Contacts of the helix formed by residues 144 - 159 (chain A) in PDB entry 2V1C
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 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A GLU* 5.1 0.9 + - - -
110A VAL* 4.4 2.6 - - - +
142A GLY* 5.6 1.3 - - - -
143A THR* 1.3 90.4 + - - +
145A VAL* 1.3 60.2 + - - +
146A GLU* 2.9 30.2 + - - +
147A GLY* 3.1 4.5 + - - -
148A ASP* 2.8 23.7 + - - +
175B GLY* 4.8 3.6 - - - -
176B GLY 5.8 1.6 - - - +
15C ARG* 5.0 11.0 - - - -
51C ASN* 3.3 33.7 - - + +
52C LEU* 5.4 4.9 - - - +
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Residues in contact with VAL 145 (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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144A THR* 1.3 72.7 - - - +
146A GLU* 1.3 72.7 + - + +
148A ASP* 4.2 0.4 - - - -
149A ALA* 2.9 32.4 + - - +
51C ASN* 5.7 1.0 - - + +
52C LEU* 4.0 19.7 - - + +
53C PHE* 3.1 44.6 - - + -
54C HIS* 6.1 2.0 - - + +
80C LEU 5.2 2.2 - - - +
83C LEU* 3.6 31.7 - - + +
84C ALA* 3.8 13.1 - - + +
89C TYR* 4.7 4.5 - - + +
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Residues in contact with GLU 146 (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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110A VAL* 3.1 21.8 - - + -
111A LEU* 2.3 32.7 - - - +
112A SER* 2.8 14.0 + - - +
113A PRO* 5.8 3.1 - - + -
144A THR* 2.9 15.6 - - - +
145A VAL* 1.3 99.6 - - + +
147A GLY* 1.3 55.0 + - - +
149A ALA* 3.2 4.3 + - - +
150A THR* 2.6 39.5 + - - -
52C LEU* 3.4 13.9 - - + +
53C PHE* 4.2 0.3 - - - -
89C TYR* 4.5 3.8 - - - -
93C HIS* 2.9 28.4 + - + -
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Residues in contact with GLY 147 (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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86A GLU* 3.7 16.2 - - - -
110A VAL* 3.7 1.0 - - - +
141A THR* 2.6 30.6 + - - -
142A GLY 3.6 11.7 - - - -
144A THR* 3.1 8.6 + - - -
146A GLU* 1.3 78.6 - - - +
148A ASP* 1.3 62.4 + - - +
150A THR* 4.1 2.0 - - - -
151A ALA* 3.1 14.2 + - - +
167A ARG* 3.6 4.0 - - - -
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Residues in contact with ASP 148 (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 GLY 4.0 0.6 + - - -
143A THR 4.8 2.4 - - - +
144A THR 2.8 16.7 + - - +
145A VAL* 4.2 0.2 - - - -
147A GLY* 1.3 78.1 - - - +
149A ALA* 1.3 61.1 + - - +
151A ALA* 3.8 1.6 - - - +
152A LEU* 3.2 34.6 + - - +
167A ARG* 3.8 9.3 + - - +
170A TYR* 2.8 26.7 + - - +
188A ARG* 4.3 13.9 + - - -
84C ALA* 2.0 48.0 - - + +
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Residues in contact with ALA 149 (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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111A LEU* 4.7 2.9 - - + -
145A VAL 2.9 21.3 + - - +
146A GLU* 3.6 3.8 - - - +
148A ASP* 1.3 76.3 - - - +
150A THR* 1.3 65.9 + - - +
152A LEU 3.3 1.2 + - - -
153A TYR* 3.0 22.7 + - - +
84C ALA 3.0 14.5 + - - +
86C PRO* 3.7 12.2 - - + +
89C TYR* 3.8 37.7 - - + -
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Residues in contact with THR 150 (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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86A GLU* 6.0 0.9 - - + -
107A LEU* 3.6 30.5 - - + -
109A GLY 5.6 1.6 - - - +
110A VAL* 4.3 1.9 - - - +
111A LEU* 3.1 48.1 + - + +
122A LEU* 4.5 2.7 - - + -
124A ILE* 4.8 3.6 - - + -
141A THR* 4.3 7.9 - - + -
146A GLU 2.6 30.0 + - - -
147A GLY* 3.9 5.5 - - - -
149A ALA* 1.3 71.9 - - - +
151A ALA* 1.3 52.5 + - - +
153A TYR* 3.0 5.7 + - - +
154A LEU* 2.8 41.5 + - + +
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Residues in contact with ALA 151 (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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139A LEU* 3.5 13.7 - - + +
141A THR* 3.6 7.1 + - - +
