Contacts of the helix formed by residues 228 - 246 (chain A) in PDB entry 3ELY
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 228 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A GLU* 5.5 0.2 - - - +
199A GLN* 5.6 0.4 - - - +
227A ASN* 1.3 71.9 - - - +
229A ILE* 1.3 63.8 + - - +
230A THR* 3.1 23.0 + - - -
231A HIS* 3.2 27.5 + - + +
232A MET* 3.0 26.0 + - - +
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Residues in contact with ILE 229 (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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192A ILE* 4.0 20.6 - - + +
195A LEU* 3.9 43.5 - - + +
196A GLU* 4.5 16.2 - - + +
199A GLN* 3.8 35.1 - - + +
205A GLY* 4.6 2.0 - - - -
206A ILE* 4.0 35.6 - - + +
221A TYR* 5.1 6.5 - - + -
227A ASN* 3.6 2.7 + - - +
228A ASN* 1.3 70.1 + - - +
230A THR* 1.3 63.4 + - - +
232A MET* 3.1 4.2 + - - +
233A VAL* 2.9 30.6 + - + +
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Residues in contact with THR 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ILE* 3.7 22.8 - - + +
196A GLU* 3.2 22.4 + - - -
228A ASN* 3.1 10.0 + - - -
229A ILE* 1.3 74.9 - - - +
231A HIS* 1.3 61.4 + - - +
233A VAL* 3.6 1.4 + - - +
234A ASN* 3.0 45.0 + - - +
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Residues in contact with HIS 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ASN* 3.2 29.2 + - + +
230A THR* 1.3 77.8 - - - +
232A MET* 1.3 70.1 + - - +
234A ASN* 3.7 4.6 + - - +
235A THR* 2.7 54.0 + - - +
238A ARG* 4.2 13.1 + - - +
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Residues in contact with MET 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ILE* 3.7 27.4 - - + +
207A VAL* 5.0 11.4 - - + -
208A ARG 5.6 1.1 - - - +
219A MET* 3.6 6.4 - - + +
227A ASN* 3.6 35.2 - - + +
228A ASN 3.0 21.3 + - - +
229A ILE 3.6 3.1 - - - +
231A HIS* 1.3 88.5 - - + +
233A VAL* 1.3 63.5 + - - +
235A THR* 3.6 9.0 + - + -
236A THR* 3.3 25.7 + - - +
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Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A PRO* 3.5 40.2 - - + +
187A TYR* 3.8 11.4 - - - +
192A ILE* 3.6 23.1 - - + -
195A LEU* 5.3 0.4 - - + -
206A ILE* 4.4 6.1 - - + -
217A HIS* 3.7 10.7 - - + -
219A MET* 4.0 11.7 - - - -
229A ILE* 2.9 25.1 + - + +
230A THR 4.0 4.3 - - - +
232A MET* 1.3 77.2 - - - +
234A ASN* 1.3 63.0 + - - +
236A THR* 3.3 5.5 + - - -
237A SER* 2.9 31.2 + - - +
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Residues in contact with ASN 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A THR* 5.2 5.7 - - - -
8A LEU* 4.7 18.7 + - + +
9A GLY 5.3 0.3 + - - -
230A THR* 3.0 36.9 + - - +
231A HIS* 4.2 3.0 - - - +
232A MET 3.4 0.2 - - - -
233A VAL* 1.3 78.3 - - - +
235A THR* 1.3 59.5 + - - +
237A SER* 3.6 9.5 + - - -
238A ARG* 2.9 59.2 + - - +
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Residues in contact with THR 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A HIS* 2.7 44.0 + - - +
232A MET* 3.8 13.7 - - + -
233A VAL 3.3 0.4 - - - -
234A ASN* 1.3 76.9 - - - +
236A THR* 1.3 58.8 + - - +
238A ARG* 3.8 14.1 + - - +
239A SER* 3.1 25.5 + - - -
242A ARG* 5.7 0.7 + - - -
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Residues in contact with THR 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ARG* 3.6 44.8 - - + +
217A HIS* 3.8 16.6 - - + +
219A MET* 3.7 11.3 - - - +
232A MET 3.3 12.6 + - - -
233A VAL 3.3 8.6 + - - -
234A ASN 3.2 0.4 - - - -
235A THR* 1.3 77.4 - - - +
237A SER* 1.3 58.5 + - - +
239A SER* 3.2 7.9 + - - -
240A LEU* 2.8 40.6 + - + +
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Residues in contact with SER 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.0 12.6 - - - -
9A GLY* 3.4 27.8 + - - -
