Contacts of the helix formed by residues 240 - 256 (chain A) in PDB entry 1L4E
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 GLY 240 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A HIS* 3.9 11.4 - - - -
134A CYS* 4.1 8.7 - - - -
143A MET* 3.6 11.2 - - - +
235A LEU 3.9 3.2 + - - -
239A GLY* 1.3 73.7 - - - -
241A PHE* 1.3 65.7 + - - -
242A ASP* 3.3 12.6 - - - -
243A LEU* 3.2 7.2 + - - +
244A VAL* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ALA* 3.8 11.7 - - + +
69A ASP 4.8 0.4 + - - -
70A HIS* 4.7 0.8 - - - -
115A VAL* 3.5 30.6 - - + +
116A GLY* 3.7 11.7 - - - -
130A VAL* 3.7 33.2 - - + -
131A ALA* 3.9 21.5 - - + -
133A GLY 3.6 21.3 - - - -
134A CYS* 3.6 25.5 - - + +
142A ALA 4.5 2.7 - - - -
143A MET* 3.7 38.1 - - + -
147A GLN* 5.2 2.5 - - - -
151A LEU* 3.5 14.2 - - + +
240A GLY* 1.3 71.9 - - - -
242A ASP* 1.3 57.9 + - - +
244A VAL* 3.3 1.1 + - - -
245A GLY 2.9 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A MET* 3.7 24.6 - - + +
68A ALA* 3.8 15.9 - - + +
70A HIS* 2.7 43.3 + - - -
115A VAL* 3.8 9.3 - - - +
174A GLU* 4.5 6.7 - - + -
176A GLY* 4.2 1.7 - - - -
179A ASN* 3.1 23.3 + - - -
240A GLY 3.6 1.6 - - - -
241A PHE* 1.3 71.3 - - - +
243A LEU* 1.3 79.2 + - - +
245A GLY* 3.2 1.7 + - - -
246A MET* 3.0 28.9 + - - +
266A LEU* 5.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A HIS* 4.6 0.2 - - + -
179A ASN 4.5 0.2 - - - +
182A PRO* 4.2 23.3 - - + -
183A ALA* 4.5 3.6 - - + +
186A MET* 4.1 14.8 - - - -
235A LEU* 4.0 14.1 - - + -
240A GLY 3.2 18.8 + - - +
242A ASP* 1.3 97.8 + - - +
244A VAL* 1.3 63.8 + - - +
246A MET* 3.2 8.3 + - - +
247A THR* 3.1 25.8 + - - -
266A LEU* 3.6 52.3 - - + +
269A SER* 4.3 10.1 - - - -
270A ALA* 3.9 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A MET* 3.8 24.9 - - + -
148A ALA* 3.7 27.6 - - + +
151A LEU* 3.6 23.6 - - + -
152A LEU* 3.5 14.3 - - + +
235A LEU* 4.1 28.7 - - + +
240A GLY 3.0 16.8 + - - +
241A PHE 3.5 7.2 - - - +
243A LEU* 1.3 76.1 - - - +
245A GLY* 1.3 63.4 + - - +
247A THR* 3.1 6.1 + - - -
248A GLY* 2.9 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A MET* 3.7 26.5 - - - -
151A LEU* 4.1 3.8 - - - +
155A VAL* 3.4 15.0 - - - +
241A PHE 2.9 15.6 + - - -
242A ASP 3.2 3.3 + - - -
244A VAL* 1.3 76.4 - - - +
246A MET* 1.3 61.9 + - - +
248A GLY* 3.0 10.7 + - - -
249A VAL* 3.0 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A MET* 3.9 7.0 - - + -
172A VAL* 4.0 9.5 - - + +
173A GLY* 3.6 43.3 - - - +
174A GLU* 3.6 27.4 - - + -
242A ASP 3.0 16.9 + - - +
243A LEU* 3.6 12.1 - - - +
244A VAL 3.2 0.4 - - - -
245A GLY* 1.3 74.1 - - - +
247A THR* 1.3 64.0 + - - +
249A VAL* 3.1 17.4 + - - +
250A MET* 3.2 20.7 + - + +
263A ASP* 5.3 1.3 - - + -
266A LEU* 4.5 5.8 - - - +
267A SER* 3.7 37.2 - - - +
270A ALA* 3.7 12.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
152A LEU* 3.9 15.3 - - + -
235A LEU* 3.9 22.9 - - + +
243A LEU 3.1 13.6 + - - -
244A VAL 3.4 7.9 - - - -
246A MET* 1.3 77.1 - - - +
248A GLY* 1.3 58.6 + - - +
250A MET* 3.1 9.2 + - - +
251A LEU* 3.0 29.5 + - + +
270A ALA* 3.3 24.2 + - - +
273A ALA* 4.0 0.3 - - - +
274A ALA* 3.8 29.4 - - + +
277A ILE* 4.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU* 3.6 19.2 - - - +
