -
320A ASN 4.7 1.9 + - - -
321A ASN* 4.1 9.5 + - - +
324A PHE* 3.8 22.4 - - + -
332A ILE* 5.1 2.8 - - + +
423A PHE* 4.5 17.3 - - + -
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Residues in contact with ALA 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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121A GLU* 6.0 0.2 - - - -
122A PRO* 3.2 15.2 - - + +
314A PHE 3.0 15.2 + - - +
315A TYR 2.9 4.4 + - - +
317A ALA* 1.3 76.9 - - - +
319A THR* 1.3 64.5 + - - +
320A ASN 3.0 4.5 + - - -
321A ASN 3.0 12.5 + - - +
324A PHE* 3.6 28.0 - - + -
408A PHE* 4.2 6.3 - - + -
409A SER* 3.5 25.6 - - - +
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Residues in contact with THR 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TYR* 4.3 3.6 - - + +
120A SER* 2.6 47.4 - - - +
121A GLU* 5.6 0.2 - - - +
122A PRO* 3.8 11.3 - - - +
125A LYS* 2.6 41.8 + - - +
153A LEU* 4.2 13.3 - - + +
154A ASP* 5.0 8.0 + - - +
157A ILE* 4.4 4.9 - - - +
315A TYR 3.1 9.1 + - - -
316A THR* 3.4 17.5 + - - -
317A ALA 3.7 1.0 - - - -
318A ALA* 1.3 72.9 - - - +
320A ASN* 1.3 63.4 + - - +
321A ASN 3.4 0.6 + - - -
322A PRO* 5.4 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
------------------------------------------------------------
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