Contacts of the helix formed by residues 139 - 149 (chain C) in PDB entry 6P59
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 ALA 139 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C ASP 3.9 6.3 + - - +
137C ALA* 3.1 10.6 - - + +
138C LEU* 1.3 74.1 - - - +
140C GLN* 1.3 55.8 + - - +
141C GLN 3.2 1.6 - - - -
142C ALA* 3.1 10.7 + - + +
143C PHE* 2.6 35.0 + - - +
92F TYR* 5.5 0.3 - - - -
94F ASP* 3.5 29.6 - - + +
96F LYS* 6.0 0.2 - - - -
97F CYS* 4.8 2.5 - - - -
101F TYR* 4.5 19.5 - - + -
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Residues in contact with GLN 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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8C GLN* 3.3 27.1 + - + +
105C GLY* 4.5 4.9 - - - +
132C ALA* 3.5 23.2 + - - +
135C GLU* 3.7 19.0 + - - +
136C ASP 4.3 2.1 - - - +
138C LEU* 3.2 33.9 + - + +
139C ALA* 1.3 83.5 + - - +
141C GLN* 1.3 62.5 + - + +
143C PHE* 3.6 12.2 - - - +
144C GLU* 3.1 24.6 + - - +
101F TYR* 3.4 30.1 - - - +
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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
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6C PRO* 5.0 6.5 - - - +
7C ASP* 4.5 26.0 + - - +
138C LEU* 3.5 44.1 + - + +
139C ALA 3.2 0.4 - - - -
140C GLN* 1.3 80.6 - - + +
142C ALA* 1.3 62.2 + - - +
144C GLU* 3.7 6.8 + - - +
145C GLU* 3.3 19.6 + - - +
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Residues in contact with ALA 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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138C LEU 3.8 3.3 + - - +
139C ALA* 3.1 21.9 + - + +
141C GLN* 1.3 76.3 - - - +
143C PHE* 1.3 64.4 + - - +
145C GLU* 3.4 15.7 + - - +
146C ALA* 3.3 19.8 + - - +
92F TYR* 5.0 2.5 + - - -
94F ASP* 5.2 4.0 - - - +
96F LYS* 5.6 6.3 - - - +
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Residues in contact with PHE 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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11C LYS* 5.7 0.7 - - - -
104C ASN* 3.8 27.6 - - - -
105C GLY* 3.8 13.2 - - - -
139C ALA 2.6 20.7 + - - +
140C GLN* 3.6 11.9 - - - +
142C ALA* 1.3 71.0 - - - +
144C GLU* 1.3 77.0 + - - +
146C ALA* 3.1 14.9 + - + +
147C ARG* 3.2 18.7 + - + +
92F TYR* 3.4 60.3 + + + -
101F TYR* 4.4 5.4 - + + -
103F THR* 4.2 2.0 - - + -
105F ILE* 3.8 20.0 - - + -
109F VAL* 4.6 7.9 - - + -
113F LEU* 3.8 20.4 - - + +
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Residues in contact with GLU 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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11C LYS* 2.8 35.5 + - - +
140C GLN 3.1 17.8 + - - +
141C GLN* 3.7 7.8 + - - +
142C ALA 3.4 0.4 - - - -
143C PHE* 1.3 82.7 - - + +
145C GLU* 1.3 62.8 + - - +
147C ARG* 3.3 24.3 + - - -
148C ARG* 3.3 52.3 + - - +
148F GLN* 5.1 3.3 + - - -
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Residues in contact with GLU 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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141C GLN 3.3 15.5 + - - +
142C ALA* 3.4 17.4 - - - +
143C PHE 3.1 0.6 - - - -
144C GLU* 1.3 76.8 - - - +
146C ALA* 1.3 61.9 + - - +
148C ARG* 3.1 7.4 + - - +
149C ARG* 3.1 22.9 + - + +
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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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142C ALA 3.3 8.2 + - - +
143C PHE* 3.1 11.2 + - - +
145C GLU* 1.3 80.8 + - - +
147C ARG* 1.3 61.4 + - - +
148C ARG 3.6 0.2 + - - -
149C ARG* 3.6 20.9 + - - +
62F LEU* 6.6 0.2 - - + -
92F TYR* 5.1 9.9 - - + +
113F LEU* 3.4 24.1 - - + +
116F LYS* 3.9 11.5 - - + +
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Residues in contact with ARG 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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11C LYS* 4.0 25.1 - - - +
17C PHE 4.5 1.4 + - - -
19C ARG* 4.0 5.9 - - - +
104C ASN* 3.7 32.5 + - - +
143C PHE* 3.2 21.4 + - + +
144C GLU* 3.6 27.2 + - - +
145C GLU 3.1 1.0 - - - -
146C ALA* 1.3 77.5 - - - +
148C ARG* 1.3 57.6 + - - +
149C ARG 3.5 3.4 + - - +
109F VAL* 3.6 30.1 - - + +
112F SER* 4.6 10.1 + - - +
113F LEU* 4.0 10.9 - - + +
116F LYS* 4.9 0.6 - - - +
147F ASP* 2.9 38.8 + - - +
148F GLN* 3.6 26.6 - - - +
87Z SER* 4.1 13.7 + - - -
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Residues in contact with ARG 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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144C GLU* 3.3 38.8 + - - +
145C GLU* 3.1 6.2 + - - +
147C ARG* 1.3 75.3 - - - +
149C ARG* 1.3 66.2 + - - +
150C THR* 3.8 9.4 + - - +
148F GLN* 4.1 27.1 + - - +
80Z LYS* 5.5 5.5 - - - +
84Z THR* 5.0 9.7 + - - -
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Residues in contact with ARG 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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145C GLU* 3.1 16.2 + - + +
146C ALA* 3.8 15.0 - - - +
147C ARG 3.5 2.3 - - - +
148C ARG* 1.3 83.2 - - - +
150C THR* 1.3 76.2 + - - +
151C ARG* 4.1 11.1 - - - +
154C GLU* 5.2 7.9 - - - +
155C ASP* 5.8 0.8 + - - -
116F LYS* 3.1 64.7 + - + +
117F ILE* 4.6 10.1 - - - +
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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