Contacts of the helix formed by residues 240 - 259 (chain A) in PDB entry 1EQR
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 THR 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A MET* 1.3 74.6 - - - +
241A ALA* 1.3 59.4 + - - +
242A PRO* 3.1 17.6 - - - +
243A GLN* 2.6 42.3 + - - +
244A VAL* 2.9 31.7 + - - +
488A VAL* 4.8 3.1 - - - -
1B MET* 5.5 8.5 - - + -
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Residues in contact with ALA 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A THR* 1.3 70.7 - - - +
242A PRO* 1.3 68.5 - - + +
244A VAL* 3.0 9.8 + - - +
245A ARG* 2.8 47.7 + - - +
472A ASN* 3.6 23.8 - - - +
474A TYR* 3.9 15.7 - - + -
488A VAL* 3.6 18.9 - - + +
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Residues in contact with PRO 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A THR* 3.1 17.3 - - - +
241A ALA* 1.3 95.1 - - + +
243A GLN* 1.3 58.0 + - + +
245A ARG* 3.5 28.7 + - - +
246A GLU* 3.0 26.7 + - - +
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Residues in contact with GLN 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A PHE 4.2 3.4 + - - -
239A MET* 3.1 26.6 - - + +
240A THR* 2.6 54.2 + - - +
241A ALA 3.1 0.6 - - - -
242A PRO* 1.3 77.0 - - + +
244A VAL* 1.3 64.4 + - - +
246A GLU* 3.3 22.4 + - - +
247A VAL* 3.2 18.6 - - - +
1B MET* 3.3 34.5 - - - +
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Residues in contact with VAL 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A VAL* 6.2 0.9 - - + -
236A THR* 3.5 32.3 - - + +
239A MET* 4.1 9.0 - - + -
240A THR 2.9 25.7 + - - +
241A ALA* 3.0 9.1 + - - +
243A GLN* 1.3 75.6 - - - +
245A ARG* 1.3 64.5 + - - +
247A VAL* 3.5 7.2 - - + +
248A MET* 3.1 40.2 + - + +
474A TYR* 3.8 22.9 - - + +
529A ALA* 3.6 17.5 - - + -
530A GLY* 4.2 14.1 - - - +
531A LEU* 4.8 0.7 - - + -
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Residues in contact with ARG 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ALA* 2.8 31.4 + - - +
242A PRO* 3.8 34.8 - - - +
244A VAL* 1.3 75.3 - - - +
246A GLU* 1.3 58.1 + - - +
249A GLU* 2.6 38.6 + - - +
269A VAL* 4.8 10.1 - - - +
429A TRP* 3.4 59.9 - - + +
431A ILE* 3.9 31.4 - - - +
455A LYS* 5.5 4.6 - - - +
472A ASN* 5.3 1.6 + - - -
474A TYR* 3.9 25.4 - - + +
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Residues in contact with GLU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A PRO 3.0 15.2 + - - +
243A GLN* 3.3 17.5 - - - +
244A VAL 3.2 0.4 - - - -
245A ARG* 1.3 80.7 - - - +
247A VAL* 1.3 65.0 + - - +
249A GLU* 3.0 7.0 + - - +
250A ALA* 3.0 18.2 + - - +
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Residues in contact with VAL 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A PHE* 3.8 17.9 - - + -
155A HIS* 4.4 13.7 - - + +
157A PHE* 4.2 18.2 - - + -
208A ARG* 5.8 4.3 - - - +
236A THR* 5.9 1.6 - - + -
239A MET* 5.0 11.4 - - - -
243A GLN 3.2 17.5 - - - +
244A VAL* 3.5 9.4 - - + +
246A GLU* 1.3 77.4 - - + +
248A MET* 1.3 78.5 + - + +
250A ALA* 3.0 22.6 + - - +
251A LEU 3.0 10.6 + - - -
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Residues in contact with MET 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A MET* 4.1 21.8 - - + -
157A PHE* 4.7 8.7 - - + -
234A VAL* 4.0 25.8 - - + -
236A THR* 6.5 0.2 - - + -
244A VAL* 3.1 36.5 + - + +
245A ARG 3.8 2.9 - - - +
247A VAL* 1.3 101.4 - - + +
249A GLU* 1.3 60.9 + - - +
250A ALA 3.4 0.5 + - - -
251A LEU* 3.5 8.1 + - + +
252A VAL 3.5 14.4 + - - -
429A TRP* 4.2 15.5 - - + -
476A MET* 3.6 11.8 - - - +
531A LEU* 4.2 13.7 - - + -
533A PHE* 3.8 28.7 - - + -
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Residues in contact with GLU 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ARG 2.6 22.6 + - - +
246A GLU* 3.4 6.5 - - - +
248A MET* 1.3 73.7 - - - +
250A ALA* 1.3 57.9 + - - +
252A VAL 3.8 0.8 + - - -
253A ARG* 2.9 40.9 + - - +
265A GLY 3.9 1.0 - - - +
266A ASP* 3.4 19.1 - - - +
267A PHE* 2.7 57.8 + - + +
429A TRP* 2.7 33.3 + - - +
476A MET* 4.0 9.4 - - - -
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Residues in contact with ALA 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A PHE* 3.9 16.6 - - + -
155A HIS* 5.4 2.2 - - - +
246A GLU 3.0 9.6 + - - +
247A VAL* 3.0 17.9 + - - +
