Contacts of the helix formed by residues 267 - 281 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268E ARG* 6.2 0.2 - - - +
530E ASP* 5.5 2.7 - - - +
233F ASP* 3.2 33.6 + - + +
236F GLU* 5.0 0.8 + - - -
265F GLY 3.7 2.0 + - - +
266F PRO* 1.3 73.6 - - - +
268F ARG* 1.3 68.2 + - - +
269F LEU 3.5 0.9 - - - -
270F ALA* 3.2 2.5 + - - +
271F GLU* 2.9 25.5 + - - +
308F TYR* 4.7 0.8 + - - -
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Residues in contact with ARG 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266E PRO 5.0 6.3 + - - -
267E ALA* 6.2 0.4 - - - +
268E ARG* 3.1 35.8 - - - +
271E GLU* 4.1 29.3 + - - +
490E ARG* 3.3 34.0 - - - +
530E ASP* 3.8 12.1 + - - +
233F ASP* 4.4 0.4 - - - +
267F ALA* 1.3 75.4 - - - +
269F LEU* 1.3 57.6 + - - +
271F GLU* 3.2 15.9 + - - +
272F GLU* 2.9 41.4 + - + +
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Residues in contact with LEU 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449E LYS* 4.0 7.2 + - - +
451E ILE* 4.0 30.5 - - + -
488E GLN* 5.5 0.7 - - - +
490E ARG* 4.1 26.9 - - - +
530E ASP* 6.0 0.2 - - - +
565E LYS* 6.1 2.0 - - - -
567E THR* 4.1 15.0 - - + +
569E VAL* 4.1 10.3 - - + -
233F ASP* 3.0 24.8 + - + +
234F ALA* 4.0 22.9 - - + +
237F ALA* 3.6 16.2 - - + +
268F ARG* 1.3 73.9 - - - +
270F ALA* 1.3 56.6 + - - +
272F GLU* 3.2 21.4 + - - +
273F ALA* 2.8 28.1 + - - +
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Residues in contact with ALA 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233F ASP* 3.0 18.8 + - - +
236F GLU* 3.9 24.5 - - + +
237F ALA* 3.9 6.5 - - - +
240F LEU* 4.2 8.7 - - + +
266F PRO* 3.5 23.6 - - + -
267F ALA 3.2 2.0 + - - +
269F LEU* 1.3 75.0 - - - +
271F GLU* 1.3 63.1 + - - +
273F ALA* 3.1 9.6 + - - +
274F PHE* 2.9 27.1 + - - -
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Residues in contact with GLU 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E ARG* 4.0 33.5 + - - +
271E GLU* 5.5 2.3 - - - +
272E GLU* 5.7 0.7 - - - +
266F PRO* 3.7 23.6 - - + +
267F ALA 2.9 27.4 + - - +
268F ARG* 3.5 16.3 + - - +
270F ALA* 1.3 75.7 - - - +
272F GLU* 1.3 65.7 + - + +
274F PHE* 3.0 12.6 + - - +
275F PHE* 2.9 24.6 + - - +
313F TYR* 5.0 4.0 - - + -
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Residues in contact with GLU 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271E GLU* 5.5 2.9 - - - +
275E PHE* 4.8 8.5 - - + -
313E TYR* 4.6 4.5 + - - +
449E LYS* 2.7 35.6 + - - +
488E GLN* 5.3 2.8 + - - +
490E ARG* 4.4 12.2 + - - -
571E TYR* 4.1 4.4 + - - -
602E FMT 3.8 19.2 - - - +
268F ARG* 2.9 25.1 + - + +
269F LEU* 3.2 20.5 + - - +
271F GLU* 1.3 76.8 - - + +
273F ALA* 1.3 57.7 + - - +
275F PHE* 3.8 6.6 - - - +
276F ARG* 2.9 37.1 + - - +
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Residues in contact with ALA 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449E LYS* 5.3 0.4 - - - +
237F ALA* 3.8 26.5 - - + +
240F LEU* 4.0 16.7 - - + +
241F GLY* 4.4 8.2 - - - +
269F LEU 2.8 13.2 + - - +
270F ALA 3.3 10.3 - - - +
271F GLU 3.1 0.2 - - - -
272F GLU* 1.3 74.3 - - - +
274F PHE* 1.3 59.9 + - - +
276F ARG* 3.9 8.8 - - - +
277F GLY* 2.9 26.7 + - - -
289F PHE* 4.3 5.5 - - - -
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Residues in contact with PHE 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240F LEU* 3.8 19.7 - - + +
266F PRO* 4.1 15.9 - - + -
270F ALA 2.9 22.3 + - - -
