Contacts of the helix formed by residues 229 - 244 (chain E) in PDB entry 5EIG
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 CYS 229 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E ASP* 5.3 5.1 + - + +
227E VAL* 3.8 2.8 - - + +
228E ASN* 1.3 79.0 - - - +
230E GLU* 1.3 66.5 + - - +
231E SER* 3.4 25.4 - - - -
232E LEU* 3.7 26.9 - - + +
233E HIS* 3.0 23.4 + - - +
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Residues in contact with GLU 230 (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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82E LYS* 3.5 15.0 + - - +
83E TYR* 2.6 36.3 + - - -
228E ASN 3.3 2.8 + - - -
229E CYS* 1.3 74.9 - - - +
231E SER* 1.3 63.5 + - - +
233E HIS* 3.4 4.7 + - - +
234E ASN* 3.2 43.5 + - - +
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Residues in contact with SER 231 (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 CYS* 3.4 14.1 - - - -
230E GLU* 1.3 77.0 - - - +
232E LEU* 1.3 68.3 + - - +
234E ASN* 3.3 11.4 + - - +
235E ARG* 3.2 36.9 + - - +
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Residues in contact with LEU 232 (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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100E LEU* 3.8 27.4 - - + -
183E ILE* 3.8 20.2 - - + -
204E ASP* 4.2 18.4 - - + +
205E ILE* 3.7 23.1 - - + -
227E VAL* 3.6 23.3 - - + -
229E CYS* 3.5 24.5 + - + +
230E GLU 3.3 0.4 - - - -
231E SER* 1.3 81.9 + - - +
233E HIS* 1.3 58.0 + - - +
235E ARG* 3.5 19.5 + - - +
236E LEU* 3.0 34.4 + - + +
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Residues in contact with HIS 233 (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 TYR* 3.4 58.4 - + + +
85E LEU* 4.4 10.3 - - + -
227E VAL* 3.8 10.7 - - + +
229E CYS 3.0 18.2 + - - +
230E GLU* 3.5 5.8 + - - +
232E LEU* 1.3 76.4 - - - +
234E ASN* 1.3 65.6 + - - +
236E LEU* 3.1 3.2 + - - +
237E ARG* 2.6 78.3 + - + +
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Residues in contact with ASN 234 (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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230E GLU* 3.2 35.7 + - - +
231E SER* 3.3 10.8 + - - +
233E HIS* 1.3 87.7 + - - +
235E ARG* 1.3 60.4 + - + +
237E ARG* 3.9 5.5 - - - +
238E PHE* 3.0 28.4 + - - +
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Residues in contact with ARG 235 (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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100E LEU* 2.9 57.0 + - + +
101E LEU* 5.2 2.2 - - - +
181E ASP* 5.3 7.3 + - - -
183E ILE* 4.9 7.9 - - - +
231E SER* 3.2 26.3 + - - +
232E LEU* 3.8 18.0 - - - +
234E ASN* 1.3 77.8 - - + +
236E LEU* 1.3 61.4 + - - +
238E PHE* 3.6 6.8 + - - +
239E LEU* 3.2 28.8 + - + +
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Residues in contact with LEU 236 (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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85E LEU* 3.6 25.9 - - + +
87E PHE* 5.6 2.0 - - + -
96E THR* 4.7 13.5 - - + +
97E ILE* 4.2 22.2 - - + -
100E LEU* 3.9 29.4 - - + -
205E ILE* 4.0 14.8 - - + -
225E VAL* 3.8 26.5 - - + -
227E VAL* 4.3 13.9 - - + -
232E LEU 3.0 25.9 + - - +
233E HIS 3.5 3.8 - - - +
235E ARG* 1.3 75.2 - - - +
237E ARG* 1.3 59.4 + - - +
239E LEU* 3.2 3.6 + - - +
240E GLN* 2.9 24.9 + - - +
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Residues in contact with ARG 237 (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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63E SER 5.3 6.7 - - - -
68E ARG* 5.1 1.6 - - - +
72E GLU* 3.2 25.2 + - - +
83E TYR* 4.7 2.2 - - - +
84E CYS 3.0 22.6 + - - +
85E LEU* 3.6 15.1 - - - +
