Contacts of the helix formed by residues 138 - 149 (chain C) in PDB entry 2P2L
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 138 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120C ARG* 3.7 8.7 - - - +
135C THR* 6.0 1.1 - - + +
136C PRO 4.1 6.7 - - - +
137C ILE* 1.3 79.2 - - - +
139C TYR* 1.3 65.4 + - - +
140C PRO* 3.5 14.0 - - - +
141C GLN* 2.9 38.8 + - - +
142C GLY* 3.0 19.4 + - - -
156C GLU* 4.2 1.5 - - - +
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Residues in contact with TYR 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C ARG* 3.5 11.6 - - - +
138C THR* 1.3 71.1 - - - +
140C PRO* 1.3 76.8 - - + +
142C GLY* 3.1 2.4 + - - -
143C LEU* 2.9 46.9 + - + +
154C TYR* 3.5 41.0 + + - -
155C LEU* 5.6 0.2 - - - -
156C GLU* 3.4 31.0 - - + +
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Residues in contact with PRO 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C THR* 3.5 15.0 - - - +
139C TYR* 1.3 97.8 - - + +
141C GLN* 1.3 56.2 + - + +
143C LEU* 3.4 9.1 + - + +
144C ALA* 3.0 30.2 + - - +
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Residues in contact with GLN 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C PHE* 3.4 20.4 - - + -
135C THR* 5.7 4.1 - - - +
136C PRO 4.1 2.3 - - - +
137C ILE* 3.4 26.5 - - + +
138C THR* 2.9 43.4 + - - +
140C PRO* 1.3 74.1 - - + +
142C GLY* 1.3 61.5 + - - +
144C ALA* 3.4 6.7 + - - +
145C MET* 3.0 24.1 + - - +
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Residues in contact with GLY 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C PHE* 4.0 15.0 - - - -
112C LEU* 3.5 9.9 - - - +
137C ILE* 4.1 1.3 - - - +
138C THR 3.0 11.5 + - - -
139C TYR 3.1 0.4 + - - -
141C GLN* 1.3 75.8 - - - +
143C LEU* 1.3 56.8 + - - +
145C MET 3.3 1.0 + - - -
146C ALA* 2.9 26.0 + - - +
154C TYR* 3.5 32.1 - - - -
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Residues in contact with LEU 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C TYR* 2.9 43.5 + - + +
140C PRO* 3.7 8.3 - - + +
142C GLY* 1.3 75.0 - - - +
144C ALA* 1.3 57.9 + - - +
146C ALA* 3.2 5.6 + - + +
147C LYS* 3.0 28.0 + - + +
154C TYR* 3.6 24.4 - - + +
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Residues in contact with ALA 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C PRO 3.0 18.1 + - - +
141C GLN* 3.6 8.1 - - - +
143C LEU* 1.3 73.8 - - - +
145C MET* 1.3 59.1 + - - +
147C LYS* 3.4 9.7 + - - +
148C GLU* 3.0 29.0 + - - +
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Residues in contact with MET 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C PHE* 3.6 64.2 - - + +
93C VAL* 3.7 25.6 - - + -
94C ARG* 3.5 56.3 - - + +
112C LEU* 3.9 4.7 - - + -
141C GLN 3.0 7.0 + - - +
142C GLY 3.6 4.3 - - - +
144C ALA* 1.3 71.2 - - - +
146C ALA* 1.3 66.8 + - - +
148C GLU* 3.1 14.5 + - - +
149C ILE* 3.1 24.7 + - - +
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Residues in contact with ALA 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C LEU* 3.6 13.4 - - + +
142C GLY 2.9 15.0 + - - +
143C LEU* 3.2 11.0 + - + +
145C MET* 1.3 76.5 - - - +
147C LYS* 1.3 60.6 + - - +
149C ILE* 3.5 1.7 + - - -
150C GLY 3.0 4.0 + - - -
151C ALA* 2.8 50.2 + - + +
153C LYS 4.3 2.9 - - - +
154C TYR* 3.8 22.4 - - + +
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Residues in contact with LYS 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C LEU* 3.0 12.7 + - + +
144C ALA* 3.6 13.2 - - - +
145C MET 3.3 0.2 - - - -
146C ALA* 1.3 75.8 - - - +
148C GLU* 1.3 64.4 + - - +
150C GLY* 3.2 13.2 + - - -
151C ALA 5.3 1.8 - - - -
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Residues in contact with GLU 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ARG* 2.7 53.7 + - - +
98C TYR* 4.7 7.2 + - + -
144C ALA 3.0 14.1 + - - +
145C MET* 3.4 18.7 - - - +
147C LYS* 1.3 77.0 - - - +
149C ILE* 1.3 60.8 + - + +
150C GLY 3.6 0.3 + - - -
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Residues in contact with ILE 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C ILE* 4.3 9.2 - - + -
93C VAL* 3.9 23.8 - - + +
94C ARG* 5.0 3.1 - - - -
98C TYR* 3.3 57.9 + - + -
110C ILE* 4.2 28.5 - - + +
112C LEU* 4.4 11.2 - - + -
145C MET* 3.1 35.9 + - - +
146C ALA 3.6 7.2 - - - +
148C GLU* 1.3 81.8 - - + +
150C GLY* 1.3 60.2 + - - +
151C ALA* 3.9 9.9 - - + +
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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