Contacts of the helix formed by residues 246 - 259 (chain A) in PDB entry 1EFA
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 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A TRP* 2.9 42.5 + - + +
244A VAL* 3.1 4.3 + - - +
245A ALA* 1.3 79.1 - - - +
247A ASP* 1.3 65.1 + - - +
248A GLN* 3.8 13.9 + - - +
249A MET* 2.8 27.9 + - - +
250A ALA* 3.0 17.3 + - - +
272A GLY* 4.4 0.2 - - - -
273A TYR 3.0 16.8 - - - +
274A ASP* 3.8 0.4 - - - +
901A NPF 3.1 30.8 + - - +
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Residues in contact with ASP 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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246A ASN* 1.3 71.5 - - - +
248A GLN* 1.3 64.8 + - + +
250A ALA* 3.1 3.5 + - - +
251A LEU 2.9 19.2 + - - -
273A TYR 2.9 18.7 + - - +
274A ASP* 3.5 1.2 + - - +
275A ASP* 2.7 8.7 + - - -
276A THR* 2.6 51.2 + - + +
279A SER* 3.4 11.9 - - - -
282A TYR* 3.5 13.7 - - - +
286A LEU* 3.4 15.7 - - + +
288A THR* 2.6 29.0 + - - -
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Residues in contact with GLN 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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74A HIS* 3.8 29.0 + - - +
220A TRP 3.4 17.7 + - - +
221A SER* 5.4 3.4 - - - +
222A ALA* 3.1 26.3 - - - +
246A ASN* 3.3 12.4 + - - +
247A ASP* 1.3 79.0 - - + +
249A MET* 1.3 61.5 + - - +
251A LEU* 3.2 11.9 + - - +
252A GLY 3.3 0.3 + - - -
274A ASP* 4.9 3.2 + - - +
276A THR* 5.1 6.3 - - + +
282A TYR* 4.1 8.1 - - - +
901A NPF 4.7 5.9 + - - -
277B GLU* 5.8 2.2 - - - +
278B ASP* 3.2 38.9 + - - +
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Residues in contact with MET 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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185A LEU* 4.3 8.5 - - + +
186A ALA 3.8 11.0 - - - +
187A GLY* 3.8 5.8 - - - -
218A GLY* 3.7 16.8 - - - -
220A TRP* 3.5 28.9 - - + -
221A SER 3.3 21.5 - - - +
222A ALA* 4.2 0.2 - - - +
224A SER* 3.6 9.9 - - - +
225A GLY* 3.6 14.0 - - - +
244A VAL* 3.5 10.8 - - + -
245A ALA* 3.3 37.0 - - + +
246A ASN* 2.8 29.7 + - - +
248A GLN* 1.3 68.6 - - - +
250A ALA* 1.3 68.4 + - - +
252A GLY* 3.0 3.5 + - - -
253A ALA* 2.8 20.8 + - - +
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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
----------------------------------------------------------
244A VAL* 3.5 18.5 - - + +
246A ASN 3.0 12.8 + - - +
247A ASP* 3.1 9.8 + - - +
249A MET* 1.3 77.1 - - - +
251A LEU* 1.3 51.7 + - - +
253A ALA* 2.9 3.9 + - - +
254A MET* 2.7 40.7 + - - +
270A VAL* 4.1 17.7 - - + -
272A GLY* 4.2 3.1 - - - -
286A LEU* 3.6 24.5 - - + -
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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
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222A ALA* 4.1 9.0 - - + -
247A ASP 2.9 12.5 + - - +
248A GLN 3.2 9.0 - - - +
249A MET 3.1 0.2 - - - -
250A ALA* 1.3 75.6 - - - +
252A GLY* 1.3 61.5 + - - +
254A MET* 3.3 10.6 + - + +
255A ARG* 3.0 21.7 + - - +
282A TYR* 3.7 48.2 - - + +
283A ILE 5.7 0.7 - - - +
251B LEU* 5.3 1.3 - - + -
278B ASP* 3.9 33.0 - - + +
281B CYS 3.5 20.4 - - - +
282B TYR* 3.9 19.3 - - + -
283B ILE* 4.8 7.5 - - + +
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Residues in contact with GLY 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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222A ALA* 3.2 25.7 - - - +
226A PHE* 3.1 24.9 - - - +
248A GLN 3.3 4.9 + - - -
249A MET 3.0 5.7 + - - -
251A LEU* 1.3 76.5 - - - +
253A ALA* 1.3 65.3 + - - +
255A ARG* 3.3 1.9 + - - +
256A ALA 3.1 17.2 + - - -
281B CYS* 4.3 8.7 - - - -
