Contacts of the helix formed by residues 237 - 254 (chain E) in PDB entry 3DV0
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 ASP 237 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25E ILE* 3.0 18.9 + - - +
26E LEU* 2.8 40.3 + - - +
83E ALA* 4.0 2.5 - - - -
234E ASP* 3.2 19.7 + - + +
235E GLY 3.2 0.2 - - - -
236E MET* 1.3 78.8 - - - +
238E PRO* 1.3 71.3 - - - +
239E LEU* 2.9 14.9 + - - +
240E ALA* 3.4 9.1 - - + +
241E VAL* 3.3 24.8 + - - +
298E ARG* 3.8 16.6 - - - +
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Residues in contact with PRO 238 (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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26E LEU* 4.7 0.2 - - + -
49E LEU* 4.3 6.4 - - + +
53E MET* 3.9 30.7 - - + -
83E ALA* 3.8 12.3 - - + -
87E ALA* 3.3 14.0 - - + +
236E MET 3.4 9.0 - - - +
237E ASP* 1.3 90.7 - - - +
239E LEU* 1.3 61.8 + - - +
242E TYR* 3.1 20.6 + - - +
295E PRO 4.2 5.2 - - - +
298E ARG* 4.4 8.7 - - - -
299E PHE* 3.6 42.4 - - + -
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Residues in contact with LEU 239 (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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25E ILE* 3.6 26.9 - - + -
26E LEU* 3.6 36.6 - - + -
38E MET* 4.1 20.6 - - + -
39E PRO* 4.0 23.3 - - + +
41E LEU* 4.0 19.1 - - + -
46E LEU* 4.3 7.6 - - + -
49E LEU* 5.2 1.3 - - + -
237E ASP* 2.9 13.6 + - - +
238E PRO* 1.3 70.5 - - - +
240E ALA* 1.3 65.6 + - - +
242E TYR* 3.2 4.5 + - - +
243E ALA* 2.9 24.8 + - - +
299E PHE* 4.1 14.1 - - + -
302E PHE* 4.4 7.6 - - + -
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Residues in contact with ALA 240 (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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23E PHE* 3.3 30.6 - - + +
24E GLN* 4.3 0.2 - - - -
25E ILE* 3.5 17.7 - - + +
233E VAL* 3.4 19.5 - - + -
234E ASP 4.2 0.9 - - - +
237E ASP* 3.4 27.0 + - + +
239E LEU* 1.3 78.1 - - - +
241E VAL* 1.3 57.4 + - - +
244E ALA* 2.9 27.4 + - - +
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Residues in contact with VAL 241 (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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83E ALA 3.7 18.8 - - - +
84E SER* 3.8 21.3 - - - +
87E ALA* 4.2 0.2 - - + -
88E SER* 3.7 26.0 - - - +
233E VAL* 4.0 9.6 - - + -
234E ASP 3.7 14.4 - - - +
235E GLY 4.0 4.7 - - - +
237E ASP 3.3 18.1 + - - +
238E PRO 4.0 3.6 - - - +
239E LEU 3.2 0.4 - - - -
240E ALA* 1.3 74.0 - - - +
242E TYR* 1.3 65.4 + - - +
243E ALA 3.2 0.2 + - - -
244E ALA* 3.2 4.3 + - - +
245E VAL* 3.0 30.4 + - + +
261E ILE* 6.3 0.9 - - + -
263E THR* 4.3 15.0 - - + -
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Residues in contact with TYR 242 (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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39E PRO* 3.9 22.7 - - + -
40E GLU 5.6 0.4 + - - -
41E LEU* 3.5 37.2 - - + +
45E GLN* 5.4 2.4 + - - -
49E LEU* 5.3 2.9 - - + -
87E ALA* 3.5 21.5 + - + +
90E PHE* 3.7 23.6 + + - -
91E ALA* 3.2 40.5 - - + +
238E PRO 3.1 17.2 + - - +
239E LEU* 3.2 5.8 + - - +
241E VAL* 1.3 79.0 - - - +
243E ALA* 1.3 59.6 + - - +
245E VAL* 3.7 0.4 + - - -
246E LYS* 2.9 47.2 + - + +
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Residues in contact with ALA 243 (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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23E PHE* 3.8 19.5 - - + -
25E ILE* 5.3 1.6 - - + -
37E ALA 5.5 1.3 - - - +
39E PRO* 4.6 16.4 - - + -
239E LEU 2.9 16.4 + - - +
240E ALA 3.6 4.0 - - - +
242E TYR* 1.3 78.7 - - - +
244E ALA* 1.3 65.6 + - - +
246E LYS* 3.1 13.4 + - - +
247E ALA* 2.9 28.0 + - - +
7G PHE* 4.4 4.4 - - + -
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Residues in contact with ALA 244 (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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23E PHE* 4.3 3.9 - - + -
231E ILE* 4.3 12.3 - - + +
233E VAL* 3.5 32.5 - - + -
240E ALA 2.9 12.9 + - - +
241E VAL* 3.7 4.5 - - - +
243E ALA* 1.3 76.3 - - - +
245E VAL* 1.3 60.5 + - - +
247E ALA* 4.0 1.9 - - - +
248E ALA* 3.1 24.3 + - - +
261E ILE* 3.5 17.3 - - + +
7G PHE* 4.2 12.3 - - + -
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Residues in contact with VAL 245 (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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88E SER* 3.5 42.2 - - - +
91E ALA* 3.8 15.0 - - + -
92E LEU* 4.3 16.2 - - + -
168E ILE* 4.6 8.1 - - + -
196E ILE* 4.7 6.9 - - + +
198E VAL* 5.3 5.8 - - + -
241E VAL* 3.0 19.4 + - + +
244E ALA* 1.3 75.9 - - + +
246E LYS* 1.3 55.1 + - - +