233E HIS* 2.6 56.0 + - + +
234E ASN* 3.9 7.0 - - - +
236E LEU* 1.3 73.8 - - - +
238E PHE* 1.3 63.0 + - - +
240E GLN* 3.1 26.9 + - - +
241E ASN* 3.5 19.2 + - - +
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Residues in contact with PHE 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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234E ASN 3.0 19.3 + - - +
235E ARG* 3.7 7.0 - - - +
237E ARG* 1.3 78.5 - - - +
239E LEU* 1.3 65.3 + - + +
241E ASN* 3.4 6.9 + - - +
242E SER* 2.6 51.4 + - - -
119F ARG* 4.0 27.1 - - + -
123F GLN* 4.3 25.6 - - + -
124F VAL* 4.0 20.9 - - + -
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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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96E THR* 3.4 38.3 - - + +
99E HIS* 3.7 34.3 - - + +
100E LEU* 3.8 15.0 - - + -
235E ARG* 3.2 18.6 + - + +
236E LEU* 3.2 2.7 + - - +
238E PHE* 1.3 88.1 - - + +
240E GLN* 1.3 60.7 + - - +
242E SER* 4.2 2.7 - - - -
243E LEU* 2.9 43.6 + - + +
124F VAL* 4.2 21.5 - - + -
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Residues in contact with GLN 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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63E SER 4.7 1.0 - - - +
68E ARG* 3.4 27.9 + - - +
72E GLU* 3.0 20.6 + - - -
85E LEU* 4.0 7.8 - - + +
86E ALA 2.9 28.1 + - - +
87E PHE* 3.8 26.5 - - + -
96E THR* 4.4 0.8 - - - +
236E LEU 2.9 17.4 + - - +
237E ARG* 3.1 32.8 + - - +
238E PHE 3.3 0.2 - - - -
239E LEU* 1.3 75.8 - - - +
241E ASN* 1.3 58.7 + - - +
244E GLY* 3.3 22.3 + - - -
245E ALA 4.2 2.3 + - - +
246E VAL* 3.7 15.2 - - + +
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Residues in contact with ASN 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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62E ARG* 3.2 32.1 + - - +
63E SER* 2.7 45.0 + - - +
237E ARG 3.5 9.1 + - - +
238E PHE* 3.4 9.0 + - - +
239E LEU 3.2 0.4 - - - -
240E GLN* 1.3 79.6 - - + +
242E SER* 1.3 63.3 + - - +
243E LEU 3.5 0.2 - - - -
244E GLY 4.1 0.4 - - - -
91F LEU* 3.5 5.0 - - - +
119F ARG* 3.5 28.1 - - - +
501F SO4 3.4 8.8 + - - -
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Residues in contact with SER 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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238E PHE* 2.6 53.8 + - - -
239E LEU* 3.3 4.7 + - - -
241E ASN* 1.3 79.7 + - - +
243E LEU* 1.3 66.1 + - - +
91F LEU* 3.4 20.2 - - - +
95F VAL* 4.6 1.6 - - - +
116F GLY 5.1 0.5 - - - +
119F ARG* 3.7 19.2 + - - +
120F TYR* 4.5 14.3 - - - +
124F VAL* 4.7 11.7 - - - -
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Residues in contact with LEU 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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95E VAL* 5.4 1.8 - - + -
96E THR* 3.8 30.5 - - + +
99E HIS* 3.7 49.8 - - + +
239E LEU* 2.9 26.4 + - + +
240E GLN* 5.5 0.2 - - - -
242E SER* 1.3 80.7 - - - +
244E GLY* 1.3 62.7 + - - +
245E ALA* 3.3 8.2 + - + +
91F LEU* 3.4 4.6 - - - +
92F ALA* 3.2 24.4 + - - -
95F VAL* 3.8 26.4 - - + +
120F TYR* 4.1 13.0 - - + -
124F VAL* 4.2 6.7 - - + -
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Residues in contact with GLY 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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62E ARG* 3.6 22.7 - - - -
240E GLN 3.3 12.4 + - - -
242E SER 3.5 1.8 - - - -
243E LEU* 1.3 79.2 - - - +
245E ALA* 1.3 56.3 + - - +
246E VAL* 2.9 14.3 + - - +
88F ALA* 3.8 1.9 - - - +
89F SER* 2.6 33.1 + - - -
91F LEU* 4.3 2.5 - - - -
92F ALA* 3.6 5.2 - - - +
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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