Contacts of the helix formed by residues 140 - 152 (chain w) in PDB entry 5OOM
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 CYS 140 (chain w).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100w VAL 3.6 14.4 - - - +
101w ASN* 4.1 19.3 - - - +
102w SER 3.7 1.1 - - - -
103w HIS* 5.3 2.5 - - + -
104w PHE* 4.5 1.2 - - - -
138w LEU* 2.9 7.2 + - - +
139w MET* 1.3 79.5 - - - +
141w PRO* 1.3 72.5 - - + +
142w GLN* 4.3 3.6 - - - -
143w GLU* 3.2 38.3 + - - +
144w ILE* 3.2 15.7 + - - +
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Residues in contact with PRO 141 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83w VAL* 4.0 9.0 - - + -
84w LEU* 6.2 1.3 - - + -
87w LEU* 3.8 28.5 - - + -
99w SER 3.2 25.6 - - - +
100w VAL* 3.3 14.8 - - + +
102w SER* 3.3 25.8 - - - +
104w PHE* 5.2 2.7 - - + -
140w CYS* 1.3 79.1 - - - +
142w GLN* 1.3 58.5 + - - -
144w ILE* 3.5 14.3 - - + +
145w VAL* 2.9 33.6 + - + +
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Residues in contact with GLN 142 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100w VAL* 2.9 42.4 + - + +
101w ASN* 3.6 18.5 + - - +
140w CYS* 3.2 5.0 - - - -
141w PRO* 1.3 77.5 - - - +
143w GLU* 1.3 57.8 + - - +
145w VAL* 3.4 4.1 + - - +
146w ASP* 2.9 49.9 + - - +
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Residues in contact with GLU 143 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137w LYS 5.1 1.3 - - - +
138w LEU* 3.7 30.3 - - + +
140w CYS* 3.2 26.0 + - - +
142w GLN* 1.3 79.3 - - - +
144w ILE* 1.3 57.4 + - - +
146w ASP* 4.4 8.1 - - - +
147w TYR* 2.9 49.7 + - - +
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Residues in contact with ILE 144 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83w VAL* 3.7 20.0 - - + -
87w LEU* 5.4 2.0 - - + -
104w PHE* 4.5 17.9 - - + -
118w ILE* 5.6 2.7 - - + -
119w ILE* 5.8 1.6 - - + -
122w MET* 3.8 21.5 - - + -
138w LEU* 3.7 37.0 - - + -
140w CYS 3.3 12.1 - - - +
141w PRO* 3.6 23.6 - - + +
142w GLN 3.1 0.6 - - - -
143w GLU* 1.3 75.2 - - - +
145w VAL* 1.3 59.7 - - - +
147w TYR* 3.3 0.8 + - - +
148w ILE* 2.9 55.0 + - + +
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Residues in contact with VAL 145 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76w LEU* 4.7 1.1 - - + +
79w ILE* 3.6 26.7 - - + +
80w GLN* 3.7 37.0 - - + +
83w VAL* 3.8 26.7 - - + -
100w VAL* 6.5 1.3 - - + -
141w PRO* 2.9 21.4 + - + +
142w GLN* 4.0 4.7 - - - +
144w ILE* 1.3 74.2 - - - +
146w ASP* 1.3 63.2 + - - +
149w ALA* 2.8 33.1 + - + +
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Residues in contact with ASP 146 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142w GLN* 2.9 41.0 + - - +
143w GLU* 4.1 10.9 + - - +
145w VAL* 1.3 82.3 - - - +
147w TYR* 1.3 55.3 - - - +
149w ALA* 3.3 7.0 - - - +
150w ASP* 2.9 33.1 + - - +
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Residues in contact with TYR 147 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130w ILE* 5.3 7.6 - - + -
131w PRO* 3.3 22.7 - - + +
134w ASP* 2.3 47.3 + - + -
138w LEU* 4.3 17.9 - - + -
143w GLU* 2.9 36.7 + - - +
144w ILE* 3.3 2.2 + - - +
146w ASP* 1.3 75.7 - - - +
148w ILE* 1.3 61.1 + - + +
150w ASP* 2.9 18.6 - - - +
151w LYS* 2.7 55.1 + - + +
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Residues in contact with ILE 148 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79w ILE* 4.5 1.8 - - + -
83w VAL* 4.1 1.1 - - + -
122w MET* 4.5 3.1 - - + -
126w PHE* 3.6 52.5 - - + +
127w GLY* 5.5 3.6 - - - -
129w GLU* 4.4 10.1 - - - +
130w ILE* 4.9 16.8 - - + -
144w ILE* 2.9 34.8 + - + +
145w VAL 4.5 1.3 - - - +
147w TYR* 1.3 83.0 - - + +
149w ALA* 1.3 57.9 + - - +
151w LYS* 3.7 5.8 - - + -
152w LYS* 3.0 48.5 + - + -
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Residues in contact with ALA 149 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76w LEU* 4.6 13.9 - - + +
79w ILE* 3.9 22.4 - - + +
145w VAL* 2.8 24.7 + - + +
146w ASP* 3.3 10.8 - - - +
147w TYR 3.2 0.4 - - - -
148w ILE* 1.3 78.4 - - - +
150w ASP* 1.3 58.6 + - - +
152w LYS* 3.0 19.1 + - - +
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Residues in contact with ASP 150 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146w ASP 2.9 15.0 + - - +
147w TYR* 2.9 34.8 - - - +
149w ALA* 1.3 72.9 - - - +
151w LYS* 1.3 65.0 + - - +
152w LYS 3.2 7.3 + - - +
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Residues in contact with LYS 151 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129w GLU* 3.8 49.6 + - + +
131w PRO* 4.3 10.6 - - - +
147w TYR* 2.7 52.5 + - + +
148w ILE* 3.7 10.8 - - + +
149w ALA 3.3 0.2 - - - -
150w ASP* 1.3 79.6 + - - +
152w LYS* 1.3 58.8 + - - +
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Residues in contact with LYS 152 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74w LEU* 3.2 33.7 - - + +
79w ILE* 3.3 20.9 - - - +
126w PHE* 3.0 35.9 - - + -
129w GLU* 3.9 19.1 - - - +
148w ILE* 3.0 31.2 + - + +
149w ALA 3.0 18.0 - - - +
150w ASP* 3.5 8.9 - - - +
151w LYS* 1.3 76.7 - - - +
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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