Contacts of the helix formed by residues 138 - 146 (chain C) in PDB entry 7CR3
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 ASN 138 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ASN* 4.1 9.4 + - - +
150B CYS* 3.1 22.6 - - - -
98C ASN 5.4 0.3 - - - +
99C GLY* 3.3 16.0 - - - +
100C TYR* 3.8 22.2 + - + -
136C GLN 3.6 4.4 + - - +
137C VAL* 1.3 71.0 - - - +
139C TYR* 1.3 66.3 + - - +
140C GLU* 2.9 43.0 + - - +
141C GLU* 2.8 45.2 + - - +
142C PHE 3.7 0.2 + - - -
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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
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87C ARG* 3.5 47.5 + - + +
90C PHE* 3.5 50.0 - + + -
91C ARG* 5.2 7.1 - - - +
94C ASP* 3.7 14.9 + - + -
99C GLY* 3.4 34.8 - - - -
101C ILE* 5.3 5.2 - - + -
137C VAL* 3.3 15.3 + - + +
138C ASN* 1.3 72.5 - - - +
140C GLU* 1.3 74.5 + - - +
142C PHE* 3.1 7.1 + - - +
143C VAL* 3.0 30.7 + - + +
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Residues in contact with GLU 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ASN* 4.9 0.9 - - - +
82B TYR* 3.5 23.7 + - - -
83B ASN* 5.1 4.2 + - - -
150B CYS* 3.3 14.6 - - - -
151B CYS* 5.9 0.2 - - - -
87C ARG* 4.5 14.4 - - - +
98C ASN 5.8 0.3 - - - +
99C GLY* 5.8 0.6 - - - -
138C ASN* 2.9 36.1 + - - +
139C TYR* 1.3 95.5 + - + +
141C GLU* 1.3 60.6 + - - +
143C VAL* 3.6 8.7 - - - -
144C GLN* 2.9 50.1 + - - +
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Residues in contact with GLU 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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150B CYS* 4.2 19.5 - - - +
152B CYS* 4.4 6.4 - - + +
129C ALA 2.9 23.9 - - - +
130C ASP* 3.8 6.4 - - - +
131C ILE* 3.1 32.4 + - + +
132C ASP* 4.6 4.6 - - - +
138C ASN* 2.8 40.2 + - + +
140C GLU* 1.3 80.7 - - - +
142C PHE* 1.3 58.8 + - - +
144C GLN* 3.8 3.4 - - - +
145C MET* 3.0 30.5 + - - +
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Residues in contact with PHE 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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340B ILE* 5.5 6.5 - - + -
344B TRP* 4.0 19.1 - + - -
86C ILE* 6.0 5.2 - - + -
90C PHE* 4.2 23.1 - + - -
125C MET* 4.7 4.5 - - + -
128C GLU* 3.3 31.6 - - + -
129C ALA* 3.4 33.0 - - + +
131C ILE* 5.6 0.2 - - - -
138C ASN 4.7 0.2 - - - +
139C TYR* 3.1 13.5 + - - +
141C GLU* 1.3 83.1 - - + +
143C VAL* 1.3 58.5 - - + +
145C MET* 3.6 7.5 - - + +
146C MET* 3.0 71.3 + - + +
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Residues in contact with VAL 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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83C GLU* 3.2 25.0 - - - +
86C ILE* 3.5 33.4 - - + -
87C ARG* 3.6 16.4 - - + -
90C PHE* 3.6 27.1 - - + -
139C TYR 3.0 15.5 + - - +
140C GLU* 3.3 17.3 - - - +
142C PHE* 1.3 77.4 - - + +
144C GLN* 1.3 62.9 + - + +
147C THR* 3.0 34.9 + - - -
148C ALA 3.4 1.7 + - - -
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Residues in contact with GLN 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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82B TYR* 5.5 3.1 + - - -
151B CYS* 2.7 48.0 - - - +
152B CYS* 3.4 27.4 + - + +
153B ARG* 4.2 20.9 + - + +
83C GLU* 3.5 21.3 - - - +
87C ARG* 4.5 9.7 - - - +
140C GLU* 2.9 37.7 + - - +
141C GLU 4.3 0.3 + - - -
143C VAL* 1.3 75.0 - - + +
145C MET* 1.3 60.3 + - - +
148C ALA* 3.9 16.0 - - - +
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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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152B CYS* 3.9 16.4 - - - -
347B TYR* 5.6 0.7 - - - -
353B ARG* 4.9 5.4 - - - +
128C GLU* 3.2 47.3 - - - +
131C ILE* 3.8 16.6 - - + -
141C GLU 3.0 19.6 + - - +
142C PHE* 3.6 4.9 - - + +
143C VAL 3.2 0.2 - - - -
144C GLN* 1.3 80.7 - - - +
146C MET* 1.3 86.6 + - + +
148C ALA 4.6 6.2 + - - +
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Residues in contact with MET 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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343B ALA* 5.4 1.1 - - + +
344B TRP* 4.5 3.4 - - + -
347B TYR* 3.4 63.0 - - + -
76C LYS* 6.0 0.3 + - - -
77C MET* 3.8 26.0 - - + +
128C GLU* 3.9 3.8 - - - -
142C PHE* 3.0 51.6 + - + +
145C MET* 1.3 90.4 - - - +
147C THR* 1.3 69.4 + - - +
148C ALA 2.9 13.2 - - - +
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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