Contacts of the helix formed by residues 283 - 299 (chain K) in PDB entry 5LN3
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 ARG 283 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133J PRO 4.8 2.6 + - - -
134J LEU* 3.2 28.5 + - - +
135J VAL 4.0 2.8 + - - -
136J SER* 3.3 18.8 + - - +
221J GLN* 3.2 33.3 + - - +
223J PHE* 3.9 15.2 - - + -
226J GLU* 3.2 20.4 + - - -
230J MET* 4.3 3.6 - - - +
281K ALA* 4.7 0.8 - - - +
282K ASP* 1.3 87.0 + - - +
284K GLU* 1.3 74.9 + - - +
285K VAL 3.2 1.8 - - - -
286K GLN* 2.9 40.1 + - - +
287K ARG* 3.7 15.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 284 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223J PHE* 5.4 2.9 - - - -
237K GLN* 3.4 23.6 - - + +
238K LYS 3.1 25.8 - - - +
239K TYR* 3.0 39.0 + - - +
281K ALA* 4.4 16.5 - - + +
283K ARG* 1.3 81.2 - - - +
285K VAL* 1.4 65.2 + - + +
287K ARG* 2.8 53.1 + - - +
288K ILE* 3.8 7.8 - - - +
251L ARG* 4.2 10.6 + - - +
113M LEU* 5.2 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 285 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236K VAL* 3.7 32.3 - - + -
237K GLN 4.7 2.5 - - - +
269K ALA 4.6 2.0 - - - +
270K ILE* 3.7 37.9 - - + +
272K THR 4.7 7.2 - - - +
273K LYS* 4.7 5.8 - - + -
281K ALA* 5.1 3.1 - - + +
282K ASP* 4.0 25.6 - - - +
284K GLU* 1.4 86.2 - - + +
286K GLN* 1.3 65.8 + - - +
287K ARG 3.4 0.4 - - - -
288K ILE* 3.2 14.8 + - + +
289K LEU* 3.2 20.3 + - - +
247L THR* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 286 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133J PRO* 4.3 22.0 + - - +
135J VAL 4.1 13.5 + - - -
136J SER* 3.7 27.2 + - - +
273K LYS* 5.6 3.4 - - - +
282K ASP 3.5 10.5 - - - +
283K ARG* 2.9 47.6 + - - +
285K VAL* 1.3 80.0 - - - +
287K ARG* 1.3 64.3 + - - +
289K LEU* 3.1 14.8 + - + +
290K LEU* 3.1 40.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 287 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239K TYR* 4.6 0.8 - - - -
240K LEU* 3.8 36.5 - - - +
248K ARG* 6.0 1.1 - - - +
283K ARG* 3.7 17.1 + - - +
284K GLU* 2.8 47.6 + - - +
286K GLN* 1.3 76.9 - - - +
288K ILE* 1.3 70.8 + - + +
290K LEU* 3.2 20.6 + - - +
291K GLU* 3.1 27.8 + - - +
113M LEU* 4.7 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 288 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235K PHE* 3.1 50.9 - - + +
236K VAL* 5.0 0.2 - - - -
237K GLN* 5.3 2.7 - - + +
270K ILE* 3.9 20.9 - - + -
284K GLU 3.8 15.9 - - - +
285K VAL* 3.4 19.7 - - + +
287K ARG* 1.3 80.9 - - + +
289K LEU* 1.3 61.2 + - - +
291K GLU* 3.2 32.0 + - - +
292K LEU* 3.5 10.5 + - + +
112M ASP* 4.6 5.6 - - - +
113M LEU* 4.2 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 289 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136J SER 5.3 2.0 - - - +
137J LEU* 6.3 2.9 - - + -
267K ILE* 6.3 2.2 - - + -
270K ILE* 4.4 17.0 - - + +
271K ALA* 5.5 3.4 - - + -
273K LYS* 4.1 17.3 - - + +
285K VAL* 3.2 8.0 + - + +
286K GLN* 3.1 16.6 + - + +
288K ILE* 1.3 75.5 - - - +
290K LEU* 1.4 65.4 + - + +
292K LEU* 3.3 26.0 + - + +
293K LEU* 3.3 33.4 + - + +
318K ASP* 3.6 41.3 - - + +
321K LEU* 5.3 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 290 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133J PRO* 5.4 8.3 - - + -
286K GLN* 3.1 41.0 + - + +
287K ARG* 3.2 15.7 + - - +
289K LEU* 1.4 76.3 - - + +
291K GLU* 1.3 65.1 + - + +
293K LEU* 3.2 25.8 + - + +
