Contacts of the helix formed by residues 268 - 282 (chain B) in PDB entry 1EKF
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 268 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ARG* 3.6 0.9 - - - -
242B ASN* 3.2 23.1 - - - +
266B LEU* 2.7 12.2 + - - -
267B PRO* 1.3 73.4 - - - +
269B VAL* 1.3 60.7 + - - -
270B VAL 3.3 1.6 - - - -
271B ARG* 3.4 6.9 + - - +
272B GLN* 3.0 27.7 + - - +
370B PLP 3.4 17.7 - - - -
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Residues in contact with VAL 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B PHE* 4.1 15.7 - - + -
92B ARG* 4.0 28.7 + - + +
95B LEU* 3.9 25.8 - - + -
96B ASN* 3.7 31.2 - - - +
99B ARG* 4.0 8.5 - - - +
267B PRO 3.6 1.1 + - - +
268B GLY* 1.3 70.0 - - - -
270B VAL* 1.3 65.6 + - + +
272B GLN* 3.4 5.9 + - - +
273B SER* 2.7 27.5 + - - -
313B THR* 5.3 2.9 - - - +
370B PLP 2.8 19.9 + - - +
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B PHE* 4.9 10.3 - - + -
269B VAL* 1.3 77.3 - - + +
271B ARG* 1.3 53.9 + - - +
273B SER* 3.0 7.9 + - - -
274B LEU* 2.8 44.7 + - + +
311B SER* 3.8 8.1 - - - -
312B GLY 3.5 31.9 - - - +
313B THR* 3.7 9.6 - - - +
316B GLN* 3.4 40.6 - - - +
349B LEU* 4.6 10.1 - - + -
370B PLP 3.0 11.3 + - - +
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Residues in contact with ARG 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ASN* 3.4 39.5 - - - +
244B PHE* 3.6 23.1 - - + -
258B THR* 4.0 7.4 + - - +
259B PRO* 3.0 26.9 + - - +
261B LEU* 3.5 37.7 - - - +
265B ILE* 4.4 3.0 - - - +
266B LEU 4.4 2.5 - - - -
267B PRO* 5.2 1.4 - - - +
268B GLY 3.4 13.9 + - - +
270B VAL* 1.3 78.7 - - - +
272B GLN* 1.3 74.7 + - - +
274B LEU 3.2 0.7 + - - -
275B LEU* 3.1 40.7 + - + +
288B GLU* 2.7 31.5 + - - +
311B SER* 3.6 13.8 + - - +
370B PLP 4.3 0.6 + - - -
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Residues in contact with GLN 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ARG* 4.5 6.7 - - - +
95B LEU* 4.9 11.4 - - + -
261B LEU* 5.0 6.9 - - - +
268B GLY 3.0 17.9 + - - +
269B VAL* 3.9 6.3 - - - +
271B ARG* 1.3 93.2 - - - +
273B SER* 1.3 56.1 + - - +
275B LEU* 3.3 14.4 + - - +
276B ASP* 2.9 62.6 + - - +
279B GLN* 5.4 1.9 + - - -
288B GLU* 5.6 1.9 + - - +
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Residues in contact with SER 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B PHE* 3.4 12.7 - - - -
92B ARG* 3.0 33.7 + - - +
269B VAL 2.7 17.7 + - - -
270B VAL* 3.0 11.1 + - - -
272B GLN* 1.3 77.4 - - - +
274B LEU* 1.3 59.3 + - - +
276B ASP* 4.2 0.2 - - - -
277B MET* 2.9 32.4 + - - +
349B LEU* 5.0 5.8 - - - -
361B TRP* 3.5 21.2 - - - -
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Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B PHE* 3.9 14.1 - - + -
256B LEU* 5.3 0.4 - - - -
270B VAL* 2.8 22.4 + - + +
271B ARG 3.6 6.5 - - - +
273B SER* 1.3 71.7 - - - +
275B LEU* 1.3 60.2 - - - +
277B MET* 3.4 3.3 + - - +
278B ALA* 2.9 32.7 + - - +
309B PHE* 3.9 28.7 - - + -
311B SER* 3.9 24.0 - - - -
316B GLN 4.7 3.4 - - - +
317B VAL* 4.7 3.6 - - + -
345B PHE* 3.6 45.1 - - + -
349B LEU* 4.2 22.4 - - + -
