Contacts of the helix formed by residues 154 - 165 (chain A) in PDB entry 3NJ8
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 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A SER* 3.1 20.1 + - - +
153A SER* 1.3 78.1 - - - +
155A TYR* 1.3 69.0 + - - +
156A SER 3.2 0.9 - - - -
157A PHE* 2.8 23.9 + - - +
158A VAL* 3.7 4.9 + - - +
196A ALA 3.5 23.6 - - - +
199A ALA* 4.2 14.4 - - + -
200A LEU* 4.3 12.2 - - - +
203A ASP* 4.8 6.6 - - - +
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Residues in contact with TYR 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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81A ALA 6.1 0.7 - - - -
84A ASP* 4.0 18.4 + - - -
150A SER* 3.0 14.9 + - - +
151A SER* 4.1 13.5 - - - +
154A ALA* 1.3 76.1 - - - +
156A SER* 1.3 57.7 + - - +
158A VAL* 2.6 53.2 + - + +
159A SER* 3.0 36.4 + - - -
162A GLN* 4.0 20.1 + - - -
203A ASP* 5.4 0.6 + - - -
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Residues in contact with SER 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ALA* 3.8 35.2 - - - -
107A ILE* 4.2 3.3 - - - +
126A HIS* 2.8 28.7 + - - -
151A SER 3.7 5.8 + - - -
152A ASN 2.6 31.2 + - - -
153A SER 3.7 2.1 - - - -
155A TYR* 1.3 78.6 - - - +
157A PHE* 1.3 55.8 + - - +
159A SER* 3.7 4.8 + - - +
160A LEU* 2.9 32.1 + - - +
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Residues in contact with PHE 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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124A LEU* 5.5 0.9 - - + -
126A HIS* 3.3 41.3 - + + +
154A ALA 2.8 14.3 + - - +
155A TYR 2.8 0.2 + - - -
156A SER* 1.3 76.3 + - - +
158A VAL* 1.3 68.6 + - + +
160A LEU* 3.2 6.9 + - + +
161A LEU* 3.0 37.2 + - + +
174A ALA* 4.6 4.0 - - + -
175A VAL 4.1 6.5 - - - -
176A THR* 3.7 22.4 - - + -
200A LEU* 3.5 26.7 - - + -
203A ASP* 5.2 3.1 - - + -
204A THR* 3.7 20.2 - - + -
207A LEU* 4.4 13.9 - - + -
219A VAL* 3.8 27.6 - - + -
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Residues in contact with VAL 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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154A ALA 4.2 2.2 - - - +
155A TYR* 2.6 39.9 + - + +
157A PHE* 1.3 69.6 - - + +
159A SER* 1.3 55.6 + - - +
161A LEU* 2.7 26.7 + - - +
162A GLN* 2.9 34.3 + - + +
203A ASP* 4.1 24.5 - - + +
207A LEU* 4.1 31.4 - - + -
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Residues in contact with SER 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASP* 2.8 29.1 + - - -
107A ILE* 3.2 16.9 - - - +
155A TYR* 3.0 22.6 + - - -
156A SER* 4.1 3.6 - - - -
158A VAL* 1.3 80.0 - - - +
160A LEU* 1.3 60.6 + - - +
162A GLN* 4.1 10.3 - - - -
163A HIS* 2.8 51.0 + - - +
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Residues in contact with LEU 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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13A PHE* 5.1 0.4 - - + -
15A ALA* 4.1 27.4 - - + -
79A LEU* 5.1 7.2 - - + -
81A ALA* 6.2 2.9 - - + -
107A ILE* 4.3 18.1 - - + +
124A LEU* 3.8 27.2 - - + +
125A VAL 4.4 0.2 - - - +
126A HIS* 4.0 32.8 - - + -
128A LEU* 5.9 1.6 - - + -
156A SER 2.9 20.8 + - - +
157A PHE* 3.4 7.0 - - + +
158A VAL 2.8 0.6 + - - -
159A SER* 1.3 76.9 - - - +
161A LEU* 1.3 58.0 + - - +
164A PHE* 3.1 57.3 + - + +
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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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124A LEU* 4.1 8.1 - - + -
157A PHE* 3.0 43.7 + - + +
158A VAL 2.7 14.1 + - - +
160A LEU* 1.3 70.5 - - - +
162A GLN* 1.3 57.9 + - - +
165A GLY* 2.7 38.4 + - - +
168A MET* 4.5 16.4 - - - -
174A ALA* 3.9 22.7 - - + -
207A LEU* 4.3 22.4 - - + -
211A ALA* 4.5 20.4 - - + -
215A TYR* 5.6 1.3 - - + -
217A VAL* 5.2 3.6 - - + -
219A VAL* 4.8 8.1 - - + -
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Residues in contact with GLN 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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155A TYR* 4.0 16.9 + - - -
158A VAL* 2.9 33.6 + - + +
159A SER* 3.7 15.1 - - - +
161A LEU* 1.3 76.9 - - + +
163A HIS* 1.3 73.7 + - + +
166A PRO* 3.1 25.6 - - - +
207A LEU* 6.3 1.8 - - + -
215A TYR* 4.8 1.3 + - - -
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Residues in contact with HIS 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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84A ASP* 4.5 10.8 - - + +
85A LYS* 5.1 4.9 - - - -
107A ILE* 3.7 19.1 - - + -
108A LYS* 3.4 44.8 - - + +
111A ALA* 3.4 24.1 - - + +
159A SER* 2.8 43.7 + - - +
162A GLN* 1.3 91.5 + - + +
164A PHE* 1.3 60.9 + - + +
165A GLY 3.3 0.4 - - - -
166A PRO* 4.0 7.9 - - - +
167A ILE* 4.2 7.4 - - - +
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Residues in contact with PHE 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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13A PHE* 3.8 41.1 - + + -
79A LEU* 6.1 0.7 - - + -
107A ILE* 4.4 7.4 - - + -
110A VAL* 3.9 12.8 - - + -
111A ALA* 3.8 32.5 - - + -
114A VAL* 4.3 10.1 - - + -
121A ILE* 3.9 13.2 - - + -
124A LEU* 3.7 26.2 - - + -
160A LEU* 3.1 50.2 + - + +
163A HIS* 1.3 78.4 - - + +
165A GLY* 1.3 57.6 + - - +
166A PRO 3.6 0.4 - - - -
167A ILE* 3.2 22.1 - - + +
168A MET* 2.7 31.6 - - + +
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Residues in contact with GLY 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* 2.7 23.5 + - - -
164A PHE* 1.3 77.4 - - - +
166A PRO* 1.3 59.5 - - - +
168A MET* 2.8 39.1 + - - +
215A TYR* 3.4 27.6 - - - -
217A VAL* 6.2 0.4 - - - -
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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