Contacts of the helix formed by residues 278 - 291 (chain A) in PDB entry 1M6X
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 ASN 278 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ARG* 5.6 4.1 + - - +
276A LYS* 3.1 4.6 - - + +
277A ASP* 1.3 78.7 - - - +
279A LEU* 1.3 66.8 + - - +
280A VAL* 3.0 6.6 + - - +
281A ARG* 3.1 19.7 + - - +
282A SER* 3.7 5.0 + - - -
5E T 4.7 6.7 - - + +
6E T 2.7 60.2 + - + +
7E C 4.0 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU* 3.9 35.2 - - + -
178A TYR* 3.9 26.5 - - + -
181A LEU* 4.1 20.9 - - + -
192A PHE* 4.1 2.9 - - + -
275A LEU* 3.6 40.4 - - + -
276A LYS* 2.8 25.6 + - + +
278A ASN* 1.3 75.9 - - - +
280A VAL* 1.3 58.3 + - - +
282A SER* 2.8 25.4 + - - +
283A TYR* 2.8 13.0 + - + +
5E T 5.4 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A PHE* 3.5 39.5 - - + -
277A ASP 3.6 15.7 - - - +
278A ASN* 3.0 2.6 + - - +
279A LEU* 1.3 78.9 - - - +
281A ARG* 1.3 63.6 + - + +
283A TYR* 4.0 5.6 - - - -
284A ASN* 2.7 57.7 + - - +
304A SER* 4.1 7.0 - - - +
24H T 4.7 8.1 - - + -
25H A 4.1 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ASN* 3.1 12.3 + - - +
280A VAL* 1.3 83.9 - - + +
282A SER* 1.3 55.6 + - - +
284A ASN* 4.3 7.5 - - - +
285A LYS* 2.7 57.5 + - - +
5E T 4.5 6.7 - - + -
6E T 3.7 29.2 - - + +
7E C 3.6 5.6 - - - +
26H G 3.1 49.0 + - - +
27H G 2.6 48.2 + - - -
28H A 4.2 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A TYR* 3.1 27.0 + - - -
278A ASN 3.7 3.4 + - - -
279A LEU* 2.8 17.7 + - - +
281A ARG* 1.3 80.1 - - - +
283A TYR* 1.3 62.5 + - - +
285A LYS* 3.1 7.2 + - - +
286A ALA* 2.7 36.7 + - - +
4E G 4.1 26.7 - - - -
5E T 4.0 16.8 + - - +
6E T 5.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A PHE* 3.6 17.9 - + - -
178A TYR* 3.5 52.5 - + + -
181A LEU* 3.8 21.1 - - + -
182A PHE* 3.1 40.2 - - + +
279A LEU 2.8 15.1 + - - +
280A VAL* 3.5 7.2 - - - +
282A SER* 1.3 82.2 + - - +
284A ASN* 1.3 67.4 + - - +
286A ALA* 3.1 1.9 + - - +
287A LEU* 2.8 42.1 + - + +
304A SER* 3.3 42.8 + - - -
306A ILE* 4.8 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A VAL* 2.7 31.6 + - - +
281A ARG* 3.6 12.4 - - - +
283A TYR* 1.3 74.8 - - - +
285A LYS* 1.3 65.9 + - - +
287A LEU* 3.1 2.5 + - - +
288A LYS* 2.8 25.6 + - - +
303A LYS* 3.7 19.7 - - + +
304A SER* 3.1 23.6 + - - -
25H A 2.9 52.9 + - + +
26H G 4.5 6.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ARG* 2.7 39.6 + - - +
282A SER* 3.4 6.1 - - - +
284A ASN* 1.3 73.7 - - - +
286A ALA* 1.3 61.5 + - - +
288A LYS* 3.2 10.7 - - + +
289A LYS* 3.1 22.8 + - + +
3E A 4.0 14.6 + - + -
4E G 3.3 38.7 + - + +
5E T 3.5 25.8 + - + +
26H G 6.1 0.2 - - - -
28H A 5.5 1.8 - - - +
29H A 4.4 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A PHE* 4.1 5.6 - - + -
178A TYR* 3.9 25.4 - - + +
282A SER 2.7 19.3 + - - +
283A TYR 3.4 3.6 - - - +
285A LYS* 1.3 68.7 - - - +
287A LEU* 1.3 66.6 + - - +
288A LYS 2.9 1.1 - - - -
289A LYS* 2.9 6.3 + - - +
290A ASN* 2.8 42.5 + - - +
3E A 6.4 0.7 - - + -
4E G 4.6 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ILE* 4.2 13.0 - - + -
164A SER* 4.9 0.2 - - - +
165A PHE* 3.9 25.0 - - + -
283A TYR* 2.8 40.1 + - + +
284A ASN* 3.5 4.7 - - - +
286A ALA* 1.3 73.3 - - - +
288A LYS* 1.3 61.6 + - - +
290A ASN* 4.6 2.2 - - - +
291A ALA* 3.1 21.1 + - - -
292A PRO* 3.9 8.7 - - + +
296A PHE* 3.6 39.3 - - + +
303A LYS* 3.3 39.0 - - + +
306A ILE* 4.4 3.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
284A ASN 2.8 12.7 + - - +
285A LYS* 3.2 17.0 - - + +
286A ALA 2.9 0.2 - - - -
287A LEU* 1.3 76.5 - - - +
289A LYS* 1.3 64.2 + - + +
291A ALA* 3.4 18.2 - - - +
296A PHE 3.7 17.2 - - - +
297A ALA* 3.5 21.1 + - - +
299A LYS* 3.9 13.5 - - - +
303A LYS* 3.6 22.1 - - - +
26H G 3.5 25.6 + - - +
27H G 5.7 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LYS* 3.1 9.6 + - + +
286A ALA* 2.9 8.6 + - - +
288A LYS* 1.3 79.7 - - + +
290A ASN* 1.3 65.3 + - - +
291A ALA* 2.9 10.3 + - - +
2E A 5.7 0.7 - - - -
3E A 3.5 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A SER* 3.6 19.5 + - - +
165A PHE* 3.9 15.8 - - - -
168A THR* 3.0 44.5 + - + +
286A ALA* 2.8 36.1 + - - +
287A LEU* 4.5 1.1 - - - +
289A LYS* 1.3 75.5 - - - +
291A ALA* 1.3 68.7 + - - +
292A PRO* 2.7 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU 3.1 13.2 + - - -
288A LYS 3.4 15.5 - - - +
289A LYS 2.9 4.8 - - - +
290A ASN* 1.3 75.7 - - - +
292A PRO* 1.3 62.0 - - - +
293A TYR* 2.8 24.7 + - - +
294A PRO* 6.0 0.2 - - + -
296A PHE* 4.1 12.3 - - + -
297A ALA* 4.9 7.6 - - + +
----------------------------------------------------------
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