Contacts of the helix formed by residues 174 - 184 (chain E) in PDB entry 5A0Q
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 174 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E THR* 4.2 5.2 + - - -
169E ALA* 2.0 42.4 + - - +
170E ILE 3.5 8.1 - - - -
171E GLY 3.2 28.9 - - - -
172E SER 3.1 0.6 - - - -
173E ALA* 1.3 73.2 - - - +
175E GLU* 1.3 54.0 + - - +
177E ALA* 3.0 9.9 + - - -
178E GLN* 2.7 35.3 + - - +
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Residues in contact with GLU 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E LYS* 4.5 19.4 - - - +
171E GLY 5.5 2.7 - - - +
172E SER 4.6 8.4 + - - +
173E ALA 3.3 1.4 - - - -
174E SER* 1.3 76.1 - - - +
176E GLY* 1.4 56.5 + - - +
178E GLN* 3.2 9.9 + - - +
179E SER* 3.1 26.3 + - - -
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Residues in contact with GLY 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E ALA 3.2 8.6 + - - -
175E GLU* 1.4 76.4 - - - +
177E ALA* 1.4 58.1 + - - +
179E SER* 3.2 10.2 + - - -
180E SER* 3.0 29.2 + - - -
204E GLN* 4.9 1.6 - - - +
205E VAL* 5.0 2.2 - - - -
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Residues in contact with ALA 177 (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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36E THR* 4.9 3.4 - - - +
38E ILE* 5.0 2.0 - - + -
169E ALA* 3.7 19.5 - - + -
173E ALA 3.2 5.1 + - - -
174E SER* 3.0 15.1 + - - +
176E GLY* 1.4 73.9 - - - +
178E GLN* 1.4 60.1 + - - +
180E SER* 3.0 18.0 + - - -
181E LEU* 3.1 24.4 + - - +
201E ILE* 4.0 9.6 - - + +
205E VAL* 3.7 24.3 - - + +
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Residues in contact with GLN 178 (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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167E ALA 3.8 15.6 + - - -
168E ARG* 2.2 60.0 + - - +
169E ALA* 4.0 10.0 - - - +
174E SER* 2.7 14.3 + - - +
175E GLU* 3.2 14.9 + - - +
177E ALA* 1.4 71.7 - - - +
179E SER* 1.4 62.1 + - - +
181E LEU* 3.2 13.2 + - - +
182E GLN* 3.1 25.5 + - - +
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Residues in contact with SER 179 (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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175E GLU 3.1 10.3 + - - -
176E GLY* 3.2 14.7 + - - -
178E GLN* 1.4 77.2 - - - +
180E SER* 1.4 52.4 + - - +
182E GLN* 3.0 22.6 - - - +
183E GLU* 2.7 25.8 - - - +
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Residues in contact with SER 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176E GLY 3.0 16.3 + - - -
177E ALA* 3.0 23.4 + - - -
179E SER* 1.4 71.2 + - - +
181E LEU* 1.3 61.7 + - - +
183E GLU* 2.8 23.1 + - - +
184E VAL* 3.5 13.6 + - - +
201E ILE* 3.7 13.1 - - - +
204E GLN* 3.6 26.6 + - - -
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Residues in contact with LEU 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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38E ILE* 4.2 9.2 - - + -
40E ILE* 4.0 19.3 - - + -
167E ALA* 3.9 34.5 - - + +
168E ARG* 4.4 0.7 - - - -
169E ALA* 3.9 28.9 - - + +
177E ALA* 3.1 19.3 - - + +
178E GLN* 3.2 14.7 + - - +
180E SER* 1.3 80.0 + - - +
182E GLN* 1.3 55.3 + - - +
184E VAL* 3.7 11.2 - - + -
185E TYR* 2.9 39.4 + - + +
189E MET* 6.3 2.0 - - + -
197E SER* 4.4 1.3 - - - +
201E ILE* 3.8 20.2 - - + +
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Residues in contact with GLN 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178E GLN* 3.1 15.5 + - - +
179E SER* 3.0 22.1 - - - +
180E SER 3.1 0.6 - - - -
181E LEU* 1.3 76.9 - - - +
183E GLU* 1.4 59.7 + - - +
185E TYR* 4.5 7.5 + - - +
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Residues in contact with GLU 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E SER* 2.7 28.1 - - - +
180E SER* 2.8 17.2 - - - +
182E GLN* 1.4 78.7 - - - +
184E VAL* 1.3 61.3 + - + +
185E TYR 3.4 5.0 + - - +
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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
----------------------------------------------------------
180E SER 3.5 18.2 - - - +
181E LEU* 3.6 17.5 - - + +
183E GLU* 1.3 77.7 - - + +
185E TYR* 1.3 70.7 + - - +
186E HIS* 3.2 8.7 + - - +
189E MET* 3.7 9.1 - - + +
197E SER* 4.1 23.6 - - - +
201E ILE* 4.4 5.6 - - + -
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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