Contacts of the helix formed by residues 174 - 180 (chain E) in PDB entry 5TWV
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 ALA 174 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172E ALA 3.3 3.1 + - - +
173E GLN* 1.3 72.4 - - - +
175E HIS* 1.3 64.9 + - - +
176E ARG* 3.3 2.6 + - - +
177E ARG* 3.6 23.7 + - + +
178E ALA 3.6 2.1 + - - -
291E VAL* 5.4 2.5 - - + -
294E THR* 4.5 10.3 - - - +
296E ILE* 4.1 32.3 - - + +
298E THR* 3.4 27.1 + - + -
292G GLU 5.8 2.0 + - - -
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Residues in contact with HIS 175 (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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173E GLN* 3.5 30.2 - - + +
174E ALA* 1.3 78.0 - - - +
176E ARG* 1.3 73.4 + - - +
178E ALA* 3.0 22.0 + - - +
179E GLU* 3.1 10.4 + - - +
298E THR* 4.3 9.6 + - - -
299E GLN 5.9 0.8 + - - -
292G GLU* 3.8 51.0 + - + -
293G THR* 5.3 5.9 - - - +
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Residues in contact with ARG 176 (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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54C ARG* 5.7 5.3 - - - +
57C GLN* 5.7 14.7 - - + +
58C ASP* 4.0 30.3 - - + +
173E GLN* 4.9 29.8 + - + +
174E ALA 3.3 0.2 - - - -
175E HIS* 1.3 89.2 - - + +
177E ARG* 1.3 63.9 + - + +
179E GLU* 3.2 22.0 + - - +
180E THR* 4.1 8.0 + - - +
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Residues in contact with ARG 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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58C ASP* 5.9 2.0 - - - -
61C THR* 3.9 38.4 + - - +
174E ALA* 3.6 20.0 + - + +
175E HIS 3.2 0.6 - - - -
176E ARG* 1.3 80.1 - - + +
178E ALA* 1.3 59.7 + - - +
180E THR* 2.5 38.6 + - - +
181E LEU* 4.3 3.3 - - - +
204E ASP* 4.7 3.6 + - - -
206E ARG* 3.9 23.9 - - - +
208E SER* 3.5 42.7 + - - -
209E MET 4.6 10.1 + - - -
210E ILE* 5.4 6.2 - - - +
291E VAL* 4.9 20.0 - - + +
292E GLU* 5.4 0.8 - - - +
293E THR* 4.8 9.7 + - - +
294E THR* 5.8 0.9 - - - +
298E THR* 5.1 5.2 - - + -
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Residues in contact with ALA 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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174E ALA 3.6 2.2 + - - -
175E HIS* 3.0 11.7 + - - +
177E ARG* 1.3 78.9 - - - +
179E GLU* 1.3 61.5 + - - +
181E LEU* 3.0 37.3 - - + +
298E THR* 3.0 34.9 - - + +
299E GLN 4.2 13.9 - - - +
300E ALA* 4.3 7.1 - - + +
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Residues in contact with GLU 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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54C ARG* 5.0 25.8 + - + -
39E LYS* 3.3 40.8 + - - +
175E HIS 3.1 10.3 + - - +
176E ARG* 3.2 16.0 + - - +
178E ALA* 1.3 70.7 - - - +
180E THR* 1.3 53.0 + - + +
181E LEU 2.6 28.0 + - - +
182E ILE* 3.9 16.6 - - + +
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Residues in contact with THR 180 (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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54C ARG* 6.2 3.8 - - + -
55C PHE* 4.1 14.6 - - + -
176E ARG 4.3 7.9 - - - +
177E ARG* 2.5 32.4 + - - +
179E GLU* 1.3 70.3 - - + +
181E LEU* 1.3 57.7 + - - +
182E ILE* 3.4 7.4 + - - -
204E ASP* 3.7 13.5 + - - -
205E LEU* 3.3 40.1 + - - +
206E ARG* 3.5 35.6 - - + +
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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