Contacts of the helix formed by residues 183 - 196 (chain E) in PDB entry 5GJQ
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 THR 183 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38E ARG* 3.4 13.2 + - - +
182E GLU* 1.3 80.6 + - - +
184E ASP* 1.3 67.5 + - - +
185E ASP* 4.2 7.4 - - - -
186E LEU* 2.9 25.1 + - - +
187E THR 3.0 10.6 + - - -
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Residues in contact with ASP 184 (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 ARG* 3.8 17.1 + - - +
39E ASP* 4.8 5.9 - - - +
40E ILE* 4.1 25.7 - - + +
183E THR* 1.3 73.1 - - - +
185E ASP* 1.3 57.5 + - - +
186E LEU 3.0 2.1 + - - -
187E THR* 3.1 3.5 + - - -
188E ILE* 3.0 41.3 + - + +
210E VAL* 6.4 0.4 - - + -
212E ARG* 5.2 5.2 - - - +
228E TYR* 6.1 0.2 - - - +
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Residues in contact with ASP 185 (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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183E THR* 3.3 6.2 - - - -
184E ASP* 1.3 77.5 - - - +
186E LEU* 1.3 56.0 + - - +
188E ILE* 4.1 12.4 - - - +
189E LYS* 3.3 23.3 + - - +
228E TYR* 4.2 29.0 + - + +
231E GLU* 5.7 2.5 - - - +
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Residues in contact with LEU 186 (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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179E GLU 3.2 24.7 - - - +
180E ALA* 4.0 8.6 - - + +
181E ILE 3.7 12.3 + - - +
182E GLU* 4.0 10.5 - - + +
183E THR* 2.9 21.8 + - - +
185E ASP* 1.3 78.0 - - - +
187E THR* 1.3 59.8 + - - +
189E LYS* 3.3 12.7 - - + +
190E LEU* 2.9 26.0 + - - +
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Residues in contact with THR 187 (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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35E VAL* 4.2 12.5 - - - +
37E GLY* 5.1 4.7 - - - -
38E ARG* 3.9 11.9 - - - -
40E ILE* 5.5 5.6 - - - -
42E VAL* 4.9 7.2 - - - -
181E ILE* 3.8 28.8 - - - +
183E THR 3.0 5.5 + - - -
184E ASP* 3.1 7.4 + - - -
186E LEU* 1.3 72.3 - - - +
188E ILE* 1.4 61.5 + - - +
190E LEU* 3.0 21.9 + - - +
191E VAL* 3.0 19.4 + - - +
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Residues in contact with ILE 188 (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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42E VAL* 4.9 2.9 - - + +
184E ASP* 3.0 32.8 + - + +
185E ASP* 4.1 5.2 - - - +
187E THR* 1.4 73.0 - - - +
189E LYS* 1.3 57.5 - - - +
191E VAL* 3.2 8.7 + - - +
192E ILE* 2.9 31.4 + - + +
208E LEU* 5.4 7.6 - - + -
210E VAL* 3.9 33.0 - - + -
220E LEU* 4.2 16.6 - - + -
228E TYR* 3.7 53.6 - - + +
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Residues in contact with LYS 189 (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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185E ASP 3.3 16.1 + - - +
186E LEU* 3.3 21.8 - - + +
188E ILE* 1.3 80.6 - - - +
190E LEU* 1.3 56.5 + - - +
192E ILE* 3.4 5.5 + - - +
193E LYS* 2.9 31.1 + - - +
228E TYR* 6.1 2.7 - - - -
232E ILE* 5.7 8.8 - - + +
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Residues in contact with LEU 190 (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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35E VAL* 4.1 23.3 - - + -
171E PHE* 4.1 11.4 - - + -
172E LEU* 4.2 12.8 - - + -
