Contacts of the helix formed by residues 239 - 260 (chain A) in PDB entry 1M1B
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 239 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLU* 3.0 22.1 - - - +
46A SER* 4.8 1.6 - - - +
48A LEU* 4.6 16.3 - - + +
49A SER* 3.8 10.1 - - - +
124A LEU* 4.4 12.5 - - - +
217A THR* 3.9 22.4 + - - +
237A TRP 3.6 0.2 + - - -
238A ALA* 1.3 84.2 - - - +
240A HIS* 1.3 70.2 + - - +
242A LEU* 3.5 4.5 + - + +
243A ARG* 3.1 52.0 + - + +
996A SPV 4.8 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A MET* 4.0 10.1 - - + -
25A GLU* 3.4 3.2 + - - +
217A THR* 4.8 15.3 + - + +
220A TYR* 6.1 3.2 - - - +
237A TRP* 4.1 24.4 - + + +
238A ALA 4.1 9.2 - - - -
239A ASN* 1.3 92.0 + - - +
241A ASN* 1.3 63.2 + - - +
243A ARG* 3.2 37.6 + - + +
244A ALA* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A MET* 3.7 16.1 - - - +
25A GLU* 2.8 35.6 + - - +
26A ALA* 4.9 0.6 - - - +
27A HIS* 3.8 12.6 - - + -
31A SER* 5.1 6.1 - - - -
34A ILE* 5.9 4.8 - - - +
35A VAL* 3.7 19.2 - - - +
240A HIS* 1.3 76.2 - - - +
242A LEU* 1.3 68.2 + - - +
244A ALA* 4.0 5.1 - - - +
245A SER* 3.0 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLU* 2.5 19.7 + - - +
27A HIS* 3.7 23.8 - - + +
48A LEU* 4.5 8.1 - - + +
49A SER* 3.6 36.6 - - - +
52A ALA* 3.4 30.5 - - + -
53A GLN* 4.4 7.9 - - + +
239A ASN* 3.6 7.9 - - + +
241A ASN* 1.3 75.8 - - - +
243A ARG* 1.3 65.8 + - + +
245A SER* 3.3 6.0 + - - -
246A VAL* 3.2 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A THR* 4.3 12.3 + - - +
239A ASN* 3.1 45.1 + - + +
240A HIS* 3.2 30.2 + - + +
241A ASN 3.3 0.2 - - - -
242A LEU* 1.3 83.8 - - + +
244A ALA* 1.3 63.5 + - - +
246A VAL* 3.4 9.2 + - - +
247A SER* 3.3 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A HIS 3.0 20.7 + - - +
241A ASN* 4.0 7.0 - - - +
243A ARG* 1.3 72.3 - - - +
245A SER* 1.3 66.5 - - - +
247A SER* 3.1 10.3 + - - -
248A ALA* 3.0 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A HIS* 4.7 11.4 + - - -
241A ASN 3.0 19.6 + - - -
242A LEU* 3.3 10.1 - - - -
244A ALA* 1.3 77.5 - - - +
246A VAL* 1.3 60.3 + - - +
248A ALA* 3.6 5.6 + - - +
249A ILE* 2.9 46.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LEU* 3.2 24.0 + - + +
243A ARG* 3.6 10.3 - - - +
244A ALA 3.1 0.4 - - - -
245A SER* 1.3 74.8 - - - +
247A SER* 1.3 56.0 + - - +
249A ILE* 3.1 5.3 + - - -
250A GLN* 2.7 68.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ARG 3.3 11.2 + - - -
244A ALA* 3.1 11.9 + - - -
246A VAL* 1.3 78.8 - - - +
248A ALA* 1.3 53.9 + - - +
250A GLN* 3.6 9.3 - - - +
251A GLN* 2.7 59.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ALA 3.0 13.2 + - - +
245A SER* 3.7 7.6 - - - +
247A SER* 1.3 79.5 - - - +
249A ILE* 1.3 58.7 + - + +
251A GLN* 4.1 5.4 - - - +
252A THR* 2.7 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A SER* 2.9 37.3 + - - +
246A VAL* 3.8 4.7 - - + +
248A ALA* 1.3 76.4 - - + +
250A GLN* 1.3 63.1 + - + +
252A THR* 4.4 3.6 - - - -
253A THR* 2.7 45.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A VAL* 2.7 49.0 + - + +
247A SER* 3.7 6.6 - - - +
249A ILE* 1.3 75.7 - - + +
251A GLN* 1.3 58.7 + - + +
253A THR* 4.0 3.7 - - - -
254A LYS* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A SER* 2.7 43.9 + - - +
248A ALA* 4.1 4.9 - - - +
250A GLN* 1.3 74.9 - - + +
252A THR* 1.3 58.7 + - - +
254A LYS* 3.2 6.5 + - - +
255A GLN* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ALA* 2.7 26.3 + - - +
249A ILE* 4.1 4.3 - - - -
251A GLN* 1.3 76.8 - - - +
253A THR* 1.3 63.7 + - - +
255A GLN* 3.4 2.1 + - - +
256A ILE* 3.0 44.2 + - + +
265A VAL* 3.9 19.7 - - + +
269A ILE* 4.2 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ILE* 2.7 39.8 + - - +
250A GLN* 4.0 4.7 - - - -
252A THR* 1.3 75.4 - - - +
254A LYS* 1.3 64.3 + - - +
256A ILE* 3.5 5.3 + - - +
257A TYR* 3.0 26.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A GLN 2.9 20.2 + - - +
251A GLN* 3.6 7.0 - - - +
253A THR* 1.3 78.7 - - - +
255A GLN* 1.3 57.8 + - - +
257A TYR* 3.1 8.4 + - + +
258A ASP* 2.9 53.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A GLN 2.9 17.4 + - - +
252A THR* 3.8 4.3 - - - +
254A LYS* 1.3 77.2 - - - +
256A ILE* 1.3 61.9 + - - +
258A ASP* 3.8 5.9 - - - +
259A ASP* 2.6 60.4 + - - +
261A SER 6.0 0.7 - - - +
264A ASN* 3.3 34.1 - - + +
265A VAL* 4.1 16.8 - - + -
268A LYS* 5.5 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A THR* 3.0 37.6 + - + +
253A THR* 4.1 4.7 - - - +
255A GLN* 1.3 72.6 - - - +
257A TYR* 1.3 61.4 + - - +
260A GLN* 2.9 28.5 + - - -
261A SER 4.0 18.4 - - - +
262A LEU* 3.7 24.7 - - + -
265A VAL* 3.9 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A THR* 3.0 22.2 + - + +
254A LYS* 3.3 8.7 - - + +
256A ILE* 1.3 81.5 - - - +
258A ASP* 1.3 79.2 + - - +
260A GLN* 3.5 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LYS* 2.9 48.5 + - - +
255A GLN* 3.8 7.4 - - - +
257A TYR* 1.3 97.0 - - - +
259A ASP* 1.3 65.8 + - - +
260A GLN* 4.4 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLN* 2.6 46.8 + - - +
258A ASP* 1.3 78.0 - - - +
260A GLN* 1.3 69.9 + - - +
261A SER* 3.0 23.1 + - - +
264A ASN* 2.9 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ILE* 2.9 17.1 + - - -
257A TYR 3.5 15.3 + - - +
258A ASP 4.4 3.4 - - - +
259A ASP* 1.3 79.9 - - - +
261A SER* 1.3 57.8 + - - +
----------------------------------------------------------
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