Contacts of the helix formed by residues 177 - 184 (chain D) in PDB entry 3V5I
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 177 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114D ALA* 4.3 13.5 - - + -
115D LEU 3.6 15.7 - - - +
116D PRO 3.6 24.2 + - - +
118D ALA 3.6 13.4 + - - +
120D VAL* 5.7 1.6 - - - -
176D THR* 1.3 73.4 - - - +
178D GLU* 1.3 64.1 + - + +
180D ALA* 3.2 5.9 + - - -
181D LYS* 3.0 18.4 + - - +
186D ILE* 3.3 13.1 - - - +
189D VAL* 4.1 15.5 - - + -
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Residues in contact with GLU 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D THR* 3.3 7.4 + - - +
177D ALA* 1.3 76.7 - - + +
179D GLU* 1.3 59.7 + - + +
181D LYS* 3.0 22.9 + - - +
182D GLU* 2.9 27.2 + - - +
189D VAL* 3.9 26.6 - - + +
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Residues in contact with GLU 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C LYS* 3.7 17.3 + - - -
174D PHE 3.8 5.7 - - - +
175D LEU* 3.3 22.7 - - + +
176D THR* 2.8 43.2 + - - +
178D GLU* 1.3 79.0 - - + +
180D ALA* 1.3 57.0 + - - +
182D GLU* 3.3 10.6 + - - +
183D TYR* 2.9 30.1 + - - +
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Residues in contact with ALA 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D VAL* 4.0 28.3 - - + -
175D LEU* 4.4 7.2 - - + +
176D THR 2.9 17.9 + - - +
177D ALA* 3.4 6.7 - - - +
178D GLU 3.2 0.2 - - - -
179D GLU* 1.3 72.7 - - - +
181D LYS* 1.3 60.4 + - - +
183D TYR* 3.2 7.0 + - - +
184D GLY 3.0 21.8 + - - -
185D LEU* 3.0 21.2 + - + -
186D ILE* 3.7 14.6 - - + -
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Residues in contact with LYS 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D ALA 3.0 12.1 + - - +
178D GLU* 3.3 21.5 + - - +
180D ALA* 1.3 74.5 - - - +
182D GLU* 1.3 64.3 + - - +
184D GLY* 3.1 14.6 + - - -
186D ILE* 3.4 21.7 - - + +
187D ASP 3.4 28.9 - - - +
188D GLU* 3.7 16.8 + - - +
189D VAL* 4.2 16.5 - - + +
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Residues in contact with GLU 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D GLN* 4.0 7.3 + - - -
178D GLU 2.9 12.8 + - - +
179D GLU* 3.3 13.7 + - - +
181D LYS* 1.3 77.4 - - - +
183D TYR* 1.3 61.3 + - - +
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Residues in contact with TYR 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D ILE* 4.2 19.2 - - + +
154D LEU* 5.9 0.9 - - + -
158D THR* 3.6 9.7 - - + +
160D GLN* 2.9 41.9 + - + +
164D LYS* 3.9 18.9 + - - +
165D ILE* 3.8 27.1 - - + +
168D ASP* 2.6 40.9 + - + +
173D ASN* 5.2 2.9 - - - -
175D LEU* 4.5 12.3 - - + -
179D GLU 2.9 16.3 + - - +
180D ALA* 3.4 10.5 - - - +
181D LYS 3.1 0.4 - - - -
182D GLU* 1.3 76.6 - - - +
184D GLY* 1.3 59.9 + - - +
185D LEU* 4.0 24.5 - - + -
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Residues in contact with GLY 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D ARG* 3.2 19.9 + - - -
157D ARG 3.3 2.1 - - - +
158D THR* 3.3 30.6 - - - +
180D ALA 3.0 3.0 + - - -
181D LYS 3.1 11.8 + - - -
182D GLU 3.3 0.4 - - - -
183D TYR* 1.3 79.5 - - - +
185D LEU* 1.3 60.7 + - - +
186D ILE 3.4 6.1 - - - -
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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