Contacts of the helix formed by residues 182 - 194 (chain E) in PDB entry 5X6E
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 HIS 182 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180E ILE* 3.6 2.0 - - - +
181E ALA* 1.3 92.1 + - + +
183E SER* 1.3 66.3 + - - +
184E SER* 4.2 1.6 - - - +
185E ALA* 3.0 16.3 + - + +
186E VAL* 3.2 15.5 + - - +
18G G 4.3 3.8 - - + -
19G T 3.3 86.8 + + + +
20G T 3.9 27.7 + - + +
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Residues in contact with SER 183 (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 MET* 4.1 10.6 - - - +
172E GLN* 4.0 37.9 - - - +
181E ALA 4.1 2.0 + - - -
182E HIS* 1.3 71.6 - - - +
184E SER* 1.3 58.6 + - - +
186E VAL* 3.2 14.3 + - - +
187E SER* 2.8 27.6 + - - -
8H A 5.2 6.7 + - - -
9H T 4.3 13.6 + - - +
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Residues in contact with SER 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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182E HIS* 4.2 0.6 - - - +
183E SER* 1.3 79.3 + - - +
185E ALA* 1.3 66.5 + - - +
187E SER* 3.1 17.7 + - - -
188E ARG* 3.2 16.9 + - - +
19G T 3.5 15.4 + - - +
20G T 2.6 35.1 + - - +
21G A 4.2 2.0 - - - -
9H T 4.3 7.2 - - - -
10H T 3.4 23.5 - - - +
11H A 3.8 4.6 + - - -
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Residues in contact with ALA 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E ILE* 3.7 15.5 - - + -
182E HIS* 3.0 12.9 + - + +
184E SER* 1.3 82.8 + - - +
186E VAL* 1.3 60.3 + - - +
188E ARG* 3.2 30.1 + - - +
189E ILE* 3.2 22.0 - - - +
17G T 4.4 10.3 - - + +
18G G 4.8 1.8 - - + +
19G T 3.5 23.1 - - + -
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Residues in contact with VAL 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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143E ILE* 4.0 23.1 - - + -
171E MET* 3.8 20.4 - - + +
172E GLN 5.3 0.4 - - - +
174E LEU* 4.2 9.2 - - + -
175E GLY* 4.1 7.2 - - - +
180E ILE* 3.6 23.8 - - + -
182E HIS 3.2 17.5 - - - +
183E SER* 3.4 13.5 - - - +
185E ALA* 1.3 76.1 - - - +
187E SER* 1.3 62.9 + - - +
189E ILE* 3.0 14.8 + - - +
190E ILE* 3.0 39.2 + - + +
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Residues in contact with SER 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171E MET* 4.1 7.2 - - - -
183E SER 2.8 14.3 + - - -
184E SER 3.1 8.9 + - - -
186E VAL* 1.3 75.7 - - - +
188E ARG* 1.3 62.8 + - - +
190E ILE* 3.9 10.5 - - - +
191E SER* 3.0 27.7 + - - -
9H T 3.9 33.9 + - - +
10H T 3.3 25.2 + - - +
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Residues in contact with ARG 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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184E SER 3.2 7.7 + - - +
185E ALA* 3.2 29.0 + - - +
187E SER* 1.3 78.3 - - - +
189E ILE* 1.3 66.2 + - + +
191E SER* 4.2 4.2 - - - -
192E LYS* 3.3 21.7 + - - +
17G T 3.2 44.4 - - - +
18G G 2.3 48.7 + - - -
19G T 3.3 20.0 + - - -
10H T 4.9 5.5 - - + +
11H A 5.3 1.4 - - - +
12H A 3.5 9.9 - - - +
13H C 5.1 0.8 - - - +
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Residues in contact with ILE 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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139E LYS* 4.9 8.1 - - + -
140E LEU* 4.6 15.7 - - + +
143E ILE* 4.0 24.7 - - + -
180E ILE* 4.3 17.7 - - + -
185E ALA 3.2 22.4 - - - +
186E VAL* 3.0 7.6 + - - +
188E ARG* 1.3 81.9 - - + +
190E ILE* 1.3 61.5 + - + +
192E LYS* 3.0 27.0 + - + +
193E LEU* 3.0 29.6 + - + +
17G T 4.1 32.5 - - + +
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Residues in contact with ILE 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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143E ILE* 4.9 11.4 - - + -
147E LEU* 5.5 4.7 - - + -
171E MET* 3.5 37.9 - - + -
174E LEU* 4.5 10.3 - - + -
186E VAL* 3.0 40.5 + - + +
187E SER* 3.9 1.8 - - - +
189E ILE* 1.3 78.5 - - + +
191E SER* 1.3 62.2 + - - +
193E LEU* 3.1 27.7 - - + +
194E LYS* 3.6 4.5 + - - +
199E ILE* 3.9 24.2 - - + +
206E PHE* 4.7 15.7 - - + -
9H T 5.9 0.7 - - - +
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Residues in contact with SER 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187E SER* 3.0 18.7 + - - -
188E ARG* 4.3 5.2 - - - -
190E ILE* 1.3 74.6 - - - +
192E LYS* 1.3 64.5 + - - +
194E LYS* 3.4 4.9 + - - +
195E GLN* 3.3 26.7 + - - +
9H T 6.0 2.6 - - - -
10H T 3.5 25.2 + - - -
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Residues in contact with LYS 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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140E LEU* 5.1 16.8 - - + -
188E ARG 3.3 14.1 + - - +
189E ILE* 3.0 18.1 + - + +
191E SER* 1.3 76.7 - - - +
193E LEU* 1.3 71.0 + - + +
195E GLN* 3.2 35.7 + - - +
196E GLU* 3.7 7.8 + - - +
213E TYR* 5.8 4.3 - - - +
16G A 5.5 11.8 + - - +
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Residues in contact with LEU 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E LEU* 5.4 6.3 - - + -
143E ILE* 5.1 4.5 - - + -
144E CYS* 4.2 18.8 - - - -
147E LEU* 4.8 9.2 - - + -
189E ILE* 3.0 48.1 + - + +
190E ILE* 3.1 16.8 + - + +
192E LYS* 1.3 83.6 - - + +
194E LYS* 1.3 50.9 + - - +
196E GLU* 2.5 33.3 - - - +
198E VAL* 3.1 30.9 - - + +
199E ILE* 4.1 13.0 - - + -
213E TYR* 3.6 27.7 - - + +
214E LEU* 4.9 4.9 - - + -
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Residues in contact with LYS 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190E ILE 3.6 2.9 + - - +
191E SER* 3.4 9.2 + - - +
192E LYS 3.2 0.6 - - - -
193E LEU* 1.3 75.7 - - - +
195E GLN* 1.3 61.8 + - - +
196E GLU 3.5 5.6 - - - +
197E LYS* 4.1 4.8 + - - +
198E VAL 4.5 1.8 - - - +
199E ILE* 3.0 66.9 + - + +
200E VAL* 3.4 24.1 - - - +
201E TYR* 4.4 6.1 - - + +
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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