Contacts of the helix formed by residues 180 - 194 (chain E) in PDB entry 4I02
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 SER 180 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E GLN* 5.7 0.7 - - - +
174E GLY* 4.9 0.2 - - - -
179E CYS* 1.3 77.3 - - - +
181E ARG* 1.3 65.1 + - - +
182E GLU* 3.1 24.9 + - - +
183E THR* 3.1 27.5 + - - -
184E VAL* 3.0 21.8 + - - +
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Residues in contact with ARG 181 (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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170E ARG* 3.5 40.0 + - + +
171E GLN* 3.8 42.5 + - - +
174E GLY* 5.2 0.2 - - - -
179E CYS 3.8 1.4 + - - -
180E SER* 1.3 72.4 - - - +
182E GLU* 1.3 79.6 + - - +
184E VAL* 3.4 7.6 + - - +
185E GLY 2.9 23.0 + - - -
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Residues in contact with GLU 182 (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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170E ARG* 5.5 0.7 - - - +
180E SER* 3.1 18.9 + - - +
181E ARG* 1.3 105.8 + - - +
183E THR* 1.3 68.1 + - - +
185E GLY* 3.2 2.5 + - - -
186E ARG* 3.0 24.5 + - - +
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Residues in contact with THR 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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140E ALA* 4.2 4.5 - - + -
179E CYS* 4.1 22.7 - - - -
180E SER* 3.1 21.4 + - - -
182E GLU* 1.3 78.2 - - - +
184E VAL* 1.3 62.7 + - - +
186E ARG* 3.3 23.3 + - - +
187E ILE* 3.0 44.4 + - + +
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Residues in contact with VAL 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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144E ILE* 4.1 11.8 - - + +
170E ARG* 3.7 24.0 - - + +
173E ILE* 3.9 19.7 - - + -
174E GLY* 3.5 31.2 - - - +
177E VAL* 4.8 0.2 - - + -
179E CYS* 4.2 8.3 - - + -
180E SER 3.0 17.9 + - - +
181E ARG 3.5 7.4 - - - +
182E GLU 3.2 0.2 - - - -
183E THR* 1.3 74.6 - - - +
185E GLY* 1.3 55.1 + - - +
187E ILE* 3.3 1.2 + - - +
188E LEU* 2.8 56.8 + - + +
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Residues in contact with GLY 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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170E ARG* 3.1 38.0 + - - -
181E ARG 2.9 11.1 + - - -
182E GLU* 3.2 4.4 + - - -
184E VAL* 1.3 77.1 - - - +
186E ARG* 1.3 61.0 + - - +
188E LEU* 3.4 2.8 + - - +
189E LYS* 3.0 23.6 + - - +
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Residues in contact with ARG 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E ALA* 5.8 1.2 - - - +
141E THR* 5.5 0.6 + - - -
182E GLU 3.0 15.3 + - - +
183E THR* 3.7 27.5 + - - +
184E VAL 3.3 0.2 - - - -
185E GLY* 1.3 77.7 - - - +
187E ILE* 1.3 75.8 + - - +
189E LYS* 3.4 8.3 + - - +
190E MET* 3.2 42.3 + - + +
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Residues in contact with ILE 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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140E ALA* 3.7 21.1 - - + -
141E THR* 3.6 33.2 - - + +
144E ILE* 3.7 26.0 - - + -
183E THR* 3.0 40.1 + - + +
184E VAL 4.0 0.2 - - - +
186E ARG* 1.3 92.5 - - - +
188E LEU* 1.3 61.7 + - - +
190E MET* 3.1 10.8 + - + +
191E LEU* 2.9 46.3 + - + +
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Residues in contact with LEU 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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144E ILE* 4.1 14.1 - - + -
148E LEU* 4.0 20.6 - - + -
170E ARG* 3.5 33.7 - - - +
173E ILE* 4.2 11.0 - - + -
184E VAL* 2.8 29.6 + - + +
185E GLY* 3.9 4.3 - - - +
187E ILE* 1.3 72.3 - - - +
189E LYS* 1.3 57.5 + - - +
191E LEU* 3.3 2.1 + - + +
192E GLU* 2.9 30.6 + - - +
197E ILE* 3.7 26.4 - - + +
204E ILE* 4.0 21.1 - - + -
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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 GLY 3.0 17.3 + - - +
186E ARG* 3.7 7.9 - - - +
187E ILE 3.2 0.2 - - - -
188E LEU* 1.3 77.2 - - - +
190E MET* 1.3 56.4 + - - +
192E GLU* 3.3 10.7 + - - +
193E ASP* 2.9 63.7 + - - +
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Residues in contact with MET 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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141E THR* 4.9 15.3 - - - +
186E ARG* 3.2 40.5 + - + +
187E ILE* 3.1 14.0 + - + +
189E LYS* 1.3 78.2 - - - +
191E LEU* 1.3 64.5 + - + +
193E ASP* 3.2 10.8 + - + +
194E GLN* 2.9 45.8 + - + +
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Residues in contact with LEU 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E THR* 4.7 15.5 - - + +
144E ILE* 4.3 6.5 - - + -
145E ALA* 4.9 14.6 - - + +
148E LEU* 3.9 27.6 - - + -
187E ILE* 2.9 36.8 + - + +
188E LEU* 3.3 6.5 + - + +
190E MET* 1.3 79.5 - - + +
192E GLU* 1.3 59.6 + - - +
194E GLN* 3.5 11.8 + - - +
195E ASN 3.3 2.9 + - - -
196E LEU* 2.9 56.4 + - + +
197E ILE* 3.6 13.4 + - + -
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Residues in contact with GLU 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 LEU 2.9 17.4 + - - +
189E LYS* 3.5 11.2 - - + +
191E LEU* 1.3 74.9 - - - +
193E ASP* 1.3 57.9 + - - +
195E ASN* 2.7 23.0 + - - -
197E ILE* 3.6 19.7 - - + +
198E SER* 3.4 5.4 - - - -
199E ALA* 2.8 47.1 + - - +
45F LYS* 3.0 26.4 + - - +
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Residues in contact with ASP 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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189E LYS* 2.9 49.6 + - - +
190E MET* 3.5 11.7 - - + +
192E GLU* 1.3 79.4 - - - +
194E GLN* 1.3 59.1 + - + +
195E ASN 3.2 2.9 + - - -
45F LYS* 3.8 18.0 + - - +
67F GLN* 4.6 7.1 + - - +
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Residues in contact with GLN 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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141E THR* 6.3 0.4 - - - +
190E MET* 2.9 40.0 + - + +
191E LEU* 3.9 16.1 - - - +
192E GLU 3.2 0.4 - - - -
193E ASP* 1.3 74.8 - - + +
195E ASN* 1.3 69.2 + - - +
196E LEU* 3.3 32.4 + - + +
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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