Contacts of the helix formed by residues 132 - 146 (chain C) in PDB entry 6P7B
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 132 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ASP* 3.4 25.1 - - - +
11C LYS* 6.4 0.2 - - - -
12C ASN* 3.9 30.3 + - - +
14C ALA* 3.9 7.6 - - + -
34C LYS* 3.4 35.0 - - - +
129C LYS* 4.9 3.5 - - - +
130C LEU* 2.7 11.9 + - - +
131C ASP* 1.3 73.3 + - - +
133C ILE* 1.3 84.8 + - - +
134C ALA 3.2 0.9 - - - -
135C ASN 3.1 3.5 + - - +
136C SER* 3.0 19.6 + - - -
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Residues in contact with ILE 133 (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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14C ALA* 3.9 15.9 - - + -
32C ILE* 4.3 29.8 - - + +
33C GLU 4.1 17.3 - - - +
34C LYS* 4.5 6.1 - - + +
109C PHE* 4.6 15.0 - - + -
127C TYR* 5.2 15.7 - - + -
129C LYS 3.8 17.7 - - - +
130C LEU* 3.6 13.9 - - + +
132C ASP* 1.3 86.5 + - - +
134C ALA* 1.3 62.7 + - - +
136C SER* 2.8 22.0 + - - +
137C PHE* 2.9 20.0 + - - +
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Residues in contact with ALA 134 (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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105C SER* 5.4 1.3 - - - -
106C ILE* 4.0 26.0 - - + -
109C PHE* 3.8 24.9 - - + -
130C LEU* 2.8 24.3 + - + +
131C ASP* 4.6 2.2 - - - -
133C ILE* 1.3 79.6 - - - +
135C ASN* 1.3 57.0 + - - +
137C PHE* 3.8 0.9 - - - +
138C ASN* 2.9 42.0 + - - +
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Residues in contact with ASN 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ASP* 3.4 15.9 + - - +
60C GLU* 2.9 39.4 + - - +
92C THR* 5.7 0.2 + - - -
101C ARG* 3.5 26.7 + - - +
105C SER* 5.6 3.1 - - - -
131C ASP 4.5 8.0 - - - +
132C ASP* 3.1 12.0 + - - +
134C ALA* 1.3 77.6 - - - +
136C SER* 1.3 63.5 + - - +
138C ASN* 3.3 8.5 + - - +
139C LEU* 3.0 24.6 + - - +
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Residues in contact with SER 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C SER* 2.9 33.0 + - - -
6C VAL 4.7 1.6 - - - -
7C ASP* 3.7 28.6 - - - +
14C ALA* 4.1 7.6 - - - +
15C TYR 4.2 2.8 - - - -
16C ALA* 4.2 11.2 + - - +
32C ILE* 4.9 0.5 - - - +
132C ASP 3.0 10.0 + - - -
133C ILE* 2.8 28.9 + - - +
135C ASN* 1.3 76.0 - - - +
137C PHE* 1.3 55.8 + - - +
139C LEU* 3.3 5.6 + - - +
140C GLY 2.9 16.8 + - - -
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Residues in contact with PHE 137 (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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16C ALA* 4.4 2.2 - - - -
18C PHE* 3.4 38.7 - + - -
29C LEU* 4.7 10.5 - - + -
32C ILE* 4.3 17.3 - - + -
108C VAL 5.5 0.2 - - - -
109C PHE* 3.5 34.8 - + + -
112C LYS* 4.1 6.7 - - + -
113C ILE* 4.2 19.3 - - + -
116C TYR* 3.6 28.3 - + + -
133C ILE 2.9 19.0 + - - +
134C ALA 3.8 2.0 - - - +
136C SER* 1.3 76.0 + - - +
138C ASN* 1.3 66.3 + - - +
140C GLY* 3.4 0.7 + - - -
141C LEU* 2.9 50.8 + - + +
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Residues in contact with ASN 138 (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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92C THR* 4.6 11.1 - - - +
93C PHE* 5.3 5.4 - - + -
101C ARG* 6.0 1.1 - - - +
105C SER* 3.0 52.4 + - - +
108C VAL* 4.2 13.0 - - + +
109C PHE* 3.7 17.1 + - - +
134C ALA* 2.9 27.0 + - - +
135C ASN* 3.8 7.2 + - - +
137C PHE* 1.3 78.0 - - - +
139C LEU* 1.3 60.4 + - - +
141C LEU* 3.8 4.3 - - - +
142C SER* 2.9 31.4 + - - -