249A GLU* 1.3 77.4 - - - +
251A LEU* 1.3 63.6 + - - +
252A VAL 3.2 0.2 - - - -
253A ARG* 3.4 8.4 + - - +
254A HIS* 3.0 25.8 + - - +
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Residues in contact with LEU 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LEU 4.8 0.9 - - - +
148A VAL* 3.8 37.2 - - + -
151A PHE* 3.6 33.6 - - + -
152A MET* 3.3 26.2 - - + -
232A ILE* 4.8 7.4 - - + -
247A VAL 3.0 7.4 + - - +
248A MET* 3.8 9.9 - - + +
249A GLU 3.5 0.2 - - - -
250A ALA* 1.3 76.5 - - - +
252A VAL* 1.3 61.8 + - + +
254A HIS* 3.4 2.9 - - + +
255A LEU* 3.1 29.6 + - + +
533A PHE* 3.7 31.6 - - + -
538A LEU* 6.2 0.2 - - + -
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Residues in contact with VAL 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A MET 3.5 2.1 + - - +
249A GLU 3.8 3.1 + - - +
250A ALA 3.2 0.6 - - - -
251A LEU* 1.3 76.3 - - + +
253A ARG* 1.3 67.5 + - - +
255A LEU* 3.0 24.7 + - + +
256A TRP* 3.0 36.4 + - + -
264A LEU* 4.2 2.7 - - + -
267A PHE* 3.9 14.4 - - + -
476A MET* 3.5 35.2 - - + -
478A ILE* 3.9 16.2 - - + -
533A PHE* 3.8 19.1 - - + -
538A LEU* 5.0 5.8 - - + -
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Residues in contact with ARG 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A GLU* 2.9 31.9 + - - +
250A ALA* 3.9 7.4 - - - +
252A VAL* 1.3 75.5 - - - +
254A HIS* 1.3 63.9 + - - +
256A TRP* 3.1 3.1 + - - +
257A LEU* 2.9 26.7 + - - +
262A VAL 4.4 1.4 - - - +
263A ASP* 4.0 19.3 + - - +
264A LEU* 4.2 15.5 - - + +
265A GLY* 3.1 46.2 + - - +
266A ASP* 3.5 24.5 + - - +
267A PHE* 3.7 17.9 - - + -
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Residues in contact with HIS 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU* 3.9 37.4 + - + +
150A ARG* 5.4 3.5 + - - +
151A PHE* 4.0 23.7 - + + +
250A ALA 3.0 19.1 + - - +
251A LEU* 3.4 9.0 - - + +
252A VAL 3.2 0.2 - - - -
253A ARG* 1.3 77.5 - - - +
255A LEU* 1.3 56.9 - - - +
257A LEU* 3.3 5.6 + - - +
258A GLU* 2.8 67.7 + - + +
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Residues in contact with LEU 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ILE* 3.9 31.4 - - + -
147A LEU* 4.0 27.8 - - + -
148A VAL* 4.0 19.3 - - + -
251A LEU* 3.1 31.4 + - + +
252A VAL* 3.0 16.7 + - + +
254A HIS* 1.3 78.0 - - + +
256A TRP* 1.3 66.1 + - + +
258A GLU* 4.8 2.5 - - - -
259A VAL* 2.8 37.5 + - + +
538A LEU* 4.4 24.9 - - + -
542A LEU* 4.2 9.0 - - + -
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Residues in contact with TRP 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A VAL* 3.0 40.6 + - + +
253A ARG 3.8 5.8 - - - +
255A LEU* 1.3 80.7 - - + +
257A LEU* 1.3 53.3 + - - +
260A LYS* 3.5 5.6 + - + -
261A GLY 2.8 10.2 + - - -
262A VAL* 2.6 61.9 + - + +
264A LEU* 3.8 23.8 - - + +
425A TRP* 3.3 46.5 - + - -
478A ILE* 3.8 18.2 - - + -
538A LEU* 4.0 19.3 - - + -
541A LEU* 3.9 26.5 - - + -
542A LEU* 3.5 36.9 - - + +
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Residues in contact with LEU 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A ARG 2.9 16.2 + - - +
254A HIS* 3.8 7.4 - - - +
256A TRP* 1.3 77.2 - - - +
258A GLU* 1.3 74.7 + - - +
261A GLY* 3.1 28.4 - - - +
262A VAL 3.4 16.1 + - - +
263A ASP* 4.8 17.5 - - + +
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Residues in contact with GLU 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LYS* 3.5 18.0 + - - -
147A LEU* 3.4 29.5 - - + +
254A HIS* 2.8 50.3 + - + +
257A LEU* 1.3 88.6 - - - +
259A VAL* 1.3 59.5 + - - +
261A GLY* 4.8 0.3 + - - -
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Residues in contact with VAL 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A THR* 4.1 13.9 - - + -
143A LYS* 4.5 14.9 + - + +
144A ILE* 3.9 24.0 - - + -
147A LEU* 3.9 17.0 - - + -
255A LEU* 2.8 24.4 + - + +
258A GLU* 1.3 75.8 - - - +
260A LYS* 1.3 63.8 + - + +
261A GLY 3.2 3.6 - - - -
542A LEU* 3.9 39.7 - - + +
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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
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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) + - + + + + + -
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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