Contacts of the helix formed by residues 142 - 153 (chain H) in PDB entry 6V3O
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 142 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208G ASP* 5.7 1.3 - - - +
122H ARG* 2.6 45.1 + - - +
140H GLU* 4.0 0.4 + - - -
141H SER* 1.3 72.5 - - - +
143H ILE* 1.3 64.9 + - + +
144H GLU* 3.1 9.9 + - - +
145H GLU* 2.6 46.0 + - - +
146H THR* 2.8 26.4 + - - -
692H GLN* 3.3 27.8 - - - +
696H ALA* 4.9 0.4 - - - -
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Residues in contact with ILE 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142H ASP* 1.3 76.9 - - + +
144H GLU* 1.3 65.9 + - + +
146H THR* 3.7 4.5 - - - -
147H LEU* 3.1 41.7 + - + +
165H LEU* 5.2 3.6 - - + -
259H PHE* 4.6 8.3 - - + -
262H ARG* 4.2 25.6 - - + +
263H VAL* 4.7 11.9 - - + -
266H ALA* 4.2 11.2 - - + -
692H GLN* 3.2 24.2 + - + +
695H THR* 3.8 31.0 - - + +
696H ALA* 3.8 21.3 - - + +
699H LEU* 4.8 12.8 - - + -
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Residues in contact with GLU 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208G ASP* 2.7 35.9 - - - +
142H ASP* 3.1 9.2 + - - +
143H ILE* 1.3 83.8 - - + +
145H GLU* 1.3 58.4 + - + +
147H LEU* 3.4 3.2 + - - +
148H LYS* 3.0 66.3 + - + +
262H ARG* 6.3 0.2 - - - -
266H ALA* 4.0 27.5 + - + +
269H ASN* 2.9 33.3 - - + +
270H ILE* 5.6 0.9 - - + -
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Residues in contact with GLU 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H ARG* 3.2 23.7 + - - -
127H LYS* 3.9 18.1 + - - +
140H GLU 4.0 0.5 - - - +
141H SER* 3.2 22.0 - - - +
142H ASP* 2.6 35.7 + - - +
144H GLU* 1.3 73.2 - - + +
146H THR* 1.3 60.5 + - - +
148H LYS* 3.3 9.9 + - + +
149H ARG* 2.9 26.9 + - - +
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Residues in contact with THR 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141H SER* 3.0 14.9 + - - -
142H ASP 2.8 18.3 + - - -
143H ILE* 3.7 5.6 - - - -
145H GLU* 1.3 77.0 - - - +
147H LEU* 1.3 65.3 + - + +
149H ARG* 3.2 11.4 + - - +
150H LEU* 3.0 28.4 + - + +
653H HIS* 4.6 1.9 + - - -
696H ALA* 3.6 29.1 - - + +
699H LEU* 5.2 1.6 - - + -
700H GLU* 3.5 38.9 + - + +
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Residues in contact with LEU 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143H ILE* 3.1 22.7 + - + +
144H GLU 3.9 3.4 - - - +
145H GLU 3.4 0.2 - - - -
146H THR* 1.3 76.8 - - - +
148H LYS* 1.3 61.7 + - - +
150H LEU* 3.1 7.3 + - + +
151H VAL* 3.0 30.5 + - - +
161H VAL* 3.6 15.7 - - + -
165H LEU* 4.7 6.3 - - + -
263H VAL* 5.3 1.3 - - + +
266H ALA* 3.7 32.3 - - + +
267H LEU* 4.4 11.2 - - + -
270H ILE* 4.1 30.3 - - + -
699H LEU* 3.4 33.9 - - + -
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Residues in contact with LYS 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144H GLU* 3.0 51.8 + - + +
145H GLU* 3.7 9.6 - - + +
146H THR 3.3 0.2 - - - -
147H LEU* 1.3 76.8 - - - +
149H ARG* 1.3 62.1 + - - +
151H VAL* 3.4 5.4 + - - +
152H SER* 3.1 29.0 + - - -
269H ASN* 4.3 15.4 - - - +
270H ILE* 4.4 11.9 - - + -
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Residues in contact with ARG 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H LYS* 4.8 4.8 - - - +
134H GLU* 3.1 26.6 + - - -
141H SER* 3.3 22.5 + - - -
145H GLU* 2.9 15.8 + - - +
146H THR* 3.5 18.6 + - - +
148H LYS* 1.3 77.0 - - - +
150H LEU* 1.3 57.6 + - + +
153H GLU* 2.9 66.9 + - + +
154H VAL* 3.2 12.4 + - + +
700H GLU* 2.7 45.8 + - - -
704H HIS* 4.6 11.2 - - - -
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Residues in contact with LEU 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146H THR* 3.0 23.2 + - + +
147H LEU* 3.1 15.7 + - + +
149H ARG* 1.3 79.7 - - + +
151H VAL* 1.3 58.8 + - - +
154H VAL* 3.1 22.2 - - + +
155H GLY 3.1 8.1 + - - -
156H LYS* 3.0 24.5 + - + -
161H VAL* 4.2 13.5 - - + -
699H LEU* 4.1 21.1 - - + -
700H GLU* 4.4 20.9 - - + +
703H MET* 3.6 46.2 - - + -
704H HIS* 4.6 7.2 - - + +
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Residues in contact with VAL 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147H LEU 3.0 19.6 + - - +
148H LYS* 4.1 3.6 - - - +
150H LEU* 1.3 77.3 - - - +
152H SER* 1.3 61.5 + - - +
155H GLY* 3.3 19.8 - - - -
156H LYS 3.2 19.0 - - - +
157H SER* 4.8 0.2 - - - -
158H PRO* 3.9 23.3 - - + -
161H VAL* 4.5 10.8 - - + -
270H ILE* 4.5 28.3 - - + +
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Residues in contact with SER 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H LYS 3.1 13.9 + - - -
151H VAL* 1.3 79.7 - - - +
153H GLU* 1.3 73.1 + - - +
155H GLY* 4.4 2.2 - - - -
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Residues in contact with GLU 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149H ARG* 2.9 48.0 + - + +
152H SER* 1.3 89.2 + - - +
154H VAL* 1.3 64.4 + - + +
155H GLY* 3.4 0.6 - - - -
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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