175E ASN* 3.8 36.8 - - + +
176E TYR* 4.3 21.8 - - + -
180E ALA* 4.6 15.7 - - + -
181E ILE* 5.5 3.8 - - + +
186E LEU 2.9 14.8 + - - +
187E THR* 3.0 11.9 + - - +
189E LYS* 1.3 77.9 - - - +
191E VAL* 1.3 57.5 + - - +
193E LYS* 3.4 4.9 + - + +
194E ALA* 2.9 25.1 + - - +
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Residues in contact with VAL 191 (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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33E VAL* 3.7 21.7 - - + +
35E VAL* 3.6 32.1 - - + -
42E VAL* 3.7 21.8 - - + +
43E LEU 4.6 2.2 - - - -
44E GLY* 4.0 22.7 - - - +
187E THR 3.0 13.3 + - - +
188E ILE* 3.2 7.2 + - - +
190E LEU* 1.3 74.0 - - - +
192E ILE* 1.3 61.2 + - - +
194E ALA* 3.1 6.6 + - - +
195E LEU* 2.9 30.0 + - + +
206E ILE* 6.5 0.7 - - + -
208E LEU* 5.1 9.4 - - + -
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Residues in contact with ILE 192 (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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188E ILE* 2.9 19.3 + - + +
189E LYS* 4.0 5.2 - - - +
191E VAL* 1.3 75.8 - - - +
193E LYS* 1.3 56.8 + - - +
195E LEU* 3.4 6.1 + - - +
196E LEU* 2.9 32.8 + - - +
206E ILE* 5.4 11.6 - - + +
228E TYR* 5.8 4.0 - - + +
229E VAL* 5.6 10.5 - - + +
232E ILE* 5.5 10.1 - - + -
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Residues in contact with LYS 193 (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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171E PHE* 4.0 21.7 - - + -
189E LYS 2.9 20.3 + - - +
190E LEU* 3.5 9.6 - - + +
192E ILE* 1.3 78.0 - - - +
194E ALA* 1.3 61.9 + - - +
196E LEU* 3.6 11.1 + - - +
197E GLU* 3.7 12.3 + - - +
232E ILE* 6.1 3.0 - - + +
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Residues in contact with ALA 194 (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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33E VAL* 4.6 5.4 - - + -
168E VAL* 3.8 24.2 - - + +
171E PHE* 3.6 15.5 - - + -
172E LEU* 3.6 28.0 - - + -
190E LEU 2.9 16.4 + - - +
191E VAL* 3.5 7.2 - - - +
193E LYS* 1.3 76.6 - - - +
195E LEU* 1.3 63.9 + - - +
197E GLU* 3.2 18.4 + - - +
198E VAL 4.1 1.7 + - - -
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Residues in contact with LEU 195 (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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31E THR* 6.0 3.1 - - + +
33E VAL* 5.0 14.8 - - + +
44E GLY* 5.5 6.7 - - - +
45E VAL 6.0 2.0 - - - -
46E GLU* 5.8 3.2 - - + +
168E VAL* 5.4 1.6 - - - -
191E VAL* 2.9 19.0 + - + +
192E ILE* 3.9 6.1 - - - +
194E ALA* 1.3 72.2 - - - +
196E LEU* 1.3 58.2 + - - +
197E GLU 3.0 6.3 + - - -
198E VAL* 3.2 4.0 + - - +
199E VAL* 3.1 29.6 + - - +
206E ILE* 4.0 27.6 - - + -
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Residues in contact with LEU 196 (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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192E ILE 2.9 18.8 + - - +
193E LYS* 3.9 7.2 - - - +
194E ALA 3.3 0.4 - - - -
195E LEU* 1.3 74.7 - - - +
197E GLU* 1.3 57.9 + - - +
198E VAL 3.3 2.7 + - - -
199E VAL* 4.2 16.7 + - - +
201E SER* 5.3 7.4 + - - +
202E GLY 6.4 0.2 - - - +
206E ILE* 5.2 2.9 - - + +
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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