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Residues in contact with ALA 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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185A LEU* 4.4 4.0 - - + -
225A GLY 3.8 1.7 + - - +
229A THR* 3.4 27.1 - - - +
242A MET* 4.2 17.7 - - + -
244A VAL* 4.7 5.4 - - + -
249A MET 2.8 13.1 + - - +
250A ALA* 3.3 12.3 - - - +
252A GLY* 1.3 75.0 - - - +
254A MET* 1.3 61.2 + - - +
256A ALA* 3.0 4.2 + - - +
257A ILE* 2.8 35.1 + - + +
270A VAL* 5.0 4.3 - - + -
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Residues in contact with MET 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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250A ALA 2.7 24.7 + - - +
251A LEU* 3.5 8.3 - - + +
253A ALA* 1.3 73.8 - - - +
255A ARG* 1.3 60.0 + - - +
257A ILE* 3.7 2.5 - - - +
258A THR* 2.9 31.3 + - - +
264A VAL* 3.7 22.2 - - + +
270A VAL* 4.4 11.2 - - + -
282A TYR* 4.1 27.1 - - + -
283A ILE 3.5 20.6 - - - +
284A PRO* 3.2 32.5 - - + +
286A LEU* 4.3 8.5 - - - -
328A THR* 3.5 18.8 - - + -
283B ILE* 4.0 7.9 - - + -
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Residues in contact with ARG 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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223A MET* 4.6 6.7 - - - +
226A PHE* 3.3 39.7 - - + -
251A LEU 3.0 12.8 + - - +
252A GLY* 3.5 10.3 - - - +
253A ALA 3.1 0.2 - - - -
254A MET* 1.3 76.1 - - - +
256A ALA* 1.3 53.5 + - - +
258A THR* 3.7 0.7 - - - -
259A GLU* 2.7 102.6 + - + +
280B SER 3.2 26.7 + - - -
281B CYS* 3.6 19.6 - - + +
282B TYR 3.8 8.1 - - - +
283B ILE* 3.2 25.3 - - + +
285B PRO* 3.9 11.0 - - - +
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Residues in contact with ALA 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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226A PHE* 3.5 34.4 - - + +
229A THR* 3.8 16.4 - - + +
230A MET* 3.7 18.9 - - + +
233A LEU* 4.3 2.0 - - + -
252A GLY 3.1 5.6 + - - +
253A ALA 3.0 8.3 + - - +
255A ARG* 1.3 77.5 - - - +
257A ILE* 1.3 66.2 + - - +
259A GLU* 3.4 2.2 + - - +
260A SER* 2.8 27.5 + - - -
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Residues in contact with ILE 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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229A THR* 4.3 10.8 - - + -
233A LEU* 4.3 8.0 - - + +
242A MET* 4.4 6.7 - - - -
253A ALA 2.8 26.3 + - - +
254A MET 3.7 4.5 - - - +
256A ALA* 1.3 72.7 - - - +
258A THR* 1.3 63.5 + - - +
260A SER* 3.0 18.6 + - - -
262A LEU* 3.3 36.8 + - + +
263A ARG 4.4 0.2 - - - -
264A VAL* 3.8 19.1 - - + +
268A ILE* 3.6 45.5 - - + +
270A VAL* 3.6 23.8 - - + -
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Residues in contact with THR 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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254A MET 2.9 18.5 + - - -
255A ARG 3.7 2.9 - - - -
257A ILE* 1.3 72.8 - - - +
259A GLU* 1.3 59.9 + - + +
260A SER 2.9 9.5 + - - -
261A GLY* 3.1 14.6 + - - -
262A LEU 3.5 12.4 + - - +
264A VAL* 3.7 14.4 + - - +
283A ILE 5.0 2.9 + - - -
283B ILE* 3.9 30.8 - - + +
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Residues in contact with GLU 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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226A PHE* 3.7 9.0 - - + -
230A MET* 5.7 5.0 - - + +
255A ARG* 2.7 70.7 + - + +
256A ALA* 3.4 5.6 + - - +
257A ILE 3.4 0.2 - - - -
258A THR* 1.3 74.7 - - + +
260A SER* 1.3 57.5 + - - +
261A GLY 3.4 0.4 - - - -
283B ILE* 6.0 2.5 - - + -
284B PRO* 5.4 0.5 - - - +
285B PRO* 3.8 14.6 - - - +
327B LYS* 5.9 0.3 - - - +
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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
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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