Contacts of the helix formed by residues 248 - 266 (chain J) in PDB entry 6LTJ
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 248 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83J GLU* 4.6 10.1 - - - +
247J THR* 1.3 91.2 + - + +
249J SER* 1.3 55.3 + - - +
250J TRP* 2.6 18.4 + - - +
251J HIS* 2.9 48.6 + - - +
252J ASN* 3.4 19.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 249 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82J MET* 4.2 10.9 - - - +
83J GLU* 3.7 9.8 + - - -
84J ALA* 3.1 46.3 - - - +
247J THR* 3.3 1.4 - - - -
248J ARG* 1.3 76.1 - - - +
250J TRP* 1.3 53.7 + - - +
252J ASN* 3.7 14.7 - - - +
253J TYR* 2.7 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 250 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78J PRO* 5.3 15.4 - - + +
246J VAL* 5.2 8.1 - - - +
247J THR* 3.0 23.8 + - - +
248J ARG* 2.6 7.3 + - - +
249J SER* 1.3 73.7 - - - +
251J HIS* 1.3 118.4 + + - +
253J TYR* 5.5 0.2 - - - -
254J MET* 2.9 64.1 + - + +
255J CYS* 5.5 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 251 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207J ARG* 4.3 20.4 + - - +
211J GLN* 6.3 0.9 - - - -
248J ARG* 2.9 45.6 + - - +
250J TRP* 1.3 109.1 - + - +
252J ASN* 1.3 61.2 + - - +
255J CYS* 2.7 48.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 252 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83J GLU* 5.3 3.6 + - - -
84J ALA 5.4 3.4 + - - -
207J ARG* 5.5 2.6 + - - -
248J ARG* 3.4 17.1 + - - +
249J SER* 3.4 21.0 + - - +
250J TRP 3.2 0.6 - - - -
251J HIS* 1.3 77.5 - - - +
253J TYR* 1.3 59.4 + - + +
255J CYS* 5.0 0.2 - - - -
256J ASN* 2.9 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 253 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J TYR* 3.8 22.1 + + - -
38J PRO* 3.7 28.8 - - + +
40J ALA* 4.2 27.1 - - + -
75J LEU* 3.6 44.3 - - + +
84J ALA* 5.7 4.0 - - + -
249J SER* 2.7 29.0 + - - +
252J ASN* 1.3 73.4 - - + +
254J MET* 1.3 61.0 + - - +
256J ASN* 4.5 5.6 - - + -
257J CYS* 2.9 37.2 + - + +
260J GLN* 5.7 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 254 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250J TRP* 2.9 56.1 + - + +
253J TYR* 1.3 74.4 - - - +
255J CYS* 1.3 66.9 + - - +
257J CYS* 3.2 14.4 - - - -
258J VAL* 3.1 38.4 + - + +
293J TYR* 6.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 255 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207J ARG* 2.8 42.0 - - - +
250J TRP* 5.5 5.2 - - - -
251J HIS* 2.7 36.3 + - - +
252J ASN 4.2 0.4 - - - +
254J MET* 1.3 77.5 - - - +
256J ASN* 1.3 62.4 + - - +
258J VAL* 3.6 7.2 - - - +
259J ILE* 2.9 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 256 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200J ASP* 6.0 0.4 + - - -
203J THR* 4.9 12.6 + - + +
204J MET* 4.3 19.7 - - - +
207J ARG* 5.5 1.9 - - - +
252J ASN* 2.9 34.5 + - - +
253J TYR* 4.2 7.6 - - + +
255J CYS* 1.3 82.8 - - - +
257J CYS* 1.3 56.8 + - - +
259J ILE* 4.1 5.3 - - - +
260J GLN* 2.9 47.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 257 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J TYR* 5.4 1.1 - - - +
75J LEU* 5.3 5.6 - - + -
76J ARG* 5.3 11.9 - - - +
253J TYR* 2.9 39.5 + - + +
254J MET* 3.2 28.3 - - - -
256J ASN* 1.3 76.4 - - - +
258J VAL* 1.3 70.2 + - - +
260J GLN* 3.1 15.1 + - - +
261J ASP* 3.0 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 258 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254J MET* 3.1 38.0 + - + +
