Contacts of the helix formed by residues 245 - 266 (chain A) in PDB entry 5MJU
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 GLN 245 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A GLY* 2.8 15.1 + - - +
242A GLU* 3.4 19.3 - - - +
243A GLN 3.2 2.0 + - - -
244A GLY* 1.3 75.3 - - - +
246A LEU* 1.4 55.8 + - - +
247A LEU 3.3 0.7 - - - -
248A VAL* 3.0 20.2 + - - +
249A ASP* 2.8 71.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A GLU 4.6 1.0 + - - +
243A GLN 4.0 10.0 + - - +
245A GLN* 1.4 76.9 - - - +
247A LEU* 1.3 61.5 + - + +
249A ASP* 3.3 11.0 + - + +
250A PHE* 3.0 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A PHE* 4.4 16.4 - - + -
237A LEU* 3.8 32.5 - - + -
240A MET* 6.4 0.2 - - - -
244A GLY* 4.5 3.5 - - - +
245A GLN 3.3 1.4 - - - +
246A LEU* 1.3 81.4 - - + +
248A VAL* 1.3 57.2 + - - +
250A PHE* 3.2 12.0 + - + +
251A PHE* 2.9 62.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ILE* 5.1 1.6 - - + -
106A THR* 3.3 24.6 - - + +
109A ALA* 3.7 33.0 - - + -
110A SER* 5.5 2.2 - - - +
237A LEU* 3.8 19.5 - - + -
244A GLY 3.3 19.3 - - - +
245A GLN* 3.0 23.4 + - - +
247A LEU* 1.3 74.6 - - - +
249A ASP* 1.3 58.5 + - - +
251A PHE* 4.6 2.2 - - - -
252A ASN* 3.0 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A GLN* 2.8 54.8 + - - +
246A LEU* 3.7 9.8 + - + +
248A VAL* 1.3 77.0 - - - +
250A PHE* 1.4 57.2 + - - +
252A ASN* 4.1 6.7 - - - +
253A SER* 3.2 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 3.0 15.2 + - + +
247A LEU* 3.3 16.6 - - + +
249A ASP* 1.4 77.6 - - - +
251A PHE* 1.3 86.8 + + - +
252A ASN 3.3 0.2 - - - -
253A SER* 3.3 7.3 + - - -
254A LEU* 3.1 50.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A VAL* 4.3 11.9 - - + -
102A SER* 3.3 32.5 - - - -
105A ILE* 3.7 40.4 - - + -
106A THR* 3.7 18.7 - - + +
233A PHE* 4.4 7.9 - + - -
247A LEU* 2.9 52.1 + - + +
248A VAL 3.4 0.2 + - - -
250A PHE* 1.3 94.9 - + - +
252A ASN* 1.3 59.6 + - - +
253A SER 3.4 0.2 - - - -
254A LEU* 3.9 11.7 - - + -
255A ASN* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A THR* 3.5 13.6 - - - +
110A SER* 6.3 1.4 - - - -
248A VAL* 3.0 19.0 + - - +
249A ASP* 4.1 8.3 - - - +
251A PHE* 1.3 75.8 - - - +
253A SER* 1.4 60.2 + - - +
254A LEU 3.4 0.2 - - - -
255A ASN 3.7 0.2 + - - -
256A GLU* 3.2 31.0 + - - +
368A ARG* 3.1 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ASP 3.2 13.4 + - - -
250A PHE* 3.3 10.6 + - - -
252A ASN* 1.4 77.2 - - - +
254A LEU* 1.4 58.6 + - - +
256A GLU* 3.5 6.6 + - - +
257A ALA* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PRO* 3.4 43.1 - - + +
102A SER* 4.0 7.0 - - - -
250A PHE* 3.1 41.4 + - + +
251A PHE* 4.0 13.5 - - + +
253A SER* 1.4 76.2 - - - +
255A ASN* 1.4 62.5 + - - +
257A ALA* 3.5 7.4 + - + +
258A THR* 3.3 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU* 4.0 9.9 + - - +
102A SER* 3.3 21.4 + - - +
103A SER* 3.0 34.1 + - - +
251A PHE 3.1 16.2 + - - +
252A ASN 3.9 0.2 - - - +
253A SER 3.4 0.2 - - - -
254A LEU* 1.4 75.3 - - - +
256A GLU* 1.3 60.6 + - - +
258A THR* 3.3 6.7 + - - -
259A MET* 3.2 34.5 + - - +
353A PHE* 4.7 1.7 - - - -
357A GLU* 5.0 1.6 - - - +
364A LYS* 4.2 4.0 - - - -
368A ARG* 2.9 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ASN* 3.2 21.4 + - - +
253A SER* 3.6 8.3 - - - +
