Contacts of the helix formed by residues 281 - 293 (chain A) in PDB entry 3EBV
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 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A GLN* 6.0 0.2 - - - +
27A PRO* 3.7 25.5 - - + +
276A ASP* 2.8 26.2 + - - +
277A ALA* 3.3 27.3 + - - +
280A GLY* 1.3 80.2 + - - +
282A ALA* 1.3 59.5 + - - +
283A TRP 3.2 2.0 - - - -
284A SER* 3.9 6.7 - - - +
285A ASN* 2.9 39.6 + - - +
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A PRO* 4.2 7.0 - - + +
276A ASP* 3.8 0.6 + - - -
279A ALA* 3.3 17.2 + - + +
280A GLY 3.1 5.0 - - - +
281A ASN* 1.3 77.4 - - - +
283A TRP* 1.3 63.4 + - - +
285A ASN* 3.7 6.8 - - - +
286A SER* 3.1 26.0 + - - -
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Residues in contact with TRP 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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7A VAL* 4.0 17.3 - - + -
30A TYR* 4.4 1.3 - - - -
223A LEU* 4.1 12.9 - - + +
224A PRO 3.7 14.6 + - - -
225A ALA* 3.6 29.1 + - - +
234A TYR* 4.5 7.4 - + - -
235A VAL 4.6 4.2 + - - -
237A PRO* 4.0 21.5 - - + -
240A VAL* 4.0 19.0 - - + +
268A ALA* 4.0 9.9 - - + -
269A MSE 3.5 29.6 - - - -
270A THR* 3.6 29.6 - - + -
276A ASP* 3.4 9.5 + - - +
279A ALA* 6.0 1.4 - - + +
281A ASN 3.2 0.8 - - - -
282A ALA* 1.3 79.8 - - - +
284A SER* 1.3 66.6 + - - +
286A SER* 4.1 0.2 - - - -
287A VAL* 2.8 66.9 + - + +
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Residues in contact with SER 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 5.7 1.1 - - - -
27A PRO* 4.1 7.3 - - - +
29A ALA* 3.9 18.0 - - - +
30A TYR* 3.5 26.7 - - - -
276A ASP* 2.6 28.7 + - - -
281A ASN* 3.6 11.6 + - - +
283A TRP* 1.3 82.8 - - - +
285A ASN* 1.3 64.9 + - - +
288A GLY* 2.8 30.3 + - - +
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Residues in contact with ASN 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PRO* 6.1 0.5 - - - +
280A GLY 4.3 6.9 + - - -
281A ASN* 2.9 35.2 + - - +
282A ALA* 3.7 7.8 - - - +
284A SER* 1.3 81.6 + - - +
286A SER* 1.3 59.6 + - - +
289A ALA* 3.3 21.3 + - - +
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Residues in contact with SER 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A PRO* 3.4 23.0 - - - +
238A SER* 4.7 0.5 + - - -
241A ASN* 3.0 21.5 + - - -
282A ALA 3.1 12.5 + - - -
285A ASN* 1.3 76.7 - - - +
287A VAL* 1.3 66.0 + - - +
289A ALA* 3.5 4.3 + - - +
290A HIS* 3.1 22.9 + - - +
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Residues in contact with VAL 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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7A VAL* 4.9 2.2 - - + -
237A PRO* 3.8 18.6 - - + -
240A VAL* 4.0 18.6 - - + -
241A ASN* 3.6 16.2 - - - +
244A LEU* 4.6 0.2 - - + -
268A ALA* 3.7 19.7 - - + -
283A TRP* 2.8 63.6 + - + +
286A SER* 1.3 68.6 - - - +
288A GLY* 1.3 60.1 + - - +
290A HIS* 3.1 1.0 + - - +
291A VAL* 2.8 36.5 + - + +
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Residues in contact with GLY 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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7A VAL* 3.9 19.0 - - - +
29A ALA* 4.3 8.5 - - - -
283A TRP* 5.5 0.4 - - - -
284A SER* 2.8 22.7 + - - +
287A VAL* 1.3 77.1 - - - +
289A ALA* 1.3 61.1 + - - +
291A VAL* 3.4 0.3 + - - -
292A HIS* 2.9 38.8 + - - -
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Residues in contact with ALA 289 (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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284A SER 4.1 0.2 + - - -
285A ASN 3.3 22.5 + - - +
286A SER* 3.8 4.5 - - - +
288A GLY* 1.3 74.2 - - - +
290A HIS* 1.3 62.3 + - - +
292A HIS* 3.5 4.3 + - - +
293A ALA* 3.1 24.4 + - - +
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Residues in contact with HIS 290 (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 ASN* 3.2 54.1 + - + +
244A LEU* 4.2 12.1 - - + -
245A ASP* 2.6 39.0 + - - -
249A LYS* 5.2 5.1 + - - -
286A SER 3.1 10.3 + - - +
287A VAL 3.1 1.1 + - - +
289A ALA* 1.3 78.3 - - - +
291A VAL* 1.3 62.7 + - - +
293A ALA* 3.2 14.7 + - + +
294A LEU* 3.3 21.2 + - + +
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Residues in contact with VAL 291 (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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5A HIS* 3.5 32.4 - - + +
6A ALA 3.6 23.3 - - - +
7A VAL* 3.9 13.7 - - + -
244A LEU* 3.6 24.7 - - + -
267A GLY* 4.1 16.6 - - - -
268A ALA 4.3 2.5 - - - +
287A VAL* 2.8 32.7 + - + +
288A GLY 4.0 0.4 - - - +
290A HIS* 1.3 73.1 - - - +
292A HIS* 1.3 59.3 + - + +
293A ALA 3.1 0.2 - - - -
294A LEU* 3.0 31.0 + - + +
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Residues in contact with HIS 292 (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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2A SER* 3.2 24.6 + - - -
5A HIS* 3.3 13.2 + - - -
7A VAL* 4.2 9.1 - - + +
28A SER 5.2 0.7 - - - -
29A ALA* 3.1 35.7 - - - +
31A ASP* 2.7 24.5 + - - -
288A GLY 2.9 26.2 + - - +
289A ALA* 3.8 3.8 - - - +
291A VAL* 1.3 75.7 - - + +
293A ALA* 1.3 57.9 + - - +
294A LEU 3.5 1.6 - - - -
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Residues in contact with ALA 293 (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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289A ALA 3.1 17.9 + - - +
290A HIS* 3.7 9.0 - - + +
291A VAL 3.1 0.6 - - - -
292A HIS* 1.3 78.9 - - - +
294A LEU* 1.3 63.6 + - - +
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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