Contacts of the helix formed by residues 267 - 281 (chain E) in PDB entry 4OMD
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 ALA 267 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E ASP* 3.1 32.5 + - + +
236E GLU* 4.9 1.0 + - - -
265E GLY 3.7 2.3 + - - +
266E PRO* 1.3 75.6 - - - +
268E ARG* 1.3 69.0 + - + +
269E LEU 3.5 1.1 - - - -
270E ALA* 3.1 2.8 + - - +
271E GLU* 2.9 23.9 + - - +
308E TYR* 4.7 0.8 + - - -
268F ARG* 6.2 0.4 - - - +
530F ASP* 5.3 3.6 - - - +
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Residues in contact with ARG 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267E ALA* 1.3 73.5 - - - +
269E LEU* 1.3 58.3 + - - +
271E GLU* 3.1 16.6 + - - +
272E GLU* 2.8 41.2 + - - +
266F PRO 5.0 5.7 + - - -
267F ALA* 6.2 0.4 - - - +
268F ARG* 3.1 34.6 - - - +
271F GLU* 4.0 29.7 + - - +
490F ARG* 3.3 34.2 - - - +
530F ASP* 3.9 10.0 + - - +
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Residues in contact with LEU 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E ASP* 2.8 27.8 + - + +
234E ALA* 4.1 12.8 - - + +
237E ALA* 3.6 14.3 - - + +
268E ARG* 1.3 74.6 - - - +
270E ALA* 1.3 54.2 + - - +
272E GLU* 3.2 22.6 + - - +
273E ALA* 2.8 28.6 + - - +
449F LYS* 4.1 14.2 + - - +
451F ILE* 3.8 35.9 - - + -
488F GLN* 5.5 0.2 - - - +
490F ARG* 4.1 27.6 - - - +
565F LYS* 6.4 1.1 - - - -
567F THR* 4.1 13.9 - - + +
569F VAL* 4.3 7.9 - - + -
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Residues in contact with ALA 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E ASP* 3.0 18.9 + - - +
236E GLU* 3.7 24.7 - - + +
237E ALA* 3.9 6.2 - - - +
240E LEU* 4.1 8.9 - - + +
266E PRO* 3.5 18.4 - - + -
267E ALA 3.1 4.5 + - - +
269E LEU* 1.3 76.2 - - - +
271E GLU* 1.3 64.4 + - - +
273E ALA* 3.1 9.2 + - - +
274E PHE* 2.9 27.8 + - - -
308E TYR* 5.1 0.2 - - + -
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Residues in contact with GLU 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266E PRO* 3.8 23.0 - - + +
267E ALA 2.9 26.1 + - - +
268E ARG* 3.5 16.4 + - - +
270E ALA* 1.3 75.8 - - - +
272E GLU* 1.3 64.7 + - + +
274E PHE* 3.0 12.5 + - - +
275E PHE* 2.9 25.3 + - - +
313E TYR* 5.1 3.8 - - + -
268F ARG* 4.1 32.9 + - - +
271F GLU* 5.5 2.4 - - - +
272F GLU* 5.5 3.1 - - - +
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Residues in contact with GLU 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E ARG* 2.8 23.5 + - + +
269E LEU* 3.4 20.9 - - - +
271E GLU* 1.3 76.2 - - + +
273E ALA* 1.3 57.2 + - - +
275E PHE* 3.9 6.1 - - - +
276E ARG* 2.9 38.1 + - - +
271F GLU* 5.7 0.9 - - - +
275F PHE* 4.7 8.3 - - + -
313F TYR* 4.5 4.9 + - - +
449F LYS* 2.7 37.4 + - - +
488F GLN* 5.3 3.6 + - - +
490F ARG* 4.5 11.3 + - - -
571F TYR* 4.1 5.1 + - - -
602F FMT 3.8 19.0 - - - +
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Residues in contact with ALA 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237E ALA* 3.8 25.6 - - + +
240E LEU* 4.0 17.5 - - + +
241E GLY* 4.4 8.0 - - - +
269E LEU 2.8 13.2 + - - +
270E ALA 3.3 10.1 - - - +
271E GLU 3.0 0.2 - - - -
272E GLU* 1.3 75.8 - - - +
274E PHE* 1.3 60.3 + - - +
276E ARG* 4.0 8.1 - - - +
277E GLY* 2.9 26.9 + - - -
289E PHE* 4.3 5.9 - - - -
449F LYS* 5.1 0.4 - - - +
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Residues in contact with PHE 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E LEU* 3.6 30.7 - - + -