248E ALA* 3.2 2.9 + - - +
249E ARG* 2.8 35.8 + - + +
261E ILE* 3.9 18.6 - - + -
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Residues in contact with LYS 246 (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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38E MET 5.3 0.4 + - - -
39E PRO* 4.0 25.3 - - - +
40E GLU 4.8 2.6 - - - +
91E ALA* 4.0 10.3 - - + +
242E TYR* 2.9 44.5 + - + +
243E ALA* 3.1 12.8 + - - +
245E VAL* 1.3 77.0 - - - +
247E ALA* 1.3 66.8 + - - +
249E ARG* 3.2 6.0 + - - +
250E GLU* 3.1 44.0 + - + +
4G THR* 3.2 39.2 + - - +
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Residues in contact with ALA 247 (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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243E ALA 2.9 17.0 + - - +
244E ALA 4.0 1.8 - - - +
246E LYS* 1.3 81.8 - - - +
248E ALA* 1.3 58.6 + - - +
250E GLU* 3.4 7.1 + - - +
251E ARG* 2.9 30.2 + - - +
4G THR* 5.6 3.4 - - + -
5G PHE 5.0 5.2 - - - +
6G GLN* 5.8 2.2 - - - -
7G PHE* 3.6 31.0 - - + +
9G PHE* 5.0 7.2 - - + -
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Residues in contact with ALA 248 (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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196E ILE* 3.2 27.0 - - + +
231E ILE* 5.4 0.2 - - + -
244E ALA 3.1 17.6 + - - +
245E VAL 3.2 2.9 + - - +
247E ALA* 1.3 79.7 - - - +
249E ARG* 1.3 61.0 + - - +
251E ARG* 3.9 4.4 - - - +
252E ALA* 3.2 18.5 + - - +
257E GLY 4.8 0.7 - - - +
259E THR* 3.5 36.5 + - + -
261E ILE* 4.2 8.5 - - + -
9G PHE* 5.6 1.3 - - - -
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Residues in contact with ARG 249 (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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91E ALA 3.5 22.4 - - - -
92E LEU* 4.4 2.9 - - + +
93E GLU* 3.0 32.2 - - - +
95E GLU* 4.7 2.4 + - - -
96E ASP* 2.8 35.3 + - - -
164E LYS 3.7 18.4 + - - -
165E ALA* 4.1 1.0 - - - +
166E VAL* 3.9 15.7 - - + -
196E ILE* 3.8 8.9 - - + +
245E VAL* 2.8 20.2 + - + +
246E LYS* 3.6 6.7 - - - +
247E ALA 3.2 0.2 - - - -
248E ALA* 1.3 76.5 - - - +
250E GLU* 1.3 64.4 + - + +
252E ALA* 3.2 2.9 + - - +
253E ILE* 3.0 57.5 + - - +
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Residues in contact with GLU 250 (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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246E LYS* 3.1 43.5 + - + +
247E ALA* 3.9 5.6 - - - +
249E ARG* 1.3 77.9 - - + +
251E ARG* 1.3 65.1 + - - +
252E ALA 3.1 0.2 - - - -
253E ILE* 3.0 33.1 - - + +
254E ASN* 3.2 17.1 + - - +
4G THR* 4.2 17.4 + - - +
6G GLN* 5.4 3.3 + - - -
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Residues in contact with ARG 251 (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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229E PRO* 3.6 32.3 - - - +
247E ALA 2.9 19.3 + - - +
248E ALA 3.9 3.1 - - - +
249E ARG 3.3 0.2 - - - -
250E GLU* 1.3 77.3 - - - +
252E ALA* 1.3 57.9 + - - +
254E ASN* 3.9 2.8 + - - +
255E GLY 3.7 1.9 + - - -
256E GLU* 2.8 93.3 + - + +
257E GLY* 4.1 8.0 + - - +
258E PRO 4.0 5.3 + - - -
259E THR* 3.1 22.2 + - - -
9G PHE* 4.0 32.2 - - + +
13G LEU* 4.8 12.3 - - - +
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Residues in contact with ALA 252 (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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166E VAL* 3.5 19.5 - - + -
194E PRO* 3.5 35.1 - - + +
195E ALA 4.6 0.7 - - - +
196E ILE* 4.6 3.4 - - + -
248E ALA 3.2 19.3 + - - +
249E ARG 3.5 5.2 - - - +
250E GLU 3.1 0.6 - - - -
251E ARG* 1.3 76.0 - - - +
253E ILE* 1.3 63.8 + - - +
254E ASN 3.2 1.6 - - - -
255E GLY* 3.1 13.3 + - - -
257E GLY 3.7 15.4 + - - +
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Residues in contact with ILE 253 (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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164E LYS* 3.3 60.9 + - + +
165E ALA 4.2 3.1 - - - +
166E VAL* 4.1 10.5 - - + -
194E PRO* 5.3 0.2 - - - -
249E ARG* 3.0 38.9 + - - +
250E GLU* 3.0 35.0 - - + +
252E ALA* 1.3 77.0 - - - +
254E ASN* 1.3 70.8 + - - +
255E GLY* 3.1 1.5 + - - -
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Residues in contact with ASN 254 (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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164E LYS* 4.8 6.1 + - - +
250E GLU* 3.2 18.2 + - - +
251E ARG* 4.1 7.0 - - - +
252E ALA 3.2 0.6 - - - -
253E ILE* 1.3 92.3 - - - +
255E GLY* 1.3 60.3 + - - +
256E GLU* 3.7 15.0 + - + +
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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