Contacts of the helix formed by residues 244 - 258 (chain A) in PDB entry 3CS0
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 SER 244 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A MSE 4.4 7.3 - - - +
153A ALA 2.9 23.6 + - - -
155A SER* 3.3 12.2 + - - -
221A LEU* 3.5 23.4 + - - -
222A ILE* 2.7 25.4 + - - -
223A GLY* 4.0 2.2 - - - -
243A PRO* 1.3 69.3 - - - +
245A ASN* 1.3 67.8 + - - +
246A MSE 3.1 1.8 - - - -
247A VAL* 3.1 10.7 + - - +
248A LYS* 2.9 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ALA 3.8 2.4 + - - -
154A ASP* 3.0 27.5 + - - +
155A SER* 3.0 32.3 + - - +
156A ASP* 3.2 24.2 + - - +
243A PRO* 3.4 1.1 - - + -
244A SER* 1.3 80.3 + - - +
246A MSE 1.3 63.0 + - + +
248A LYS* 3.5 16.5 + - - +
249A ASN* 3.3 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A SER* 4.1 19.5 - - - +
195A TYR* 4.0 29.8 - - + +
197A ASN* 4.1 20.9 - - - +
242A ILE* 3.8 15.0 - - + -
243A PRO* 3.3 35.2 + - + +
244A SER 3.1 0.6 - - - -
245A ASN* 1.3 79.3 - - + +
247A VAL* 1.3 65.7 + - - +
249A ASN* 3.1 1.7 + - - +
250A LEU* 2.9 32.1 + - + +
326A ALA* 4.3 10.5 - - + +
327A GLN* 5.1 7.4 - - - +
330A THR* 3.6 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A VAL* 3.7 27.8 - - + -
136A ILE* 4.0 16.6 - - + -
152A MSE 3.3 26.5 - - + -
221A LEU* 5.6 0.2 - - + -
224A ILE* 3.6 26.0 - - + -
242A ILE* 4.2 6.0 - - + +
243A PRO 3.5 15.5 - - - +
244A SER* 3.1 10.9 + - - +
246A MSE 1.3 76.9 - - - +
248A LYS* 1.3 51.5 + - - +
250A LEU* 4.9 4.5 - - - -
251A THR* 2.7 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A MSE 4.0 28.0 - - - -
153A ALA 5.9 1.1 - - - -
244A SER 2.9 16.1 + - - +
245A ASN* 3.9 17.6 - - - +
246A MSE 3.2 0.2 - - - -
247A VAL* 1.3 78.5 - - - +
249A ASN* 1.3 65.8 + - - +
251A THR* 4.7 4.2 - - + +
252A SER* 3.4 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ASN* 3.3 16.6 + - - +
246A MSE 3.1 2.0 + - - +
248A LYS* 1.3 81.6 - - - +
250A LEU* 1.3 69.5 + - - +
251A THR 3.0 2.1 + - - -
252A SER* 3.2 6.9 + - - -
253A GLN* 3.0 27.7 + - - +
327A GLN 5.3 0.2 + - - -
330A THR* 2.9 44.8 + - + +
331A MSE 4.6 11.4 - - - +
332A PRO* 5.4 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ASP* 3.3 22.0 - - - +
134A SER* 2.9 30.5 - - - +
136A ILE* 3.9 17.9 - - + -
246A MSE 2.9 27.4 + - + +
247A VAL 4.4 0.7 - - - +
249A ASN* 1.3 76.0 - - - +
251A THR* 1.3 64.1 + - - +
253A GLN* 3.6 3.7 + - - +
254A MSE 3.2 37.3 + - + +
260A VAL* 3.7 16.7 - - + +
262A ARG* 3.8 15.7 - - - +
330A THR* 3.7 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE* 4.5 22.4 - - + -
101A VAL* 3.9 16.8 - - - +
136A ILE* 4.3 6.4 - - - +
138A LEU* 3.8 25.9 - - + +
152A MSE 5.8 1.1 - - + -
247A VAL* 2.7 25.0 + - + +