155A VAL* 3.8 12.6 - - - -
156A SER* 3.1 21.1 + - - -
244A VAL 2.9 11.6 + - - -
245A GLY 3.0 5.5 + - - -
247A THR* 1.3 75.4 - - - +
249A VAL* 1.3 59.6 + - - +
251A LEU* 4.4 1.6 - - - -
252A GLY 2.9 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 3.7 33.4 - - + -
66A MET* 4.3 8.5 - - + -
155A VAL* 3.6 13.5 - - + -
159A THR* 3.7 19.5 - - + +
170A PHE* 4.7 8.1 - - + -
171A GLY 5.0 0.4 - - - +
172A VAL* 3.5 24.9 - - + -
245A GLY 3.0 15.7 + - - +
246A MET* 3.1 8.0 + - - +
248A GLY* 1.3 75.9 - - - +
250A MET* 1.3 58.5 + - - +
252A GLY* 3.2 0.5 + - - -
253A ALA* 2.9 29.3 + - - +
260A VAL* 4.3 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A VAL* 3.9 30.3 - - + -
246A MET* 3.2 13.9 + - + +
247A THR* 3.1 7.7 + - - +
249A VAL* 1.3 77.8 - - - +
251A LEU* 1.3 61.4 + - - +
253A ALA* 4.0 1.0 - - - +
254A ALA* 3.1 24.9 + - - +
260A VAL* 4.4 14.1 - - + +
262A LEU* 4.6 7.0 - - + -
267A SER 3.7 22.2 - - - +
270A ALA* 3.9 18.8 - - + +
271A ALA* 3.5 30.5 - - + +
274A ALA* 4.1 13.0 - - + -
281A VAL* 3.9 13.1 - - + +
285A LEU* 4.3 14.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
4A LEU* 5.0 1.6 - - + -
7A LEU* 4.6 11.8 - - + +
8A LEU* 4.0 28.7 - - + -
11A ILE* 4.6 4.7 - - + +
152A LEU* 4.2 30.7 - - + -
156A SER* 3.6 14.4 - - - +
247A THR* 3.0 26.6 + - + +
248A GLY 4.0 0.2 - - - +
250A MET* 1.3 76.3 - - - +
252A GLY* 1.3 58.3 + - - +
254A ALA* 3.5 1.6 + - - +
255A ARG* 3.0 29.8 + - - +
274A ALA* 4.2 17.3 - - + +
277A ILE* 4.6 8.7 - - + -
278A ALA* 4.3 2.0 - - + -
281A VAL* 3.4 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 5.3 0.4 - - - -
156A SER* 3.5 27.7 + - - -
159A THR* 4.1 9.0 - - - -
160A CYS* 3.9 5.0 - - - +
248A GLY 2.9 16.9 + - - -
249A VAL 3.7 0.9 - - - -
251A LEU* 1.3 78.4 - - - +
253A ALA* 1.3 59.8 - - - +
255A ARG* 3.4 6.9 + - - +
256A CYS* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A THR* 3.8 6.5 - - + +
170A PHE* 4.0 21.1 - - + -
249A VAL 2.9 13.6 + - - +
252A GLY* 1.3 75.0 - - - +
254A ALA* 1.3 59.0 + - - +
256A CYS* 3.2 7.4 + - - +
257A GLY 2.9 8.7 + - - -
258A LEU 2.8 32.9 + - - +
260A VAL* 3.2 34.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
11A ILE* 3.8 12.6 - - + +
12A PRO* 3.3 14.0 - - - +
250A MET 3.1 18.4 + - - +
251A LEU 3.8 4.0 - - - +
253A ALA* 1.3 77.4 - - - +
255A ARG* 1.3 58.5 + - - +
257A GLY* 2.9 16.6 + - - -
258A LEU 4.1 0.2 + - - -
281A VAL* 3.9 24.2 - - + -
284A TYR* 3.6 33.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.5 42.9 + - + +
10A ASP* 3.2 46.2 + - - +
11A ILE* 3.9 10.0 - - + +
12A PRO* 3.5 12.0 - - - +
160A CYS* 4.8 9.0 - - + -
251A LEU 3.0 17.7 + - - +
252A GLY* 3.6 6.1 - - - +
254A ALA* 1.3 76.9 - - - +
256A CYS* 1.3 59.8 + - - +
257A GLY 3.4 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PRO* 5.1 0.4 - - - -
51A GLY* 3.8 10.0 - - - -
160A CYS* 2.0 53.6 - - + -
163A ALA* 3.3 24.5 - - - -
170A PHE* 5.6 0.4 - - + -
252A GLY 3.0 13.6 + - - +
253A ALA* 3.4 8.7 - - - +
255A ARG* 1.3 75.7 - - - +
257A GLY* 1.3 61.7 + - - +
258A LEU* 3.4 15.9 + - + +
----------------------------------------------------------
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