255J CYS* 3.6 9.2 - - - +
257J CYS* 1.3 84.1 - - - +
259J ILE* 1.3 68.8 + - + +
261J ASP* 3.3 11.3 + - + +
262J PHE* 3.0 37.5 + - + +
284J THR* 5.1 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 259 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203J THR* 3.5 42.2 - - + +
206J CYS* 3.8 15.5 - - + +
207J ARG* 4.8 12.6 - - + -
210J PHE* 3.5 42.4 - - + -
255J CYS* 2.9 28.0 + - + +
256J ASN* 4.1 4.9 - - - +
258J VAL* 1.3 84.9 - - + +
260J GLN* 1.3 59.9 + - - +
262J PHE* 4.2 2.9 - - + +
263J GLN* 2.8 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 260 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J TYR* 3.0 52.7 + - + -
174J ALA* 6.3 0.4 - - - +
203J THR* 4.4 7.7 - - + +
253J TYR* 5.6 2.0 - - - -
256J ASN* 2.9 35.2 + - - +
257J CYS* 3.1 15.4 + - - +
259J ILE* 1.3 77.2 - - - +
261J ASP* 1.3 56.2 + - - +
263J GLN* 3.3 24.5 - - - +
264J ALA* 2.9 31.9 + - - +
356J LEU* 5.1 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 261 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257J CYS* 3.0 20.9 + - - +
258J VAL* 3.5 12.8 - - - +
259J ILE 3.2 0.2 - - - -
260J GLN* 1.3 77.2 - - - +
262J PHE* 1.3 64.1 + - + +
264J ALA* 3.1 6.5 + - - +
265J SER* 3.0 32.2 + - - -
282J MET* 5.0 5.0 - - - +
279K PHE* 5.6 2.6 - - - -
283K MET* 3.4 33.4 - - - +
290K ARG* 3.6 13.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 262 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206J CYS* 4.8 4.5 - - - -
210J PHE* 3.4 42.0 - + + -
258J VAL* 3.0 23.9 + - + +
259J ILE* 4.2 5.6 - - + +
261J ASP* 1.3 76.7 - - + +
263J GLN* 1.3 61.8 + - - +
265J SER 5.1 0.2 - - - -
266J VAL* 2.9 49.1 + - + +
267J LEU* 4.0 2.2 - - - +
282J MET* 3.4 55.0 - - + -
283J PRO 3.4 24.2 - - - -
284J THR* 3.8 17.7 - - - -
295J CYS* 4.5 3.8 - - + -
297J PHE* 5.0 3.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 263 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199J GLY* 3.9 9.9 + - - +
202J ILE* 3.3 31.3 - - + +
203J THR* 3.4 32.5 + - + +
206J CYS* 5.0 5.2 - - + -
259J ILE* 2.8 24.7 + - + +
260J GLN* 3.3 20.9 - - - +
262J PHE* 1.3 74.2 - - - +
264J ALA* 1.3 65.1 + - - +
265J SER 3.4 0.3 + - - -
267J LEU* 3.8 30.1 + - + +
354J ASN* 5.2 2.6 + - - +
356J LEU* 4.6 15.5 - - + +
357J ILE* 4.0 20.7 - - + +
358J GLN 5.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260J GLN 2.9 19.9 + - - +
261J ASP* 3.1 7.1 + - - +
263J GLN* 1.3 77.3 - - - +
265J SER* 1.3 66.5 + - - +
356J LEU* 3.8 44.9 - - + +
358J GLN* 6.0 1.6 - - - +
287K VAL* 4.7 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 265 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261J ASP* 3.0 13.1 + - - -
264J ALA* 1.3 85.7 + - - +
266J VAL* 1.3 66.6 + - - +
267J LEU 5.2 0.9 - - - -
282J MET* 3.7 30.7 - - - +
301J ARG* 5.6 0.6 + - - -
287K VAL* 3.2 32.6 - - - +
288K ASP* 5.7 1.8 - - - -
290K ARG* 5.0 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 266 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262J PHE* 2.9 41.7 + - + +
264J ALA 3.8 0.2 - - - -
265J SER* 1.3 84.4 - - - +
267J LEU* 1.3 71.8 + - + +
280J ALA* 4.9 7.4 - - + +
281J GLN 5.6 1.6 - - - -
282J MET* 4.7 11.7 - - + +
297J PHE* 4.0 31.4 - - + -
300J GLU 4.8 1.1 - - - +
301J ARG* 2.8 55.8 + - + +
----------------------------------------------------------
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