254A LEU 3.3 0.2 - - - -
255A ASN* 1.3 76.3 + - - +
257A ALA* 1.4 62.5 + - - +
259A MET* 3.2 11.6 + - - +
260A LYS* 3.2 46.9 + - - +
364A LYS* 2.9 38.3 + - - +
368A ARG* 3.9 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A SER 3.0 17.0 + - - +
254A LEU* 3.7 10.8 - - + +
255A ASN 3.4 0.2 - - - -
256A GLU* 1.4 74.0 - - - +
258A THR* 1.3 60.3 + - + +
260A LYS* 3.2 12.9 + - - +
261A LEU* 3.1 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 4.1 18.6 - - + +
98A PRO* 3.8 33.4 - - + +
99A LEU* 3.9 22.5 - - - +
254A LEU* 3.3 17.8 + - + +
255A ASN* 3.3 13.3 + - - -
256A GLU 3.4 0.2 - - - -
257A ALA* 1.3 75.6 - - + +
259A MET* 1.4 59.1 + - - +
260A LYS 3.2 0.4 - - - -
261A LEU* 3.5 20.9 + - + +
262A VAL* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU* 3.7 25.8 - - - -
255A ASN* 3.2 29.3 + - - +
256A GLU* 3.2 20.1 + - - +
257A ALA 3.2 0.8 - - - -
258A THR* 1.4 75.8 - - - +
260A LYS* 1.3 60.7 + - - +
262A VAL* 3.3 31.9 - - + +
263A ALA* 3.9 4.2 + - - +
350A PRO* 4.4 1.6 - - - +
353A PHE* 3.7 10.5 - - + -
354A LYS* 3.5 58.3 - - + +
357A GLU* 3.4 24.7 - - - +
364A LYS* 4.4 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A GLU* 3.2 39.5 + - - +
257A ALA* 3.2 11.6 + - - +
259A MET* 1.3 78.4 - - - +
261A LEU* 1.4 63.2 + - + +
262A VAL 3.2 0.4 - - - -
263A ALA* 3.2 17.9 + - - +
264A ILE* 3.3 23.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A MET* 6.0 3.6 - - + -
95A LEU* 4.0 24.0 - - + -
257A ALA* 3.1 21.8 + - + +
258A THR* 3.7 24.5 - - + +
260A LYS* 1.4 77.9 - - + +
262A VAL* 1.4 54.9 + - - +
264A ILE* 3.3 21.3 + - + +
265A ILE* 3.1 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 5.3 3.4 - - + -
95A LEU* 3.8 13.0 - - + +
258A THR 3.0 11.5 + - - +
259A MET* 3.3 41.3 - - + +
261A LEU* 1.4 72.6 - - - +
263A ALA* 1.4 60.8 + - - +
265A ILE* 3.8 2.8 - - + +
266A MET* 2.9 34.2 + - + +
350A PRO* 3.4 48.5 - - + +
351A ILE* 3.9 12.3 - - + +
354A LYS* 3.9 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A MET 4.1 8.3 - - - +
260A LYS* 3.2 12.9 + - - +
262A VAL* 1.4 81.3 - - - +
264A ILE* 1.3 61.2 + - + +
266A MET* 3.3 25.3 - - - +
267A TRP* 3.7 13.7 - - - -
354A LYS* 4.8 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A MET* 6.4 0.4 - - + -
260A LYS* 3.3 22.2 + - + +
261A LEU* 3.4 27.1 - - + +
262A VAL 3.2 0.6 - - - -
263A ALA* 1.3 75.2 - - + +
265A ILE* 1.4 66.6 + - + +
266A MET 3.2 4.7 + - - -
267A TRP* 3.4 19.2 + - - +
268A TYR* 4.3 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 4.4 6.1 - - + +
91A MET* 3.7 47.3 - - + +
92A LEU* 4.0 26.0 - - + -
94A MET* 3.8 26.2 - - + -
95A LEU* 3.7 22.2 - - + -
261A LEU* 3.1 21.0 + - + +
262A VAL* 3.5 6.3 + - + +
264A ILE* 1.4 77.6 - - + +
266A MET* 1.3 62.2 + - - +
267A TRP 3.2 0.4 - - - -
268A TYR* 3.1 14.2 + - - +
269A ALA* 3.5 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 3.7 15.7 - - + +
262A VAL* 2.9 31.7 + - + +
263A ALA* 3.3 18.8 - - - +
264A ILE 3.2 0.2 - - - -
265A ILE* 1.3 76.3 - - - +
267A TRP* 1.3 63.2 + - + +
269A ALA* 3.3 23.0 - - + +
334A GLN* 4.0 26.9 + - - +
351A ILE* 3.8 31.9 - - + -
354A LYS* 3.8 33.2 - - + -
355A CYS* 6.2 1.1 - - - -
358A GLU* 5.8 2.9 - - - +
----------------------------------------------------------
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