Contacts of the helix formed by residues 152 - 164 (chain A) in PDB entry 6LGV
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 ASP 152 (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* 4.0 3.8 + - - -
151A VAL* 1.3 70.1 - - - +
153A VAL* 1.3 57.8 + - - +
154A VAL* 3.7 4.9 + - - +
155A GLY* 2.9 26.1 + - - -
156A MET* 2.9 28.3 + - - +
270A TYR* 4.0 26.4 + - + +
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Residues in contact with VAL 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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138A PRO* 3.6 40.9 - - + +
139A LEU* 4.2 15.0 - - + -
142A ARG* 4.0 33.2 - - + +
151A VAL* 3.0 26.7 + - + +
152A ASP* 1.3 73.7 + - - +
154A VAL* 1.3 71.1 + - + +
156A MET* 3.4 0.4 + - - -
157A LEU* 2.9 27.7 + - - +
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Residues in contact with VAL 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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152A ASP* 3.3 4.8 + - - +
153A VAL* 1.3 85.5 - - + +
155A GLY* 1.3 60.6 + - - +
157A LEU* 3.3 14.7 + - + +
158A LYS* 2.9 51.9 + - + +
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Residues in contact with GLY 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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152A ASP* 2.9 25.7 + - - -
154A VAL* 1.3 76.2 - - - +
156A MET* 1.3 55.5 + - - +
158A LYS* 3.2 9.6 + - - +
159A SER 2.8 22.0 + - - -
270A TYR* 2.7 25.5 + - - -
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Residues in contact with MET 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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98A LEU* 4.1 23.1 - - - -
137A THR* 4.6 0.9 - - - -
138A PRO* 3.7 31.4 - - + -
141A THR* 4.6 8.5 - - + -
151A VAL* 3.5 32.5 - - + -
152A ASP 2.9 13.4 + - - +
153A VAL 3.8 3.8 - - - +
155A GLY* 1.3 73.7 - - - +
157A LEU* 1.3 66.1 + - - +
159A SER* 3.3 1.6 + - - -
160A ILE* 2.9 28.3 + - + +
266A LEU* 3.9 28.0 - - + -
270A TYR* 3.6 29.4 - - + -
271A PHE* 4.7 4.5 - - + -
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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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134A VAL* 3.5 37.7 - - + +
135A PHE* 4.0 24.9 - - + -
138A PRO* 3.9 9.4 - - + +
153A VAL 2.9 15.1 + - - +
154A VAL* 3.4 17.7 - - + +
156A MET* 1.3 76.1 - - - +
158A LYS* 1.3 64.9 + - + +
160A ILE* 3.1 5.3 + - - +
161A LEU* 2.8 46.3 + - + +
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Residues in contact with LYS 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 VAL* 2.9 39.2 + - + +
155A GLY* 3.5 9.4 - - - +
157A LEU* 1.3 80.0 - - - +
159A SER* 1.4 64.0 + - - +
161A LEU* 3.1 22.4 + - + +
162A GLN* 3.0 23.1 + - - +
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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
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155A GLY 2.8 10.3 + - - -
156A MET 3.7 6.7 - - - -
158A LYS* 1.4 72.8 - - - +
160A ILE* 1.3 56.7 + - - +
162A GLN* 3.2 8.2 + - - +
163A ILE* 2.9 43.1 + - - +
266A LEU* 3.9 19.5 - - - -
269A ILE* 4.3 10.2 - - - +
270A TYR* 2.5 31.3 + - - -
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Residues in contact with ILE 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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133A GLY 4.2 2.0 - - - +
134A VAL* 3.8 38.1 - - + +
137A THR* 4.2 10.8 - - + -
138A PRO* 4.0 28.5 - - + -
156A MET* 2.9 22.7 + - + +
157A LEU* 3.6 4.5 - - - +
159A SER* 1.3 75.1 - - - +
161A LEU* 1.3 60.8 + - - +
163A ILE* 4.5 1.1 - - - +
164A VAL* 2.8 45.7 + - + +
165A VAL 3.3 0.9 + - - -
262A LEU* 4.5 12.3 - - + -
266A LEU* 3.9 29.8 - - + -
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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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134A VAL* 3.9 15.0 - - + -
135A PHE* 5.8 3.8 - - + -
157A LEU* 2.8 34.9 + - + +
158A LYS* 3.4 25.4 - - + +
160A ILE* 1.3 77.7 - - - +
162A GLN* 1.3 55.7 + - - +
165A VAL* 3.3 31.8 + - + +
166A ILE* 2.9 39.3 + - + +
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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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39A MET* 3.7 20.7 - - + +
158A LYS 3.0 12.6 + - - +
159A SER* 3.7 11.7 - - - +
160A ILE 3.2 0.2 - - - -
161A LEU* 1.3 76.1 - - - +
163A ILE* 1.3 67.9 + - + +
166A ILE* 4.1 16.5 - - + +
167A PRO* 3.1 22.5 - - - +
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Residues in contact with ILE 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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35A GLY* 4.3 12.6 - - - +
38A LEU* 3.8 29.2 - - + -
39A MET* 3.6 16.3 - - + -
42A MET* 3.6 10.9 - - + +
159A SER* 2.9 26.4 + - - +
162A GLN* 1.3 82.9 - - + +
164A VAL* 1.3 65.5 + - + +
167A PRO* 3.2 16.5 - - - +
262A LEU* 4.1 24.9 - - + -
265A THR* 4.2 24.9 - - + -
266A LEU* 5.1 2.2 - - + -
269A ILE* 5.1 5.2 - - + -
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Residues in contact with VAL 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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42A MET* 3.4 33.7 - - + -
130A THR* 3.4 22.0 - - + +
134A VAL* 4.8 1.3 - - + -
160A ILE* 2.8 25.0 + - + +
163A ILE* 1.3 90.8 - - + +
165A VAL* 1.3 72.3 + - + +
166A ILE 3.6 0.7 - - - -
167A PRO* 3.5 3.4 - - - +
168A ILE* 3.1 31.1 + - + +
259A ASN* 5.5 0.9 - - - +
262A LEU* 3.8 30.3 - - + -
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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