266E PRO* 4.2 15.9 - - + -
270E ALA 2.9 21.4 + - - -
271E GLU* 3.0 10.3 + - - +
273E ALA* 1.3 76.0 - - - +
275E PHE* 1.3 58.8 + - - +
277E GLY* 3.3 1.6 + - - -
278E VAL* 3.0 34.1 + - - +
289E PHE* 3.7 33.7 - + - -
291E TRP* 3.7 21.3 - + - -
308E TYR* 4.1 18.8 - + - -
311E SER* 5.0 4.7 - - - -
313E TYR* 3.6 25.4 - + + -
314E THR* 3.7 25.8 - - + -
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Residues in contact with PHE 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271E GLU 2.9 15.9 + - - +
272E GLU* 3.9 4.3 - - - +
274E PHE* 1.3 75.1 - - - +
276E ARG* 1.3 62.0 + - - +
278E VAL* 3.4 7.2 - - + +
279E SER* 2.7 45.1 + - - -
313E TYR* 3.1 31.4 - + + -
601E FMT 3.8 21.5 - - - -
602E FMT 3.6 12.6 - - - -
272F GLU* 4.6 10.1 - - + -
275F PHE* 3.1 53.8 - + + -
276F ARG* 3.8 20.6 - - + -
280F GLN* 4.4 8.1 - - - -
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Residues in contact with ARG 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244E PRO* 6.3 1.6 - - + -
272E GLU 2.9 27.0 + - - +
273E ALA* 4.0 5.8 - - - +
275E PHE* 1.3 75.8 - - - +
277E GLY* 1.3 55.5 + - - +
280E GLN* 2.7 59.9 + - + +
281E GLY 3.5 1.2 + - - -
275F PHE* 3.8 17.3 - - + -
447F GLN* 2.9 50.1 + - - -
449F LYS* 3.7 37.6 - - - +
571F TYR* 4.3 0.6 - - - -
601F FMT 3.7 9.9 + - - -
602F FMT 3.1 25.2 + - - +
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Residues in contact with GLY 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E LEU 5.9 0.7 - - - -
244E PRO* 5.4 6.1 - - - -
273E ALA 2.9 19.0 + - - -
274E PHE 3.6 1.8 - - - -
276E ARG* 1.3 78.3 - - - +
278E VAL* 1.3 58.1 + - - +
281E GLY* 2.9 20.5 + - - -
286E GLY* 3.4 0.2 - - - -
287E SER* 2.8 37.8 + - - -
289E PHE* 4.3 4.3 - - - -
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Residues in contact with VAL 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274E PHE 3.0 13.2 + - - +
275E PHE* 3.4 13.9 - - - +
277E GLY* 1.3 76.0 - - - +
279E SER* 1.3 66.2 + - - +
284E GLY 4.3 2.6 - - - +
286E GLY* 3.3 22.1 + - - -
287E SER 4.0 12.8 - - - +
289E PHE* 4.2 5.6 - - + -
313E TYR* 3.8 42.4 - - + +
390E TRP* 3.4 41.2 + - + +
601E FMT 4.5 8.5 - - - -
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Residues in contact with SER 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E PHE* 2.7 44.2 + - - -
276E ARG* 3.7 2.2 - - - -
278E VAL* 1.3 81.4 - - - +
280E GLN* 1.3 78.0 + - - +
284E GLY* 3.5 22.7 - - - +
601E FMT 5.1 0.7 + - - -
279F SER* 4.5 10.1 - - - -
280F GLN* 4.3 8.2 + - - +
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Residues in contact with GLN 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244E PRO* 5.3 2.2 - - + -
245E ASN* 3.7 8.9 + - - +
276E ARG* 2.7 45.9 + - + +
279E SER* 1.3 93.1 - - - +
281E GLY* 1.3 68.0 + - - +
283E GLY* 3.5 4.7 + - - -
284E GLY* 3.1 13.3 + - - +
275F PHE* 4.5 3.0 - - - -
279F SER* 4.1 12.9 + - - +
447F GLN* 4.8 3.1 - - - +
601F FMT 3.9 19.0 + - - +
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Residues in contact with GLY 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244E PRO* 3.6 17.6 - - - +
276E ARG 3.5 2.8 + - - -
277E GLY* 2.9 24.5 + - - -
280E GLN* 1.3 75.8 - - - +
282E ARG* 1.3 69.7 + - - -
284E GLY 2.9 3.8 + - - -
286E GLY* 2.9 21.3 + - - -
287E SER* 3.6 12.1 - - - -
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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