294K ASN* 3.0 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 291 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287K ARG* 3.1 26.2 - - - +
288K ILE* 3.2 15.3 + - - +
290K LEU* 1.3 76.1 - - + +
292K LEU* 1.3 63.4 + - - +
294K ASN* 3.1 24.4 + - - +
295K GLN* 3.1 17.0 + - - +
111M ILE* 3.3 47.8 - - + +
112M ASP* 2.9 37.0 + - - +
113M LEU* 4.0 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 292 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235K PHE* 4.9 15.9 - - + -
264K ILE* 6.3 4.3 - - + -
267K ILE* 4.7 16.4 - - + -
270K ILE* 4.0 27.1 - - + -
288K ILE* 3.5 12.6 - - + +
289K LEU* 3.3 15.0 + - + +
290K LEU 3.3 0.6 - - - -
291K GLU* 1.3 76.4 - - - +
293K LEU* 1.4 65.8 + - + +
295K GLN* 3.5 17.1 + - - +
296K MET* 3.4 26.9 + - - +
321K LEU* 6.4 3.1 - - + -
326K ARG* 5.8 0.7 - - - -
112M ASP* 4.1 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 293 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137J LEU* 6.0 6.7 - - + -
139J MET* 5.9 7.6 - - + -
289K LEU* 3.3 36.8 - - + +
290K LEU* 3.4 31.6 - - + +
292K LEU* 1.4 80.9 - - + +
294K ASN* 1.4 61.9 + - - +
297K ASP* 2.9 30.8 + - - +
320K ALA* 4.7 11.7 - - + +
321K LEU* 5.6 4.0 - - + -
326K ARG* 3.2 45.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 294 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290K LEU* 3.0 25.5 + - - +
291K GLU* 3.3 18.4 - - - +
293K LEU* 1.4 76.2 - - - +
295K GLN* 1.4 54.1 + - - +
297K ASP* 3.4 8.4 + - - +
298K GLY* 2.8 30.5 + - - -
111M ILE* 5.9 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 295 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251K PHE* 3.3 33.8 - - + +
255K LYS* 3.9 38.9 - - + +
262K ILE* 5.6 5.9 - - - +
291K GLU* 3.1 13.9 + - - +
292K LEU* 3.8 22.0 - - - +
293K LEU 3.4 0.2 - - - -
294K ASN* 1.4 73.4 - - - +
296K MET* 1.3 67.4 + - + +
298K GLY* 3.3 3.9 + - - +
299K PHE* 3.2 23.0 + - + +
300K ASP* 4.6 0.3 - - - +
307K VAL* 5.2 9.7 - - - +
111M ILE* 6.5 0.9 - - + -
112M ASP* 4.7 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 296 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200K ARG* 3.7 29.4 - - + +
292K LEU* 3.4 14.0 + - + +
293K LEU 3.7 0.7 - - - +
295K GLN* 1.3 77.7 - - + +
297K ASP* 1.4 52.5 + - - +
299K PHE 2.7 30.1 + - - +
300K ASP* 3.3 21.0 - - - +
307K VAL* 4.0 25.8 - - + -
309K MET* 4.1 14.8 - - + -
325K GLY 5.2 3.6 - - - +
326K ARG* 3.2 59.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 297 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293K LEU* 2.9 17.9 + - - +
294K ASN* 3.4 11.0 - - - +
296K MET* 1.4 61.2 - - - +
298K GLY* 1.4 61.8 + - - +
299K PHE 3.4 5.2 + - - +
301K GLN* 6.1 0.3 - - - +
325K GLY 5.6 1.1 - - - +
326K ARG* 3.4 23.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 298 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255K LYS* 6.2 3.1 - - - -
294K ASN 2.8 15.4 + - - -
295K GLN* 3.3 6.8 + - - -
297K ASP* 1.4 76.4 - - - +
299K PHE* 1.4 57.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 299 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255K LYS* 5.5 19.1 - - + -
258K ALA* 5.6 1.3 - - + -
295K GLN* 3.2 11.6 + - + +
296K MET 2.7 13.7 - - - +
297K ASP 3.6 5.4 - - - +
298K GLY* 1.4 77.7 - - - +
300K ASP* 1.4 86.4 + - - +
301K GLN* 3.5 7.7 - - - +
302K ASN* 3.0 50.0 - - + +
303K VAL* 4.1 3.1 - - + -
304K ASN* 3.5 24.7 - - + -
305K VAL* 3.8 29.4 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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