Contacts of the helix formed by residues 278 - 289 (chain A) in PDB entry 3EWS
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 GLU 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ARG* 3.8 19.5 + - - +
248A ILE* 5.0 1.6 - - - +
276A THR* 3.7 7.2 + - - +
277A PHE* 1.3 78.4 - - - +
279A ASP* 1.3 74.4 + - + +
280A SER* 3.2 24.4 + - - +
281A VAL* 2.7 26.1 + - + +
282A TRP* 3.1 6.4 + - - +
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Residues in contact with ASP 279 (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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277A PHE 3.5 2.7 + - - -
278A GLU* 1.3 76.5 - - + +
280A SER* 1.3 57.9 + - - +
282A TRP* 3.3 8.1 + - - +
283A LYS* 3.0 54.8 + - - +
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Residues in contact with SER 280 (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 ILE* 3.6 21.5 - - - +
254A GLN* 5.9 1.9 + - - -
278A GLU* 3.2 29.7 + - - +
279A ASP* 1.3 77.5 + - - +
281A VAL* 1.3 64.6 + - - +
283A LYS* 3.7 4.3 + - - +
284A PHE* 3.3 23.4 + - - +
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Residues in contact with VAL 281 (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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56A ARG* 5.5 1.1 - - - +
244A ALA* 4.1 16.2 - - + -
245A ASP* 4.2 9.6 - - + +
248A ILE* 3.5 28.9 - - + -
272A LEU* 5.5 0.7 - - + -
274A SER* 3.3 30.1 - - - +
276A THR* 3.5 14.8 - - - +
277A PHE* 4.1 8.3 - - + -
278A GLU* 2.7 36.0 + - + +
280A SER* 1.3 72.1 - - - +
282A TRP* 1.3 56.0 + - - +
284A PHE* 3.4 4.0 + - - +
285A ALA* 3.0 27.4 + - - +
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Residues in contact with TRP 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 6.5 0.7 - - + -
135A ILE* 4.0 23.8 - - + -
277A PHE* 3.9 41.2 - + + +
278A GLU 3.1 9.8 + - - +
279A ASP* 3.6 11.7 - - - +
280A SER 3.3 0.2 - - - -
281A VAL* 1.3 78.0 - - - +
283A LYS* 1.3 86.8 + - - +
285A ALA* 3.3 4.6 + - + +
286A GLN* 3.1 59.1 + - + +
292A PRO* 5.9 1.8 - - + -
294A VAL* 4.0 24.0 - - + -
296A LYS* 5.5 7.6 - - - -
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Residues in contact with LYS 283 (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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279A ASP* 3.0 38.7 + - - +
280A SER* 4.4 4.0 - - - +
281A VAL 3.5 0.2 - - - -
282A TRP* 1.3 93.0 - - - +
284A PHE* 1.3 60.0 - - - +
286A GLN* 3.2 28.6 + - - +
287A LYS* 3.1 30.8 + - + +
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Residues in contact with PHE 284 (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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241A LEU* 3.5 36.1 - - + -
244A ALA* 4.7 6.7 - - + -
247A MET* 5.4 6.1 - - + -
248A ILE* 3.8 23.1 - - + -
254A GLN* 3.9 47.8 - - + +
257A SER* 4.1 9.2 - - - -
258A ILE* 4.1 9.4 - - + -
272A LEU* 4.0 10.1 - - + -
280A SER 3.3 18.3 + - - +
281A VAL 3.6 4.0 - - - +
282A TRP 3.1 0.6 - - - -
283A LYS* 1.3 75.8 - - - +
285A ALA* 1.3 66.3 + - - +
287A LYS* 2.9 21.3 + - + +
288A VAL* 3.2 34.6 + - + +
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Residues in contact with ALA 285 (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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135A ILE* 3.8 25.1 - - + -
272A LEU* 3.8 33.4 - - + -
277A PHE* 5.0 1.6 - - + -
281A VAL 3.0 17.6 + - - +
282A TRP* 3.6 11.0 - - + +
284A PHE* 1.3 76.3 - - - +
286A GLN* 1.3 57.9 + - - +
288A VAL 3.1 0.7 + - - +
289A VAL* 2.9 34.7 + - - +
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Residues in contact with GLN 286 (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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135A ILE* 5.1 2.2 - - + -
282A TRP* 3.1 45.3 + - + +
283A LYS* 3.2 45.0 + - - +
284A PHE 3.2 0.2 - - - -
285A ALA* 1.3 76.5 - - - +
287A LYS* 1.3 60.7 + - + +
288A VAL 3.8 0.3 + - - -
289A VAL 4.4 12.6 + - - +
290A PRO* 5.0 3.3 - - - +
292A PRO* 5.8 3.4 - - + -
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Residues in contact with LYS 287 (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 GLN* 5.8 2.7 - - - -
258A ILE* 3.6 33.9 - - + +
261A GLN* 4.3 8.3 - - - +
262A ARG* 5.7 4.4 - - - +
283A LYS* 3.1 22.7 - - + +
284A PHE* 2.9 15.6 + - - +
286A GLN* 1.3 79.6 - - + +
288A VAL* 1.3 60.1 + - - +
290A PRO* 5.6 2.5 - - - +
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Residues in contact with VAL 288 (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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239A PHE* 3.8 20.0 - - + -
241A LEU* 3.9 14.6 - - + -
257A SER 5.2 0.7 - - - +
258A ILE* 3.4 23.8 - - + +
261A GLN* 3.1 37.5 + - + +
270A MET* 4.4 2.6 - - - +
272A LEU* 4.6 2.9 - - + -
284A PHE* 3.3 39.7 - - + +
285A ALA 3.1 3.7 + - - +
287A LYS* 1.3 80.2 - - - +
289A VAL* 1.3 68.5 + - + +
290A PRO* 3.2 10.5 - - - +
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ASN* 3.7 17.0 - - + -
134A LEU 3.9 11.7 - - - +
135A ILE* 4.0 12.8 - - + -
239A PHE* 5.9 0.7 - - + -
241A LEU* 6.0 0.2 - - + -
270A MET* 3.6 30.5 - - + +
271A LEU 4.6 0.7 - - - -
272A LEU* 3.6 33.7 - - + +
285A ALA 2.9 16.3 + - - +
286A GLN* 4.4 6.5 - - - +
288A VAL* 1.3 90.0 - - + +
290A PRO* 1.3 58.2 - - - +
292A PRO* 3.0 25.7 - - + +
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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
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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