271F GLU* 3.0 10.3 + - - +
273F ALA* 1.3 75.5 - - - +
275F PHE* 1.3 63.5 + - - +
277F GLY* 3.3 1.7 + - - -
278F VAL* 3.1 29.6 + - - +
289F PHE* 3.5 34.6 - + - -
291F TRP* 3.6 28.5 - + - -
308F TYR* 4.0 19.7 - + + -
311F SER* 5.1 4.9 - - - -
313F TYR* 3.5 25.8 - + + -
314F THR* 3.4 28.3 - - + -
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Residues in contact with PHE 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272E GLU* 4.5 9.9 - - + -
275E PHE* 3.1 53.2 - + + -
276E ARG* 3.8 26.2 - - + -
279E SER* 4.4 2.5 - - - -
280E GLN* 4.5 5.2 - - - -
271F GLU 2.9 15.9 + - - +
272F GLU* 3.8 5.4 - - - +
274F PHE* 1.3 76.0 - - - +
276F ARG* 1.3 65.2 + - - +
278F VAL* 3.4 6.6 - - + +
279F SER* 2.9 44.3 + - - -
313F TYR* 3.2 31.0 - + + +
601F FMT 4.2 10.8 - - - -
602F FMT 3.5 16.2 - - - -
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Residues in contact with ARG 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E PHE* 3.8 10.3 - - + -
447E GLN* 2.9 47.7 + - - -
448E ARG* 4.6 0.2 - - - +
449E LYS* 3.8 36.3 - - - +
571E TYR* 4.2 0.8 - - - -
601E FMT 3.6 10.3 + - - -
602E FMT 2.9 30.3 + - - +
244F PRO* 5.9 2.0 - - + +
272F GLU 2.9 31.1 + - - +
273F ALA* 4.0 6.7 - - - +
275F PHE* 1.3 72.7 - - - +
277F GLY* 1.3 55.6 + - - +
280F GLN* 2.7 64.7 + - + +
281F GLY 3.5 0.7 + - - -
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Residues in contact with GLY 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240F LEU 5.9 0.9 - - - -
244F PRO* 5.5 5.8 - - - -
273F ALA 2.9 18.4 + - - -
274F PHE 3.6 1.8 - - - -
275F PHE 3.1 0.6 - - - -
276F ARG* 1.3 77.3 - - - +
278F VAL* 1.3 57.0 + - - +
281F GLY* 2.9 21.0 + - - -
287F SER* 2.8 38.7 + - - -
289F PHE* 4.4 4.7 - - - -
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Residues in contact with VAL 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274F PHE 3.1 13.7 + - - +
275F PHE* 3.4 14.6 - - + +
277F GLY* 1.3 74.1 - - - +
279F SER* 1.3 65.1 + - - +
284F GLY 4.2 3.1 - - - +
286F GLY* 3.3 21.5 + - - -
287F SER 4.0 11.7 - - - +
289F PHE* 4.4 4.5 - - + -
313F TYR* 3.9 42.0 - - + +
390F TRP* 3.3 42.5 + - + +
601F FMT 4.3 11.9 - - - -
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Residues in contact with SER 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279E SER* 4.4 9.5 + - - -
280E GLN* 4.1 11.2 + - - +
275F PHE* 2.9 43.5 + - - -
278F VAL* 1.3 81.7 - - - +
280F GLN* 1.3 79.1 + - - +
284F GLY* 3.5 22.5 - - - +
601F FMT 5.0 1.4 + - - -
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Residues in contact with GLN 280 (chain F).
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* 4.4 3.0 - - - -
279E SER* 4.3 12.5 + - - -
447E GLN* 5.0 3.6 - - - +
601E FMT 3.7 22.9 + - - +
244F PRO* 5.3 1.3 - - + -
245F ASN* 3.7 9.3 + - - +
276F ARG* 2.7 44.1 + - + +
279F SER* 1.3 93.1 - - - +
281F GLY* 1.3 67.5 + - - +
283F GLY* 3.5 4.9 + - - -
284F GLY* 3.2 12.4 + - - +
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Residues in contact with GLY 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244F PRO* 3.6 20.3 - - - +
276F ARG 3.5 2.8 + - - -
277F GLY* 2.9 21.0 + - - -
279F SER 3.8 0.2 - - - -
280F GLN* 1.3 77.2 - - - +
282F ARG* 1.3 70.0 + - - -
284F GLY 2.9 6.1 + - - -
286F GLY* 2.9 21.1 + - - -
287F SER* 3.7 8.7 - - - -
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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