Contacts of the helix formed by residues 285 - 301 (chain A) in PDB entry 2XMS
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 285 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A MET* 3.6 21.7 - - + +
275A ALA 4.8 4.5 - - - +
276A ASP* 2.9 27.6 + - - +
277A SER* 3.6 23.3 - - - -
281A PRO 2.8 12.9 + - - +
284A THR* 1.3 90.5 + - - +
286A PRO* 1.4 65.1 - - - +
287A GLY 3.2 3.3 + - - +
288A LYS* 3.5 12.3 + - + +
289A LEU* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PRO* 3.7 25.6 - - + +
68A LEU* 3.7 14.8 - - + +
71A PHE* 3.9 20.9 - - + -
281A PRO 4.0 0.6 - - - +
282A GLN 3.8 16.2 - - - +
283A LEU 3.8 12.1 - - - +
284A THR 3.3 8.7 - - - +
285A GLN* 1.4 89.2 - - - +
287A GLY* 1.3 54.2 + - - +
289A LEU* 4.4 1.8 - - + -
290A THR* 2.6 39.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 3.4 33.3 - - - -
73A ASP* 5.1 2.5 - - - +
285A GLN 3.2 1.0 - - - -
286A PRO* 1.3 81.0 - - - +
288A LYS* 1.3 63.2 + - - +
290A THR* 3.4 3.3 - - - +
291A GLU* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LEU* 5.1 11.9 - - + -
274A MET* 3.2 34.7 - - + +
275A ALA* 5.5 8.7 + - - +
285A GLN* 3.5 14.6 + - + +
287A GLY* 1.3 74.3 - - - +
289A LEU* 1.3 58.9 + - - +
291A GLU* 3.2 12.1 + - + +
292A ALA* 2.9 26.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 4.0 21.1 - - + -
74A MET* 4.8 0.5 - - - +
153A VAL* 4.9 5.2 - - + -
155A ILE* 4.1 12.6 - - + -
244A MET* 4.0 15.7 - - + -
246A VAL* 4.1 15.0 - - + -
272A LEU* 3.9 22.4 - - + -
274A MET* 4.1 6.3 - - + +
281A PRO 4.7 1.1 - - - -
282A GLN* 3.8 36.6 - - + +
285A GLN 3.1 18.2 + - - +
286A PRO* 3.9 4.0 - - + +
288A LYS* 1.3 76.6 - - - +
290A THR* 1.3 64.6 + - - +
292A ALA* 3.7 4.3 - - - -
293A PHE* 2.9 27.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 3.6 12.7 - - - +
71A PHE* 3.9 6.6 - - - +
73A ASP* 3.7 16.4 - - + +
74A MET* 3.4 49.0 - - + +
77A ILE* 3.8 9.9 - - + +
286A PRO 2.6 22.4 + - - -
287A GLY* 3.4 7.9 - - - -
289A LEU* 1.3 78.8 - - - +
291A GLU* 1.3 59.2 + - - +
293A PHE* 3.2 4.0 + - - +
294A LYS* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLY 3.1 11.3 + - - +
288A LYS* 3.2 13.8 + - + +
290A THR* 1.3 79.2 - - - +
292A ALA* 1.3 62.8 + - - +
294A LYS* 3.3 23.9 + - - +
295A TYR* 2.8 55.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A MET* 3.8 16.1 - - + +
272A LEU* 3.6 38.8 - - + -
288A LYS 2.9 16.9 + - - +
289A LEU 3.8 4.5 - - - +
291A GLU* 1.3 76.0 - - - +
293A PHE* 1.3 55.8 + - - +
295A TYR* 3.2 11.3 + - - +
296A PHE* 2.8 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ILE* 3.9 33.7 - - + -
69A PHE* 6.1 1.6 - + - -
74A MET* 3.8 29.6 - - + -
77A ILE* 4.1 10.3 - - + -
