Contacts of the helix formed by residues 160 - 165 (chain E) in PDB entry 5ITX
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 PRO 160 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158E ASP 4.8 0.2 - - - +
159E ARG* 1.4 87.2 - - + +
161E ILE* 1.3 56.5 + - - +
162E CYS 3.1 0.7 - - - +
163E GLU* 2.7 55.6 + - + +
164E ALA 2.9 8.7 + - - -
190E PRO 3.7 4.0 - - - +
191E PHE* 3.4 36.6 - - + -
192E GLU 3.5 7.9 - - - +
274E ARG* 3.9 7.0 - - - +
288E LEU* 3.9 25.4 - - + +
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Residues in contact with ILE 161 (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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159E ARG 3.4 1.4 + - - -
160E PRO* 1.3 69.0 - - - +
162E CYS* 1.3 60.5 + - - +
164E ALA* 3.2 4.9 + - + -
165E LEU* 2.8 44.0 + - + +
171E PHE* 5.1 4.7 - - + -
183E LEU* 3.9 26.9 - - + -
188E ILE* 4.4 8.5 - - + -
189E PRO 3.9 5.6 - - - +
190E PRO* 3.3 19.6 + - + +
192E GLU 2.8 19.0 + - - +
194E ALA* 3.7 29.6 - - + -
197E VAL* 4.3 10.8 - - + -
198E LEU* 4.8 5.2 - - + -
225E LEU* 4.1 22.0 - - + -
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Residues in contact with CYS 162 (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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160E PRO* 2.9 0.4 + - - -
161E ILE* 1.3 77.1 - - - +
163E GLU* 1.3 67.2 - - - +
165E LEU* 3.9 9.4 + - - +
166E LEU 3.9 1.7 + - - -
179E ARG* 2.8 35.0 + - - +
183E LEU* 3.7 17.3 - - + -
190E PRO* 3.1 38.9 + - + -
191E PHE* 3.6 28.5 - - - -
273E ASP* 4.7 2.0 - - - -
279E ILE* 3.8 17.9 - - + -
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Residues in contact with GLU 163 (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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159E ARG* 4.4 1.8 - - + -
160E PRO* 2.7 35.9 + - + +
162E CYS* 1.3 72.3 - - - +
164E ALA* 1.3 68.5 + - - +
165E LEU 3.1 1.3 - - - -
166E LEU* 3.0 17.7 + - - +
167E ASP* 3.6 5.7 + - - +
179E ARG* 4.2 3.1 - - - +
191E PHE* 4.4 3.3 - - - -
273E ASP* 3.3 27.1 - - + +
274E ARG* 2.5 81.2 + - - +
275E HIS* 4.8 6.9 - - + +
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Residues in contact with ALA 164 (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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156E ALA 4.3 16.8 - - - +
157E PHE* 5.0 3.4 - - + -
159E ARG* 4.2 8.0 - - - +
160E PRO 2.9 7.8 + - - +
161E ILE* 3.5 11.0 - - + +
163E GLU* 1.3 74.7 - - - +
165E LEU* 1.3 53.6 + - - +
167E ASP* 2.8 37.4 + - - +
171E PHE* 3.3 14.7 - - + -
194E ALA* 3.6 29.8 - - + -
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Residues in contact with LEU 165 (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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161E ILE* 2.8 30.4 + - + +
162E CYS* 3.9 6.5 - - - +
163E GLU 3.1 0.4 - - - -
164E ALA* 1.3 72.2 - - - +
166E LEU* 1.3 57.1 + - - +
167E ASP 3.3 0.2 - - - -
171E PHE* 3.2 46.7 - - + +
174E ILE* 3.1 25.2 - - + +
179E ARG* 4.1 24.7 - - + +
182E ILE* 4.9 3.4 - - + -
183E LEU* 3.8 38.6 - - + -
225E LEU* 4.7 13.0 - - + -
229E CYS* 4.0 19.7 - - - -
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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