Contacts of the helix formed by residues 159 - 167 (chain A) in PDB entry 3V30
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 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A ILE* 4.2 6.1 - - - -
150A PRO 5.5 3.4 - - - -
151A HIS 5.5 0.4 - - - -
152A ILE 4.2 7.2 - - - -
153A LEU* 3.7 20.6 - - - -
157A ARG 3.5 2.2 + - - -
158A GLU* 1.3 75.1 - - - +
160A ALA* 1.3 66.1 + - - +
161A LEU* 3.6 4.5 + - - -
162A SER* 3.0 31.6 + - - -
163A LEU* 3.1 26.4 + - - +
185A ILE* 3.5 16.2 - - - +
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Residues in contact with ALA 160 (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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128A LEU* 4.3 8.3 - - + -
129A ILE* 3.6 27.6 - - + +
132A SER* 3.6 27.2 - - - +
150A PRO 4.4 11.5 + - - +
152A ILE 4.7 1.8 + - - -
159A SER* 1.3 72.3 - - - +
161A LEU* 1.3 58.2 + - - +
163A LEU* 3.4 0.6 + - - -
164A ALA* 2.9 31.9 + - - +
176A LEU* 3.7 19.3 - - + -
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Residues in contact with LEU 161 (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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150A PRO 5.4 1.4 + - - +
159A SER* 3.2 7.4 + - - +
160A ALA* 1.3 79.0 - - - +
162A SER* 1.3 57.2 + - - +
164A ALA* 3.8 0.5 - - - +
165A SER* 2.9 36.8 + - - +
173A VAL* 3.9 42.6 - - + +
176A LEU* 3.7 14.3 - - + +
177A LEU* 4.0 8.7 - - + -
181A VAL* 3.8 20.8 - - + +
182A ASP 3.5 20.2 - - - +
183A ILE* 3.8 14.4 - - + -
185A ILE* 4.5 2.5 - - + -
193A PRO* 3.5 26.5 - - + -
209A LEU* 4.6 0.9 - - + -
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Residues in contact with SER 162 (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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157A ARG 6.1 0.2 - - - -
159A SER* 3.0 24.7 + - - -
161A LEU* 1.3 77.1 - - - +
163A LEU* 1.3 58.2 + - - +
165A SER* 3.7 6.2 - - - -
166A THR* 2.8 33.5 + - - -
185A ILE* 3.7 6.8 + - - +
187A ASP* 4.7 5.1 + - - +
193A PRO* 3.5 26.6 - - - +
196A TYR* 3.7 24.0 - - - -
9B LEU* 4.1 7.6 - - - -
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Residues in contact with LEU 163 (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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125A PHE* 4.1 4.7 - - + -
129A ILE* 3.5 28.7 - - + +
133A ALA* 3.8 32.6 - - + +
158A GLU* 4.0 20.6 - - + -
159A SER 3.1 15.8 + - - +
160A ALA 4.1 2.0 - - - +
162A SER* 1.3 74.0 - - - +
164A ALA* 1.3 66.0 + - - +
166A THR* 3.4 7.2 + - + +
167A GLY* 3.3 16.8 + - - -
169A TYR* 4.7 0.2 - - - -
6B MET* 4.1 13.5 - - + -
7B PRO* 3.6 30.1 - - + +
8B PRO 4.7 2.5 - - - +
9B LEU* 3.8 24.2 - - + -
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Residues in contact with ALA 164 (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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132A SER* 3.7 14.9 + - - +
160A ALA 2.9 19.0 + - - +
161A LEU 3.8 3.1 - - - +
163A LEU* 1.3 76.7 - - - +
165A SER* 1.3 61.8 + - - +
167A GLY 3.2 2.9 + - - -
168A GLY 3.1 4.0 + - - -
169A TYR* 3.0 30.3 + - + -
172A ILE* 3.6 32.1 - - + -
173A VAL* 4.0 12.3 - - + -
176A LEU* 4.3 2.9 - - + -
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Residues in contact with SER 165 (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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161A LEU* 2.9 25.0 + - - +
162A SER 3.7 3.8 - - - -
164A ALA* 1.3 73.6 - - - +
166A THR* 1.3 66.8 + - - +
168A GLY* 3.0 11.4 + - - -
173A VAL* 3.5 12.7 - - - +
193A PRO* 3.5 39.4 - - - +
196A TYR* 4.5 0.7 - - - -
197A ALA* 3.7 11.6 - - - +
202A HIS* 3.5 10.2 - - - -
205A CYS* 4.0 15.0 - - - -
209A LEU* 3.9 4.9 - - - +
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Residues in contact with THR 166 (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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162A SER 2.8 23.1 + - - -
163A LEU* 3.6 12.3 - - + +
164A ALA 3.3 0.2 - - - -
165A SER* 1.3 76.7 - - - +
167A GLY* 1.3 57.6 + - - +
196A TYR* 3.4 23.2 - - - +
200A GLY* 5.0 1.9 - - - -
202A HIS* 2.9 20.1 + - - -
7B PRO* 5.5 5.8 - - + -
8B PRO 3.8 13.9 - - - +
9B LEU* 3.3 16.1 - - + +
10B PRO* 3.6 23.4 - - + +
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Residues in contact with GLY 167 (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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133A ALA 5.4 0.9 - - - -
163A LEU 3.3 5.0 + - - -
164A ALA 3.2 6.2 + - - -
165A SER 3.2 0.6 - - - -
166A THR* 1.3 78.3 - - - +
168A GLY* 1.3 62.0 + - - +
169A TYR* 3.3 35.1 + - - -
202A HIS* 3.6 11.2 - - - -
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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