78A ILE* 5.0 0.2 - - + -
127A ILE* 4.3 15.9 - - + -
129A VAL* 4.6 9.6 - - + -
153A VAL* 4.0 29.2 - - + -
244A MET* 4.0 5.3 - - + +
289A LEU* 2.9 20.1 + - + +
290A THR* 3.2 7.8 + - - +
292A ALA* 1.3 72.5 - - - +
294A LYS* 1.3 60.6 + - - +
296A PHE* 3.3 13.6 + + - +
297A LEU* 2.9 63.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU* 5.9 1.7 + - - +
77A ILE* 3.7 18.3 - - + +
290A THR 3.0 12.3 + - - +
291A GLU* 3.4 16.8 - - - +
292A ALA 3.2 0.2 - - - -
293A PHE* 1.3 77.4 - - - +
295A TYR* 1.3 83.8 + - + +
297A LEU* 3.3 3.0 + - - +
298A GLN* 3.0 41.8 + - - +
304A ALA* 3.8 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLU* 2.8 53.6 + - + +
292A ALA* 3.2 10.1 + - - +
294A LYS* 1.3 92.5 + - - +
296A PHE* 1.3 61.6 + - - +
298A GLN* 3.6 23.1 - - - +
299A GLY* 2.9 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ILE* 4.4 8.1 - - + -
152A LEU 3.6 17.5 - - - -
153A VAL* 4.0 22.7 - - + -
242A PRO* 3.6 38.8 - - + -
243A VAL 3.6 7.2 - - - -
244A MET* 3.5 35.7 - - + -
268A GLN 5.4 0.2 - - - -
270A SER* 4.4 9.9 - - - +
292A ALA 2.8 17.5 + - - +
293A PHE* 3.4 18.8 - + - +
294A LYS 3.3 0.2 - - - -
295A TYR* 1.3 77.0 - - - +
297A LEU* 1.3 57.6 + - + +
299A GLY* 3.4 2.6 + - - -
300A MET* 3.0 48.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 3.6 31.4 - - + -
81A PHE* 3.8 22.0 - - + -
127A ILE* 3.6 31.0 - - + -
293A PHE* 2.9 43.6 + - + +
294A LYS 3.6 4.0 - - - +
296A PHE* 1.3 73.6 - - + +
298A GLN* 1.3 69.0 + - - +
300A MET* 3.2 13.8 + - - +
301A GLY 3.0 5.5 + - - -
302A TYR* 3.0 33.0 + - + +
303A MET 5.5 0.2 - - - +
304A ALA* 3.9 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LYS* 3.0 37.4 + - - +
295A TYR* 3.6 23.4 - - - +
296A PHE 3.4 0.2 - - - -
297A LEU* 1.3 76.8 - - - +
299A GLY* 1.3 56.0 + - - +
301A GLY* 2.9 21.1 + - - -
302A TYR 3.3 14.6 - - - +
303A MET* 5.0 1.1 - - - -
304A ALA* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PRO* 6.1 0.2 - - - -
295A TYR 2.9 19.8 + - - -
296A PHE* 3.4 2.2 + - - -
297A LEU 3.3 0.2 - - - -
298A GLN* 1.3 71.7 - - - +
300A MET* 1.3 59.3 - - - +
301A GLY* 3.4 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ILE* 3.9 24.0 - - + -
150A GLU* 3.7 28.0 - - + +
151A GLY* 4.5 0.4 - - - -
242A PRO* 3.8 28.7 - - + -
296A PHE* 3.0 45.9 + - + +
297A LEU* 3.2 13.6 + - - +
299A GLY* 1.3 75.2 - - - +
301A GLY* 1.3 57.9 + - - +
302A TYR* 3.7 31.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A GLN 2.9 13.8 + - - -
299A GLY 3.2 1.3 - - - -
300A MET* 1.3 79.2 - - - +
302A TYR* 1.3 66.6 + - - +
303A MET* 4.1 1.6 + - - +
----------------------------------------------------------
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