248A LYS* 4.7 4.9 - - + +
249A ASN 3.0 0.4 + - - -
250A LEU* 1.3 76.1 - - - +
252A SER* 1.3 72.2 + - - +
254A MSE 2.9 19.8 + - - +
255A VAL* 3.1 20.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LYS* 3.4 14.8 + - - -
249A ASN* 3.2 10.7 + - - -
251A THR* 1.3 81.3 - - - +
253A GLN* 1.3 70.3 + - - +
255A VAL* 3.2 13.6 + - - +
256A GLU* 3.2 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ASN 3.0 9.8 + - - +
250A LEU* 3.6 9.1 - - - +
251A THR 3.0 0.6 - - - -
252A SER* 1.3 83.2 + - - +
254A MSE 1.3 65.9 + - - +
256A GLU* 2.9 15.5 + - - -
257A TYR* 3.2 25.0 + - + +
259A GLN 4.0 5.4 - - - +
260A VAL* 2.8 21.6 - - + +
261A LYS* 2.7 35.2 + - - +
330A THR 3.4 17.0 + - - -
331A MSE 3.7 2.2 + - - -
332A PRO* 3.4 45.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 4.2 7.5 - - - +
129A GLY* 3.7 37.0 - - - -
130A LYS 3.8 2.0 - - - +
131A ASP* 3.7 21.8 - - + +
136A ILE* 3.4 26.5 - - + +
137A ALA 4.4 0.7 - - - -
138A LEU* 3.8 26.0 - - + -
250A LEU* 3.2 30.5 + - + +
251A THR* 2.9 10.0 + - - +
253A GLN* 1.3 78.4 - - - +
255A VAL* 1.3 64.2 + - - +
258A GLY* 2.8 28.2 + - - +
259A GLN* 4.1 9.1 + - - -
260A VAL* 3.9 12.1 - - + -
419A ALA* 5.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A TYR* 3.3 49.2 + - + +
128A VAL* 4.8 7.8 - - - +
138A LEU* 5.0 8.1 - - + -
251A THR* 3.1 26.2 + - + +
252A SER* 3.4 15.5 - - - +
254A MSE 1.3 77.2 - - - +
256A GLU* 1.3 67.7 + - + +
257A TYR 3.4 0.7 + - - -
258A GLY 4.7 0.3 + - - -
419A ALA* 4.9 6.6 - - - +
----------------------------------------------------------
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 SER* 3.2 10.9 + - - +
253A GLN* 2.9 5.2 + - - +
255A VAL* 1.3 82.6 - - + +
257A TYR* 1.3 97.5 + - + -
382A ASP* 5.8 0.2 - - - +
417A ASN* 4.7 4.0 + - - -
419A ALA* 5.5 0.9 - - - -
----------------------------------------------------------
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 GLN* 3.2 23.0 + - + +
254A MSE 3.3 0.8 + - - -
255A VAL 3.4 1.6 + - - -
256A GLU* 1.3 109.9 + - + +
258A GLY* 1.3 61.1 + - - +
259A GLN 3.3 14.8 - - - +
261A LYS* 3.8 36.6 - - + -
378A ASN* 3.5 25.1 - - - +
381A LYS* 6.2 0.7 - - - -
382A ASP* 3.9 23.1 - - - -
417A ASN* 3.3 27.0 - - + +
418A ILE 3.6 0.5 + - - -
419A ALA* 3.3 7.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL 3.5 20.4 - - - +
129A GLY* 3.7 8.6 - - - -
130A LYS 4.4 1.9 + - - +
254A MSE 2.8 13.7 + - - -
257A TYR* 1.3 76.9 - - - +
259A GLN* 1.3 61.4 + - - +
362A VAL* 5.2 1.0 - - - +
418A ILE* 4.0 5.9 - - - +
419A ALA* 3.9 16.0 - - - +
422A ARG* 3.4 21.5 + - - -
----------------------------------------------------------
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