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Residues in contact with LEU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B PHE* 3.9 13.9 - - + -
256B LEU* 5.2 3.4 - - + +
258B THR* 3.8 19.5 - - + -
271B ARG* 3.1 47.2 + - + +
272B GLN* 3.7 17.7 - - - +
274B LEU* 1.3 74.9 - - - +
276B ASP* 1.3 58.6 + - - +
278B ALA* 3.4 1.3 + - - +
279B GLN* 2.9 46.0 + - - +
286B VAL* 3.7 24.7 - - + -
287B VAL 4.8 3.1 - - - +
288B GLU* 3.8 28.9 - - + +
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Residues in contact with ASP 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ARG* 3.1 32.4 + - - -
272B GLN* 2.9 44.9 + - - +
273B SER 3.6 4.5 - - - +
275B LEU* 1.3 74.4 - - - +
277B MET* 1.3 57.3 + - - +
279B GLN* 3.3 13.9 + - - +
280B THR* 2.9 33.5 + - - +
361B TRP* 3.9 13.9 - - + -
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Residues in contact with MET 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B SER 2.9 18.9 + - - +
274B LEU* 3.6 5.2 - - + +
276B ASP* 1.3 76.4 - - - +
278B ALA* 1.3 63.3 + - - +
280B THR* 3.1 16.6 + - - -
281B TRP* 3.2 22.4 + - + +
345B PHE* 3.9 25.4 - - + +
348B GLU* 3.5 43.7 - - + +
349B LEU* 3.6 21.5 - - + -
352B ILE* 3.9 15.7 - - + -
361B TRP* 3.5 32.9 - - + -
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Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B LEU* 3.9 19.1 - - + -
274B LEU 2.9 21.2 + - - +
275B LEU 4.0 1.8 - - - +
277B MET* 1.3 73.1 - - - +
279B GLN* 1.3 61.0 + - - +
280B THR 3.5 0.2 + - - -
281B TRP* 3.5 23.5 + - + +
282B GLY* 3.6 7.8 + - - -
283B GLU 4.7 1.7 + - - -
284B PHE* 4.1 14.3 - - + +
286B VAL* 3.7 25.0 - - + +
345B PHE* 4.0 7.7 - - + -
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Residues in contact with GLN 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B GLN* 5.4 1.4 + - - -
275B LEU* 2.9 40.3 + - - +
276B ASP* 3.7 12.2 + - - +
277B MET 3.2 0.2 - - - -
278B ALA* 1.3 74.4 - - - +
280B THR* 1.3 67.2 + - - +
282B GLY* 3.4 12.6 + - - -
286B VAL* 3.7 30.8 - - + +
288B GLU* 5.8 2.0 + - - -
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Residues in contact with THR 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ASP* 2.9 18.8 + - - +
277B MET* 3.1 12.0 + - - -
279B GLN* 1.3 79.5 - - - +
281B TRP* 1.3 71.4 + - + +
282B GLY* 3.2 1.0 + - - -
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Residues in contact with TRP 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B MET* 3.2 16.1 + - + +
278B ALA* 3.8 13.5 - - - +
279B GLN 3.3 0.4 - - - -
280B THR* 1.3 84.9 - - + +
282B GLY* 1.3 63.3 + - - +
283B GLU* 3.2 24.4 + - - +
284B PHE* 4.1 18.8 - + + -
341B LEU* 3.5 23.6 - - + -
344B ARG* 3.4 59.7 - - + +
345B PHE* 3.4 33.2 - + - -
348B GLU* 2.5 31.4 + - + -
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Residues in contact with GLY 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ALA 3.6 5.1 + - - -
279B GLN* 3.4 12.7 + - - -
280B THR 3.2 3.9 - - - -
281B TRP* 1.3 78.6 - - - +
283B GLU* 1.3 60.2 + - - +
284B PHE 3.6 5.2 - - - -
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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