147A GLY 3.1 15.4 + - - +
148A ASP 3.8 4.0 - - - +
150A THR* 1.3 76.7 - - - +
152A LEU* 1.3 59.3 + - + +
154A LEU* 3.0 12.4 + - - +
155A GLN* 2.7 35.2 + - - +
167A ARG* 3.4 33.4 - - - +
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Residues in contact with LEU 152 (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 ASP* 3.2 26.7 + - - +
149A ALA 3.9 3.4 - - - +
151A ALA* 1.3 81.5 - - + +
153A TYR* 1.3 63.0 + - - +
155A GLN* 3.4 27.3 + - - +
156A ARG* 3.1 38.1 + - + +
167A ARG* 6.2 1.1 - - - +
84C ALA* 4.4 3.4 - - + +
85C GLU* 4.3 29.6 - - + +
86C PRO* 4.2 12.1 - - + -
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Residues in contact with TYR 153 (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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111A LEU* 4.5 13.9 - - + -
119A PRO* 3.2 26.8 - - + +
124A ILE* 2.5 45.9 - - + +
149A ALA 3.0 13.4 + - - +
150A THR* 3.2 13.9 - - - +
152A LEU* 1.3 78.5 - - - +
154A LEU* 1.3 83.7 + - + +
156A ARG* 3.3 9.9 + - + +
157A LEU* 2.2 61.6 + - + +
86C PRO* 4.2 12.1 - - + +
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Residues in contact with LEU 154 (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 VAL* 3.7 19.5 - - + -
107A LEU* 3.6 28.7 - - + -
124A ILE* 3.6 22.9 - - + -
127A LEU* 6.0 4.3 - - + -
139A LEU* 4.2 17.5 - - + -
141A THR* 4.2 9.4 - - + -
150A THR* 2.8 22.0 + - + +
151A ALA* 3.4 7.4 - - - +
153A TYR* 1.3 100.4 - - + +
155A GLN* 1.3 58.2 + - - +
157A LEU* 3.3 3.2 + - + +
158A LEU* 2.8 47.3 + - + +
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Residues in contact with GLN 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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139A LEU* 4.1 12.8 - - + +
151A ALA 2.7 17.8 + - - +
152A LEU* 3.4 33.1 + - - +
154A LEU* 1.3 72.8 - - - +
156A ARG* 1.3 69.3 + - + +
159A GLU* 2.9 26.5 + - + +
165A ILE* 3.4 27.2 - - + +
196B VAL* 4.6 25.5 - - + +
197B SER* 5.7 3.2 - - - -
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Residues in contact with ARG 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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152A LEU* 3.1 25.4 + - - +
153A TYR* 3.4 11.2 - - + +
155A GLN* 1.3 85.4 - - + +
157A LEU* 1.3 64.4 + - - +
159A GLU* 3.2 18.6 - - - +
160A PRO* 3.4 4.7 - - - +
86C PRO* 5.1 16.8 - - - +
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Residues in contact with LEU 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 ILE* 3.6 12.3 - - + -
128A LEU* 4.2 28.7 - - + -
153A TYR* 2.2 57.6 + - + +
154A LEU* 3.6 6.1 - - + +
156A ARG* 1.3 80.4 - - - +
158A LEU* 1.3 59.4 + - + +
160A PRO* 3.0 25.9 - - + +
161A LEU* 3.6 4.9 - - - +
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Residues in contact with LEU 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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84A VAL* 5.1 1.1 - - + -
124A ILE* 6.4 0.4 - - + -
127A LEU* 3.3 29.6 - - + -
128A LEU* 3.6 21.3 - - + -
131A VAL* 4.0 16.3 - - + +
137A VAL* 3.3 41.3 - - + -
139A LEU* 4.6 5.4 - - + -
154A LEU* 2.8 32.2 + - + +
157A LEU* 1.3 73.4 - - + +
159A GLU* 1.3 66.4 + - - +
160A PRO 3.4 0.2 - - - -
161A LEU* 2.9 27.8 + - + +
163A ALA* 5.2 1.8 + - + +
165A ILE* 3.5 18.0 - - + +
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Residues in contact with GLU 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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155A GLN* 2.9 16.3 + - + +
156A ARG* 3.2 18.4 - - - +
158A LEU* 1.3 74.3 - - - +
160A PRO* 1.3 60.1 - - + +
161A LEU 2.5 22.2 - - - +
163A ALA 5.3 3.9 - - - +
165A ILE* 3.7 7.9 - - - +
197B SER* 4.9 16.5 + - - -
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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