Contacts of the helix formed by residues 154 - 163 (chain A) in PDB entry 3NTV
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 GLN 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A ASN* 4.8 4.1 + - - +
132A LEU* 3.5 31.8 - - + +
152A LYS 3.4 0.2 + - - -
153A ALA* 1.3 88.8 - - - +
155A SER* 1.3 64.5 + - - +
156A LYS 3.4 2.9 - - - -
157A LYS* 3.1 36.0 + - + +
158A PHE* 2.9 34.6 + - + -
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Residues in contact with SER 155 (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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148A ILE* 4.4 6.3 - - - +
149A ASP 3.7 16.4 - - - -
150A ALA* 2.7 32.1 + - - -
152A LYS 4.0 6.1 - - - -
153A ALA 3.0 5.1 + - - -
154A GLN* 1.3 73.9 - - - +
156A LYS* 1.4 62.7 + - - +
158A PHE* 3.3 10.8 + - - +
159A PHE* 3.1 21.7 + - - +
200A LYS* 4.2 8.4 - - - +
204A TYR* 3.4 23.6 - - - +
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Residues in contact with LYS 156 (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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154A GLN 3.4 0.6 - - - -
155A SER* 1.4 74.2 + - - +
157A LYS* 1.3 67.3 + - + +
159A PHE* 3.2 5.4 + - - +
160A GLU* 3.0 29.1 + - - +
200A LYS 5.8 0.4 - - - +
203A ASP* 4.7 17.6 + - - +
204A TYR* 3.9 30.1 - - + -
207A TRP* 3.6 53.8 - - + +
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Residues in contact with LYS 157 (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 LEU* 3.8 24.7 - - + +
154A GLN* 3.1 32.5 + - + +
156A LYS* 1.3 80.7 - - + +
158A PHE* 1.3 57.8 + - - +
160A GLU* 3.1 15.8 + - - +
161A ILE* 2.9 38.1 + - + +
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Residues in contact with PHE 158 (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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78A ILE* 3.7 31.9 - - + -
130A ASN* 5.0 1.3 - - - -
131A ALA* 3.7 32.8 - - + -
132A LEU* 3.7 22.2 - - + -
148A ILE* 4.6 10.7 - - + +
149A ASP 5.9 0.2 - - - -
152A LYS* 3.5 23.8 - - + -
153A ALA* 3.8 8.7 - - + -
154A GLN* 2.9 46.3 + - - -
155A SER* 3.6 10.3 - - - +
157A LYS* 1.3 78.4 - - - +
159A PHE* 1.4 62.5 + - - +
161A ILE* 3.3 1.3 + - + -
162A TYR* 3.0 41.9 + + + +
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Residues in contact with PHE 159 (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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148A ILE* 4.1 12.0 - - + +
155A SER 3.1 12.9 + - - +
156A LYS* 3.2 8.5 + - - +
158A PHE* 1.4 75.3 - - - +
160A GLU* 1.4 57.7 + - + +
163A THR* 2.7 51.8 + - + +
172A VAL* 3.8 30.3 - - + -
204A TYR* 3.6 18.8 - - - +
207A TRP* 3.4 30.5 - + + -
208A LEU* 3.5 28.3 - - + -
211A GLN* 4.6 8.1 - - + -
214A TYR* 3.7 41.5 - + - -
228A SER* 4.9 0.2 - - - -
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Residues in contact with GLU 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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156A LYS* 3.0 21.6 + - - +
157A LYS* 3.1 18.4 + - - +
159A PHE* 1.4 77.0 - - + +
161A ILE* 1.3 62.5 + - + +
163A THR* 4.1 3.3 + - - -
164A PRO* 3.3 18.9 - - - +
207A TRP* 3.6 32.3 + - + -
211A GLN* 5.7 0.9 - - - +
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Residues in contact with ILE 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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131A ALA 4.4 2.9 - - - +
132A LEU* 3.7 43.5 - - + +
135A PHE* 3.3 35.0 - - + +
157A LYS* 2.9 31.4 + - + +
158A PHE* 3.9 5.8 - - + +
160A GLU* 1.3 73.5 - - + +
162A TYR* 1.4 84.3 + - + +
164A PRO* 3.3 12.5 - - - +
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Residues in contact with TYR 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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76A LEU* 3.7 28.9 - - + -
78A ILE* 3.9 18.8 - - + -
101A ILE* 3.5 10.7 - - + +
131A ALA* 2.5 33.2 + - + -
134A GLN* 3.4 23.9 + - - +
135A PHE* 3.6 13.9 + + - -
138A VAL* 3.6 25.8 - - + -
146A ILE* 3.5 17.9 - - + +
158A PHE* 3.0 33.6 + - + +
159A PHE* 5.6 0.2 - - - -
161A ILE* 1.4 89.2 - - + +
163A THR* 1.3 59.2 + - + +
164A PRO* 3.2 3.4 - - - -
165A LEU* 2.9 36.0 + - + +
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Residues in contact with THR 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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146A ILE* 3.9 13.0 - - + -
148A ILE* 5.8 0.2 - - + -
159A PHE* 2.7 47.0 + - + +
160A GLU* 4.1 3.1 + - - -
162A TYR* 1.3 75.5 - - - +
164A PRO* 1.4 61.2 - - - +
165A LEU 3.0 0.2 - - - -
166A LEU* 2.9 21.0 + - + +
172A VAL* 3.8 22.9 - - + -
214A TYR* 3.1 25.9 + - - +
230A LYS* 2.9 15.7 + - - -
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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