Contacts of the helix formed by residues 244 - 257 (chain A) in PDB entry 4N7X
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 ASP 244 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 4.2 17.9 + - - +
239A LYS* 5.1 0.4 - - - -
243A PHE* 1.3 73.3 - - - +
245A GLU* 1.3 59.0 + - - +
246A SER* 2.9 19.1 + - - -
247A THR* 2.5 44.7 + - - -
248A CYS* 2.9 30.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A TYR* 2.6 39.0 + - - -
239A LYS* 3.0 18.1 + - - +
244A ASP* 1.3 74.1 - - - +
246A SER* 1.3 64.3 + - - +
248A CYS* 3.2 1.8 + - - +
249A ARG* 2.9 67.2 + - - +
297A TRP* 4.3 3.5 + - - -
301A PRO* 5.1 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LYS 3.4 22.2 + - - -
117A GLY* 3.7 11.8 - - - -
118A ASP* 4.0 5.7 + - - +
244A ASP* 2.9 9.9 + - - -
245A GLU* 1.3 79.4 - - - +
247A THR* 1.3 60.8 + - - +
249A ARG* 3.6 8.7 + - - +
250A THR* 2.9 25.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 5.5 0.3 + - - -
63A PRO* 3.7 37.3 - - + +
118A ASP* 5.7 2.9 - - - +
121A LEU* 3.8 13.0 - - + +
243A PHE* 4.0 18.2 - - + -
244A ASP* 2.5 37.0 + - - -
246A SER* 1.3 74.4 + - - +
248A CYS* 1.3 60.9 + - - +
250A THR* 3.1 7.6 + - - -
251A LEU* 2.9 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A GLY 4.6 0.7 - - - -
235A TYR* 3.6 34.3 - - + +
238A GLY* 3.6 31.2 - - - -
239A LYS* 3.6 19.5 - - - +
243A PHE* 3.6 13.9 - - - -
244A ASP 2.9 25.9 + - - +
245A GLU 3.6 4.3 - - - +
247A THR* 1.3 76.7 - - - +
249A ARG* 1.3 56.9 + - - +
251A LEU* 3.9 6.6 - - - +
252A ALA* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ILE* 5.1 0.2 - - - -
115A ALA* 3.2 25.6 + - + +
116A LYS* 4.4 6.9 - - - +
117A GLY* 4.9 4.3 - - - -
235A TYR* 4.3 0.7 - - + -
245A GLU* 2.9 51.6 + - - +
246A SER* 3.7 9.6 - - - +
248A CYS* 1.3 72.5 - - - +
250A THR* 1.3 66.5 + - - +
252A ALA* 3.4 2.1 + - - +
253A ILE* 3.3 29.6 + - - +
297A TRP* 2.9 72.3 + - + +
300A LYS* 3.4 36.8 + - - +
301A PRO* 3.5 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ILE* 3.4 23.7 - - + +
117A GLY* 3.5 2.0 - - - -
118A ASP* 2.8 46.6 + - - +
121A LEU* 3.8 24.7 - - + -
122A SER* 4.0 7.2 - - - -
125A ILE* 4.5 4.7 - - + -
246A SER 2.9 9.6 + - - -
247A THR* 3.1 10.6 + - - -
249A ARG* 1.3 80.4 - - - +
251A LEU* 1.3 57.1 + - - +
254A ALA* 2.9 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PRO* 3.5 27.1 - - + +
66A ALA* 3.9 10.5 - - + -
67A ALA* 4.0 9.6 - - + +
70A LEU* 5.0 4.7 - - + -
121A LEU* 4.8 1.3 - - + -
125A ILE* 3.8 19.5 - - + -
234A GLY* 3.3 16.6 - - - +
238A GLY* 3.9 14.8 - - - +
243A PHE* 3.6 35.2 - - + -
247A THR* 2.9 22.3 + - + +
248A CYS 3.9 2.0 - - - +
250A THR* 1.3 73.8 - - - +
252A ALA* 1.3 67.6 + - - +
254A ALA* 4.4 2.7 - - - -
255A VAL* 2.9 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A GLY 3.7 0.9 - - - +
231A LEU* 3.2 37.2 - - + +
234A GLY* 3.7 1.9 - - - -
235A TYR* 3.7 20.0 - - + +
248A CYS 3.0 17.9 + - - +
249A ARG 3.5 6.5 - - - +
250A THR 3.3 0.2 - - - -
251A LEU* 1.3 77.0 - - - +
253A ILE* 1.3 57.2 + - + +
256A GLY* 2.9 22.2 + - - -
293A LEU* 4.9 1.1 - - + -
297A TRP* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A SER* 3.8 9.8 - - - +
111A MET* 3.9 18.2 - - + +
112A ILE* 3.5 25.4 - - + -
115A ALA* 3.8 29.6 - - + -
231A LEU* 4.1 7.2 - - + -
249A ARG 3.3 12.4 + - - +
251A LEU 3.3 0.2 - - - -
252A ALA* 1.3 74.8 - - - +
254A ALA* 1.3 60.6 + - - +
257A MET* 2.9 56.1 + - + +
290A GLY* 4.9 4.0 - - - +
293A LEU* 4.2 19.1 - - + -
294A ALA* 4.7 4.5 - - + -
297A TRP* 4.2 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ALA* 5.1 0.9 - - + -
71A HIS* 2.8 22.7 + - + +
104A SER* 3.1 22.4 - - - +
108A SER* 4.5 3.1 - - - +
112A ILE* 3.9 10.9 - - + +
122A SER* 5.2 2.9 - - - +
125A ILE* 4.2 32.1 - - + -
250A THR* 2.9 20.8 + - + +
251A LEU* 4.0 3.4 - - - +
253A ILE* 1.3 76.7 - - - +
255A VAL* 1.3 57.9 + - + +
257A MET 4.0 3.8 + - - -
258A GLN 4.5 0.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
67A ALA* 4.3 13.0 - - + +
70A LEU* 3.8 39.7 - - + -
71A HIS* 3.6 14.4 - - + +
75A MET* 3.8 32.8 - - + +
230A GLY* 3.4 17.9 - - - +
233A SER* 4.5 0.2 - - - -
234A GLY* 4.1 4.7 - - - +
251A LEU* 2.9 21.2 + - - +
254A ALA* 1.3 77.2 - - - +
256A GLY* 1.3 62.7 + - - +
257A MET 3.4 0.6 + - - -
258A GLN* 3.8 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ASN* 3.1 23.1 + - - -
230A GLY* 3.9 13.2 - - - -
231A LEU* 3.8 15.7 - - - -
252A ALA 2.9 19.5 + - - -
253A ILE 3.4 0.2 + - - -
255A VAL* 1.3 79.4 - - - +
257A MET* 1.3 60.4 + - - +
258A GLN 3.6 0.9 - - - -
282A PHE* 3.4 16.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A SER* 3.6 5.0 - - - -
105A GLY* 3.4 16.1 + - - -
107A ALA* 3.8 22.2 - - + +
108A SER* 3.8 16.0 + - - +
111A MET* 3.8 12.8 - - + -
227A ASN* 5.1 1.6 - - - +
231A LEU* 5.4 2.7 - - + -
253A ILE* 2.9 39.5 + - + +
254A ALA 4.2 4.0 - - - -
255A VAL 3.4 0.4 - - - -
256A GLY* 1.3 79.8 - - - +
258A GLN* 1.3 66.8 + - - +
286A HIS* 3.5 50.4 + - + +
287A ASN* 3.7 21.3 - - - +
290A GLY* 4.4 4.7 - - - -
----------------------------------------------------------
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