Contacts of the helix formed by residues 158 - 167 (chain A) in PDB entry 3CVW
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 THR 158 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A PRO* 3.3 1.8 - - - +
157A ILE* 1.3 85.3 - - - +
159A TYR* 1.3 63.7 + - - +
160A GLN* 4.5 5.2 - - - -
161A LYS* 3.3 21.7 + - - +
162A PHE* 3.2 22.7 + - - +
305A PHE* 3.6 8.4 - - - -
415A PHE 5.8 4.0 - - - +
12D G 4.0 27.1 - - - +
13D C 3.5 18.5 + - - -
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Residues in contact with TYR 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A THR* 1.3 73.1 - - - +
160A GLN* 1.3 75.7 + - - +
162A PHE* 3.2 9.5 + + - +
163A LEU* 3.0 50.1 + - + +
292A PRO* 4.1 3.0 - - + +
293A PRO* 3.4 25.1 - - + +
298A GLY* 2.9 29.8 + - - -
301A MET* 3.2 19.1 - - + +
302A TRP* 3.4 65.7 - + + -
305A PHE* 4.2 13.6 - - + -
8C 64T 3.6 17.6 + - - +
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Residues in contact with GLN 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A THR* 3.5 3.7 - - - -
159A TYR* 1.3 91.3 - - - +
161A LYS* 1.3 62.7 + - - +
163A LEU* 3.6 21.4 + - - +
164A GLY* 3.5 14.4 + - - -
292A PRO 5.0 1.2 + - - -
293A PRO* 4.2 15.6 - - - +
6C G 5.3 0.4 - - - +
7C G 3.9 31.0 + - - +
8C 64T 3.6 21.6 + - - +
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Residues in contact with LYS 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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151A ASN* 3.5 34.8 + - - +
155A ALA 5.6 0.6 + - - -
156A PRO* 4.2 15.6 - - + +
158A THR* 3.3 20.1 + - - +
159A TYR 3.3 0.2 - - - -
160A GLN* 1.3 75.6 - - - +
162A PHE* 1.3 65.6 + - - +
164A GLY* 3.2 11.1 + - - -
165A ILE* 3.3 20.7 + - + +
13D C 3.4 44.4 + - - +
14D T 5.4 10.5 - - - +
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Residues in contact with PHE 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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142A TYR* 5.5 1.1 - + + -
147A VAL* 3.8 24.5 - - + -
156A PRO* 3.8 18.8 - - + +
158A THR 3.2 15.9 + - - +
159A TYR* 3.3 16.2 - + - +
161A LYS* 1.3 77.6 - - - +
163A LEU* 1.3 66.5 + - + +
165A ILE* 3.2 3.6 + - - +
166A VAL* 3.1 46.7 + - + +
301A MET* 3.7 14.1 - - - -
304A GLU* 3.4 28.7 - - + -
305A PHE* 3.7 36.1 - + + -
308A THR* 3.2 24.7 - - - -
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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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159A TYR* 3.0 54.4 + - + +
160A GLN* 3.7 29.8 - - - +
161A LYS 3.3 0.4 - - - -
162A PHE* 1.3 78.7 - - + +
164A GLY* 1.3 60.8 + - - +
166A VAL* 3.5 10.0 - - + +
167A GLU* 3.2 32.1 + - - +
292A PRO* 4.5 18.2 - - + +
301A MET* 4.5 17.3 - - + -
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Residues in contact with GLY 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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160A GLN 3.5 7.0 + - - -
161A LYS 3.2 8.2 + - - -
163A LEU* 1.3 79.1 - - - +
165A ILE* 1.3 64.4 + - - +
167A GLU* 3.6 21.1 - - - +
168A GLN* 3.5 24.6 + - - +
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Residues in contact with ILE 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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147A VAL* 3.5 41.5 - - + +
150A LYS* 4.3 19.5 - - + +
151A ASN* 3.4 30.3 - - + +
156A PRO* 4.1 14.1 - - + -
161A LYS* 3.3 18.8 - - + +
162A PHE 3.2 6.4 + - - +
164A GLY* 1.3 79.8 - - - +
166A VAL* 1.3 60.8 + - - +
168A GLN* 3.3 23.8 - - + +
169A LEU* 3.4 12.3 - - + +
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Residues in contact with VAL 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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142A TYR* 3.3 49.4 + - + +
147A VAL* 4.0 17.7 - - + -
162A PHE* 3.1 55.6 + - + +
163A LEU* 3.5 16.2 - - + +
165A ILE* 1.3 75.5 - - - +
167A GLU* 1.3 67.0 + - + +
168A GLN 3.2 2.5 - - - -
169A LEU* 3.2 16.5 + - - +
301A MET* 4.7 8.5 - - - -
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Residues in contact with GLU 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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142A TYR* 4.9 4.0 - - - -
163A LEU* 3.2 21.8 + - - +
164A GLY* 3.6 19.6 - - - +
166A VAL* 1.3 78.5 - - + +
168A GLN* 1.3 62.0 + - + +
169A LEU 3.3 7.1 + - - +
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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