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Residues in contact with LEU 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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5C SER* 4.7 0.2 - - - -
6C VAL 3.9 18.4 - - - +
58C ILE* 3.7 21.1 - - + +
59C LEU 3.6 7.0 - - - -
60C GLU* 3.6 43.7 - - + +
89C ARG* 3.7 32.1 + - + +
90C ASN 4.5 3.8 - - - +
91C PRO* 5.4 0.4 - - + -
92C THR* 3.9 17.2 - - + +
135C ASN* 3.0 19.8 + - - +
136C SER* 3.6 4.9 - - - +
138C ASN* 1.3 76.1 - - - +
140C GLY* 1.3 63.5 + - - +
142C SER* 3.3 3.3 + - - -
143C TYR* 3.0 22.5 + - - +
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Residues in contact with GLY 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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3C ILE* 5.4 3.0 - - - +
5C SER* 3.6 24.4 - - - -
18C PHE* 4.1 10.3 - - - -
58C ILE* 5.3 2.0 - - - -
136C SER 2.9 11.7 + - - -
137C PHE 3.8 1.6 - - - -
139C LEU* 1.3 76.3 - - - +
141C LEU* 1.3 55.8 + - - +
143C TYR* 3.2 9.3 + - - +
144C MET* 2.9 34.4 + - - +
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Residues in contact with LEU 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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18C PHE* 4.6 3.9 - - + -
27C ILE* 4.9 7.9 - - + -
108C VAL* 5.4 3.1 - - + -
112C LYS* 3.7 31.0 - - + -
116C TYR* 3.5 35.0 - - + +
137C PHE* 2.9 50.1 + - + +
138C ASN* 4.0 5.6 - - - +
140C GLY* 1.3 71.7 - - - +
142C SER* 1.3 61.3 + - - +
144C MET* 3.1 19.6 + - + +
145C GLU* 2.9 41.0 + - + +
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Residues in contact with SER 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ARG* 2.9 20.3 + - - -
92C THR* 3.7 22.4 - - - +
138C ASN 2.9 18.3 + - - -
139C LEU 3.3 4.5 + - - -
141C LEU* 1.3 74.6 - - - +
143C TYR* 1.3 63.4 + - - +
145C GLU* 3.3 15.0 + - - +
146C SER* 2.9 22.9 + - - -
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Residues in contact with TYR 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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1C MET* 5.2 1.8 - - + +
3C ILE* 3.8 32.8 - - + -
56C VAL* 4.0 20.0 - - + +
58C ILE* 3.6 28.7 - - + -
87C ILE* 3.6 33.3 - - + +
89C ARG* 4.0 19.8 - - - +
139C LEU 3.0 13.0 + - - +
140C GLY 3.2 7.2 + - - +
142C SER* 1.3 77.2 - - - +
144C MET* 1.3 56.4 + - - +
146C SER* 2.7 28.8 + - - -
147C LEU* 2.9 41.0 + - + +
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Residues in contact with MET 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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3C ILE* 3.4 36.6 - - + -
18C PHE* 4.8 10.5 - - + -
20C TYR* 3.4 43.5 - - + -
27C ILE* 3.5 30.1 - - + -
140C GLY 2.9 29.9 + - - +
141C LEU* 3.1 24.4 + - + +
143C TYR* 1.3 76.3 - - - +
145C GLU* 1.3 62.4 + - + +
147C LEU* 3.2 20.9 + - + +
148C LEU* 4.1 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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112C LYS* 4.1 23.4 + - - +
141C LEU* 2.9 29.5 + - + +
142C SER* 3.7 12.2 + - - +
144C MET* 1.3 78.2 - - + +
146C SER* 1.3 59.8 + - - +
147C LEU 3.1 1.3 + - - -
148C LEU* 3.9 11.8 + - - +
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Residues in contact with SER 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ARG* 4.1 13.2 + - - -
142C SER 2.9 11.1 + - - -
143C TYR* 2.7 39.8 + - - -
145C GLU* 1.3 74.3 - - - +
147C LEU* 1.3 62.6 + - - +
148C LEU* 4.7 3.3 - - - -
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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
------------------------------------------------------------
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