Contacts of the helix formed by residues 177 - 184 (chain E) in PDB entry 5IYB
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 ASP 177 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1366A PHE* 4.5 6.5 - - + -
1370A GLY* 3.0 21.1 - - - -
1371A ILE* 3.5 9.1 + - - -
173E ILE* 3.2 29.5 - - + +
174E GLN* 3.3 30.3 + - + +
175E ALA 3.2 1.2 - - - -
176E GLY* 1.3 77.1 - - - +
178E PRO* 1.3 77.1 - - - +
179E VAL* 3.6 9.5 + - - +
180E ALA* 3.0 16.4 + - + +
181E ARG* 2.7 33.0 + - - +
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Residues in contact with PRO 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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1366A PHE* 4.1 8.5 - - + +
1367A THR* 3.0 29.8 - - - +
1368A VAL 3.5 19.1 - - - +
1370A GLY* 4.2 6.7 - - - +
134E GLU* 6.0 4.3 - - - +
139E ILE* 3.8 12.4 - - + +
176E GLY 3.6 5.6 - - - +
177E ASP* 1.3 95.2 - - - +
179E VAL* 1.3 55.9 + - - +
181E ARG* 3.7 17.7 + - + +
182E TYR* 2.9 27.0 + - - +
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Residues in contact with VAL 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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1369A LEU 3.4 25.8 - - - +
1370A GLY* 4.4 3.8 - - - -
1372A GLU* 6.2 1.8 - - + +
139E ILE* 4.1 11.7 - - + -
140E THR* 5.5 6.1 - - + -
145E VAL* 4.8 14.8 - - + -
148E HIS* 3.9 42.2 - - + +
173E ILE* 5.4 0.4 - - + -
177E ASP* 3.3 11.4 + - - +
178E PRO* 1.3 74.2 - - - +
180E ALA* 1.3 66.0 + - - +
182E TYR* 3.3 7.9 + - + +
183E PHE* 3.1 32.5 + - + +
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Residues in contact with ALA 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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173E ILE* 4.7 10.9 - - + +
174E GLN 3.4 24.0 - - - +
175E ALA* 3.7 12.1 - - - +
177E ASP* 3.0 15.8 + - + +
179E VAL* 1.3 77.6 - - - +
181E ARG* 1.3 58.2 + - - +
184E GLY 3.0 20.1 + - - -
185E ILE* 3.1 35.2 + - + +
209E VAL* 5.3 1.3 - - + -
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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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128E GLU* 5.2 0.2 - - - -
129E GLN* 3.0 28.5 + - - +
130E PHE* 3.2 34.5 - - + +
131E LEU* 4.2 2.8 - - - +
134E GLU* 2.9 42.0 + - - -
175E ALA 3.9 12.8 - - - +
176E GLY* 3.3 24.2 + - - -
177E ASP 2.7 19.4 + - - +
178E PRO* 3.8 15.0 - - + +
180E ALA* 1.3 70.9 - - - +
182E TYR* 1.3 59.7 + - - +
184E GLY* 2.8 21.2 + - - +
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Residues in contact with TYR 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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16E THR* 4.1 11.8 + - + -
19E GLN 4.0 1.9 + - - -
20E LEU* 3.3 63.9 + - + +
23E ASP* 4.4 7.0 - - + +
24E ARG* 3.3 11.3 + - - -
130E PHE* 4.2 7.8 - + - -
134E GLU 6.0 1.1 - - - -
135E LEU* 5.3 5.8 - - + -
138E ASN* 3.0 35.7 + - - -
139E ILE* 4.3 14.6 - - + -
140E THR* 3.4 22.4 + - + -
178E PRO 2.9 19.8 + - - +
179E VAL* 3.3 11.4 + - + +
181E ARG* 1.3 76.0 - - - +
183E PHE* 1.3 83.4 + + - +
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Residues in contact with PHE 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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23E ASP* 3.0 31.9 - - + -
24E ARG* 2.8 34.6 + - + +
101E ARG* 5.5 0.7 + - - -
140E THR* 4.7 7.0 - - + -
148E HIS* 3.4 47.3 - - + -
150E VAL* 3.5 29.2 - - + -
179E VAL* 3.1 17.5 + - + +
180E ALA* 4.2 4.0 - - - +
182E TYR* 1.3 97.9 - + - +
184E GLY* 1.3 60.4 + - - +
185E ILE* 3.2 13.3 + - + +
191E VAL* 4.9 5.2 - - + -
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Residues in contact with GLY 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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24E ARG* 3.2 14.4 - - - -
101E ARG* 3.7 12.8 + - - -
128E GLU* 3.2 22.1 - - - +
180E ALA 3.0 2.7 + - - -
181E ARG* 2.8 18.6 + - - -
183E PHE* 1.3 78.6 - - - +
185E ILE* 1.3 63.8 + - - +
186E LYS* 3.7 2.4 + - - +
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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