Contacts of the helix formed by residues 177 - 183 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ALA* 4.2 10.1 - - + -
115A LEU 3.6 15.3 - - - +
116A PRO* 3.6 23.1 + - + +
118A ALA 3.6 13.6 + - - +
120A VAL* 5.7 1.8 - - - -
176A THR* 1.3 73.6 - - - +
178A GLU* 1.3 63.3 + - + +
180A ALA* 3.2 8.6 + - - +
181A LYS* 3.0 18.2 + - - +
186A ILE* 3.4 9.4 - - - +
189A VAL* 3.9 19.7 - - + +
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Residues in contact with GLU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A THR* 3.3 7.0 + - - +
177A ALA* 1.3 77.2 - - + +
179A GLU* 1.3 58.3 + - + +
181A LYS* 3.1 20.1 + - - +
182A GLU* 2.9 28.7 + - - +
189A VAL* 3.8 26.7 - - + +
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Residues in contact with GLU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PHE 3.9 5.4 - - - +
175A LEU* 3.3 23.1 - - + +
176A THR* 2.8 45.4 + - - +
178A GLU* 1.3 79.3 - - + +
180A ALA* 1.3 57.8 + - - +
182A GLU* 3.4 9.5 + - - +
183A TYR* 2.9 29.7 + - - +
145G LYS* 3.7 16.5 + - - -
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Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A VAL* 4.0 28.5 - - + -
175A LEU* 4.3 6.7 - - + +
176A THR 2.8 17.5 + - - +
177A ALA* 3.4 6.5 - - - +
179A GLU* 1.3 75.4 - - - +
181A LYS* 1.3 63.6 + - - +
183A TYR* 3.3 7.5 + - - +
184A GLY 3.1 4.0 + - - -
185A LEU* 3.0 36.1 + - + -
186A ILE* 3.6 13.0 + - + -
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Residues in contact with LYS 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ALA 3.0 11.9 + - - +
178A GLU* 3.4 20.2 + - - +
180A ALA* 1.3 74.0 - - - +
182A GLU* 1.3 61.3 + - - +
184A GLY* 2.9 19.8 + - - -
186A ILE* 3.4 24.2 - - + +
187A ASP 3.5 28.5 - - - +
188A GLU* 3.8 16.3 + - - +
189A VAL* 4.2 17.2 - - + +
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Residues in contact with GLU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A GLN* 4.0 6.6 + - - -
178A GLU 2.9 12.8 + - - +
179A GLU* 3.4 13.7 - - - +
180A ALA 3.3 0.2 - - - -
181A LYS* 1.3 77.4 - - - +
183A TYR* 1.3 59.6 + - - +
184A GLY 3.5 0.2 + - - -
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Residues in contact with TYR 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ILE* 4.2 16.6 - - + +
154A LEU* 5.7 1.1 - - + -
158A THR* 3.5 11.1 - - + +
160A GLN* 3.0 45.8 + - + +
164A LYS* 3.9 14.9 + - - +
165A ILE* 3.7 27.6 - - + +
168A ASP* 2.7 40.8 + - + +
173A ASN* 5.3 2.7 - - - -
175A LEU* 4.5 14.4 - - + -
179A GLU 2.9 17.0 + - - +
180A ALA* 3.5 10.1 - - - +
181A LYS 3.1 0.4 - - - -
182A GLU* 1.3 77.4 - - - +
184A GLY* 1.3 59.0 + - - +
185A LEU* 4.1 21.1 - - + -
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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