12A TRP* 5.0 1.8 - - - +
187A TYR* 4.8 0.2 - - - +
217A HIS* 2.7 28.6 + - - -
233A VAL* 2.9 16.5 + - - +
234A ASN* 3.3 12.0 + - - -
236A THR* 1.3 75.3 - - - +
238A ARG* 1.3 56.5 + - - +
240A LEU* 3.3 5.0 + - - +
241A LEU* 2.9 35.6 + - - +
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Residues in contact with ARG 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.8 25.9 - - + +
231A HIS* 4.2 16.8 + - - +
234A ASN* 2.9 44.6 + - - +
235A THR* 3.8 24.2 + - - +
237A SER* 1.3 74.7 - - - +
239A SER* 1.3 58.4 + - - +
241A LEU* 3.4 9.3 + - + +
242A ARG* 2.9 38.3 + - - +
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Residues in contact with SER 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A THR* 3.1 16.3 + - - -
236A THR* 3.2 12.8 + - - -
238A ARG* 1.3 76.2 - - - +
240A LEU* 1.3 64.2 + - - +
242A ARG* 3.3 26.4 + - - +
243A ARG* 3.1 46.1 + - - +
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Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TRP* 3.6 25.1 - - + +
27A TYR* 2.7 20.1 + - - +
208A ARG* 3.7 19.7 - - - +
214A ASN* 3.5 37.7 - - - +
216A THR 4.2 1.1 - - - +
217A HIS* 3.6 43.1 - - + -
236A THR* 2.8 33.6 + - + +
237A SER 3.7 3.4 - - - +
239A SER* 1.3 74.2 - - - +
241A LEU* 1.3 61.4 + - - +
243A ARG* 3.7 5.7 + - - +
244A MET* 3.3 13.9 + - - +
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Residues in contact with LEU 241 (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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8A LEU* 3.9 38.1 - - + +
11A VAL* 4.6 6.1 - - + -
12A TRP* 3.8 29.2 - - + +
15A GLN* 3.5 29.6 + - - +
237A SER 2.9 24.2 + - - +
238A ARG* 3.7 8.3 - - + +
240A LEU* 1.3 75.9 - - - +
242A ARG* 1.3 62.7 + - - +
244A MET* 3.3 7.3 + - - +
245A THR* 3.3 27.8 + - + +
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Residues in contact with ARG 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A THR 5.7 0.8 + - - -
238A ARG* 2.9 20.9 + - - +
239A SER* 3.6 40.5 + - - +
241A LEU* 1.3 75.7 - - - +
243A ARG* 1.3 65.6 + - - +
245A THR* 2.8 26.0 + - - +
246A ARG* 3.4 14.3 + - - +
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Residues in contact with ARG 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 3.8 11.3 - - + -
30A SER* 3.6 22.6 + - - +
31A ASP* 3.5 33.6 + - + +
32A ILE* 3.7 12.9 - - - +
208A ARG* 5.7 1.6 - - - +
212A SER 5.6 0.6 + - - -
214A ASN* 2.9 30.9 + - - +
239A SER* 3.1 32.5 + - - +
240A LEU* 4.0 8.2 - - - +
242A ARG* 1.3 79.6 - - + +
244A MET* 1.3 60.2 + - - +
246A ARG 4.5 4.5 - - - -
247A PRO* 3.0 35.2 - - - +
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Residues in contact with MET 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TRP* 3.8 22.0 - - + +
15A GLN* 3.7 37.7 - - + +
16A LEU* 3.8 24.7 - - - +
19A LEU* 4.5 16.6 - - + -
27A TYR* 3.4 46.4 - - + -
240A LEU 3.3 7.4 + - - +
241A LEU* 3.6 10.5 - - + +
242A ARG 3.3 0.6 - - - -
243A ARG* 1.3 79.0 - - - +
245A THR* 1.3 61.8 + - + +
247A PRO* 3.4 13.2 - - - +
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Residues in contact with THR 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A LEU* 3.3 15.5 - - + +
242A ARG* 2.8 23.0 + - - +
244A MET* 1.3 77.9 - - + +
246A ARG* 1.3 74.2 + - - +
247A PRO* 3.6 5.0 - - - +
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Residues in contact with ARG 246 (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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31A ASP* 5.7 0.3 - - - +
242A ARG* 3.4 12.6 + - - +
243A ARG* 3.2 10.0 - - - +
245A THR* 1.3 96.7 + - - +
247A PRO* 1.4 63.8 - - - +
248A SER* 3.4 4.3 + - - -
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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