Contacts of the helix formed by residues 124 - 135 (chain C) in PDB entry 2I62
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 LYS 124 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116C CYS* 3.7 4.4 - - - -
121C ASN* 3.1 24.5 - - - +
122C ARG 3.8 13.0 - - - +
123C MET* 1.3 83.0 - - - +
125C GLY* 1.3 66.8 + - - +
126C PRO* 3.4 14.1 - - + -
127C GLU* 3.4 8.4 + - + +
128C LYS 3.3 15.6 + - - -
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Residues in contact with GLY 125 (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 VAL* 3.6 23.1 - - - -
113C THR* 5.2 8.2 + - - +
116C CYS* 3.9 6.5 - - - +
124C LYS* 1.3 71.8 - - - +
126C PRO* 1.4 62.8 - - - +
128C LYS* 3.2 2.3 + - - +
129C GLU* 2.9 37.9 + - - +
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Residues in contact with PRO 126 (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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124C LYS* 3.4 14.8 - - + -
125C GLY* 1.4 89.0 - - - +
127C GLU* 1.3 56.4 + - - +
129C GLU* 3.4 6.9 + - + +
130C GLU* 3.0 30.7 + - - +
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Residues in contact with GLU 127 (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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224A ASP* 5.5 3.1 - - - +
227A GLU* 4.8 9.9 - - - +
228A GLU* 5.9 1.8 - - - +
123C MET* 3.6 37.4 - - + +
124C LYS* 3.4 12.3 + - + +
126C PRO* 1.3 78.9 - - - +
128C LYS* 1.3 57.4 + - - +
130C GLU* 3.4 5.1 + - - +
131C LYS* 3.0 30.9 + - + +
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Residues in contact with LYS 128 (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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73C LEU* 2.9 47.5 + - + +
76C CYS* 4.1 3.8 - - - -
77C GLU* 2.7 25.1 + - - +
112C VAL* 3.9 9.0 - - + -
115C VAL* 4.0 13.2 - - - -
116C CYS* 3.7 26.5 - - - -
119C GLU* 2.6 37.9 + - - -
123C MET* 3.8 10.4 - - - -
124C LYS 3.3 2.6 + - - -
125C GLY 3.2 8.6 + - - +
127C GLU* 1.3 79.6 - - - +
129C GLU* 1.3 57.7 + - - +
131C LYS* 3.2 5.1 + - - +
132C LEU* 2.9 28.4 + - - +
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Residues in contact with GLU 129 (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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73C LEU* 5.5 1.3 - - + -
98C TRP* 4.0 20.1 + - + -
108C TRP 5.3 0.3 + - - -
109C SER* 4.3 16.3 + - - -
112C VAL* 3.4 32.6 - - + +
125C GLY 2.9 24.6 + - - +
126C PRO* 3.8 6.5 - - + +
128C LYS* 1.3 69.4 - - - +
130C GLU* 1.3 62.2 + - - +
132C LEU* 3.8 4.5 - - - +
133C ARG* 2.9 65.7 + - - +
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Residues in contact with GLU 130 (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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245B SER* 3.2 37.4 + - - -
101C LYS* 3.6 20.8 + - - -
126C PRO 3.0 17.1 + - - +
127C GLU* 4.0 4.7 - - - +
129C GLU* 1.3 76.5 - - - +
131C LYS* 1.3 57.3 + - - +
133C ARG* 3.9 9.1 + - - +
134C ARG* 2.9 53.6 + - - +
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Residues in contact with LYS 131 (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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224A ASP* 2.8 36.0 + - - +
228A GLU* 4.6 1.0 + - - -
76C CYS* 3.2 27.4 - - - +
77C GLU* 2.4 51.3 + - - +
123C MET* 4.6 8.7 - - + +
127C GLU* 3.0 19.3 + - + +
128C LYS* 3.5 6.7 - - - +
130C GLU* 1.3 77.7 - - - +
132C LEU* 1.3 56.4 + - - +
134C ARG* 3.7 6.5 - - - +
135C ALA* 3.0 29.4 + - + +
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Residues in contact with LEU 132 (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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69C ILE* 4.0 25.1 - - + +
72C LEU* 3.7 23.3 - - + +
73C LEU* 3.8 24.9 - - + -
76C CYS* 3.8 27.5 - - + -
82C ILE* 4.0 7.0 - - + -
98C TRP* 3.8 19.7 - - + -
128C LYS 2.9 16.8 + - - +
129C GLU* 3.8 4.3 - - - +
131C LYS* 1.3 74.9 - - - +
133C ARG* 1.3 67.4 + - - +
135C ALA* 3.0 11.7 + - - +
136C ILE* 3.2 34.5 + - + +
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Residues in contact with ARG 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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249B ASN* 5.0 2.3 + - - +
98C TRP* 2.8 71.4 + - + +
99C LEU* 3.3 37.8 + - + +
101C LYS* 3.5 43.3 - - - +
105C ALA* 5.9 0.4 - - - +
129C GLU* 2.9 55.9 + - - +
130C GLU* 3.9 13.2 + - - +
132C LEU* 1.3 73.4 - - - +
134C ARG* 1.3 64.7 + - - +
136C ILE 3.4 11.3 + - - +
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Residues in contact with ARG 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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242B ASN* 3.5 25.9 - - - +
243B TYR 3.0 21.4 + - - -
245B SER* 3.5 29.3 - - - +
248B SER 2.8 21.7 + - - -
249B ASN* 3.4 32.2 + - - +
250B ASN* 2.9 33.5 + - - +
251B GLU* 4.1 13.9 - - + +
130C GLU* 2.9 31.3 + - - +
131C LYS* 3.7 6.1 - - - +
133C ARG* 1.3 77.5 - - - +
135C ALA* 1.3 59.1 + - - +
136C ILE 3.3 0.7 + - - -
137C LYS* 2.9 21.7 + - - -
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Residues in contact with ALA 135 (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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251B GLU* 4.1 3.3 + - - +
76C CYS* 4.4 4.5 - - + +
79C PHE 4.3 6.3 - - - +
80C THR* 3.8 18.6 - - - +
82C ILE* 2.8 47.8 + - + -
131C LYS* 3.0 16.0 + - + +
132C LEU* 3.0 11.6 + - - +
134C ARG* 1.3 77.9 - - - +
136C ILE* 1.3 56.1 + - - +
137C LYS* 3.2 13.0 + - - +
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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