Contacts of the helix formed by residues 109 - 120 (chain C) in PDB entry 2ISZ
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 SER 109 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78C LYS* 3.8 2.9 - - - +
107C VAL 3.5 0.4 + - - -
108C MET* 1.3 73.6 - - - +
110C GLU* 1.3 60.3 + - - +
111C ASP* 3.5 15.1 + - - +
112C VAL* 3.2 19.0 + - - +
113C GLU* 3.1 28.1 + - - +
92D LEU* 4.9 0.2 - - - +
100D GLU* 2.8 31.3 + - - -
103D ARG* 3.6 9.9 - - - +
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Residues in contact with GLU 110 (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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74C ALA* 5.7 1.7 - - - +
77C ARG* 3.9 15.9 + - - +
78C LYS* 3.9 8.0 - - - +
109C SER* 1.3 71.0 - - - +
111C ASP* 1.3 59.4 + - - +
113C GLU* 3.1 20.3 + - - +
114C ARG* 2.8 65.9 + - - +
138C LEU* 4.4 5.0 - - + -
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Residues in contact with ASP 111 (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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109C SER* 3.7 14.0 + - - +
110C GLU* 1.3 78.9 + - - +
112C VAL* 1.3 63.1 + - - +
114C ARG* 3.3 21.7 + - - +
115C ARG* 3.1 25.5 + - - +
92D LEU* 3.8 19.1 - - + -
93D PRO* 6.0 0.4 - - + -
96D GLU* 3.0 22.3 - - - +
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Residues in contact with VAL 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C MET* 4.1 4.9 - - + -
109C SER* 3.2 11.3 + - - +
111C ASP* 1.3 76.4 - - - +
113C GLU* 1.3 65.3 + - - +
115C ARG* 2.9 18.2 + - - +
116C LEU* 2.9 31.8 + - + +
86D LEU* 4.1 9.9 - - + -
90D ILE* 4.3 9.9 - - + -
92D LEU* 3.9 16.1 - - + +
100D GLU* 3.2 42.2 - - + +
104D TRP* 4.0 20.6 - - + -
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Residues in contact with GLU 113 (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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77C ARG* 2.9 48.0 + - - +
78C LYS* 2.8 44.1 + - + +
81C LEU* 3.5 15.4 - - + +
108C MET* 3.3 22.7 - - + -
109C SER 3.1 17.4 + - - +
110C GLU* 3.3 12.7 - - - +
112C VAL* 1.3 76.0 - - - +
114C ARG* 1.3 61.4 + - - +
116C LEU* 3.1 14.4 + - - +
117C VAL* 3.2 18.5 + - - +
138C LEU* 4.2 6.7 - - + -
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Residues in contact with ARG 114 (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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110C GLU* 2.8 46.5 + - - +
111C ASP* 3.7 23.5 + - - +
113C GLU* 1.3 73.9 - - - +
115C ARG* 1.3 62.3 + - + +
116C LEU 3.3 0.3 + - - -
117C VAL* 3.4 15.9 + - - +
118C LYS* 3.3 21.8 + - - +
138C LEU* 2.9 48.4 + - + +
139C GLY* 4.8 13.0 - - - +
140C VAL* 5.8 1.8 - - + -
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Residues in contact with ARG 115 (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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111C ASP 3.1 17.4 + - - +
112C VAL 2.9 9.2 + - - +
114C ARG* 1.3 77.0 - - + +
116C LEU* 1.3 58.3 + - - +
118C LYS* 3.6 25.3 + - - +
119C VAL* 3.0 44.3 + - - +
89D VAL 5.4 0.2 + - - -
90D ILE* 2.9 36.4 + - + +
91D GLY* 3.2 26.9 + - - +
92D LEU* 4.6 9.0 - - + -
93D PRO* 5.1 4.7 - - + -
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Residues in contact with LEU 116 (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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81C LEU* 4.5 20.4 - - + +
82C ALA* 5.5 0.2 - - - -
85C LEU* 3.8 40.8 - - + -
108C MET* 3.8 24.0 - - + -
112C VAL* 2.9 33.4 + - + +
113C GLU* 3.1 8.9 + - - +
115C ARG* 1.3 77.3 - - - +
117C VAL* 1.3 59.9 + - - +
118C LYS 3.2 0.2 - - - -
119C VAL* 4.3 7.2 - - + +
120C LEU* 2.8 54.6 + - + +
90D ILE* 4.1 15.5 - - + -
104D TRP* 5.7 0.2 - - + -
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Residues in contact with VAL 117 (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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81C LEU* 4.5 7.9 - - + -
113C GLU 3.2 16.3 + - - +
114C ARG* 3.7 8.7 - - - +
115C ARG 3.4 0.2 - - - -
116C LEU* 1.3 75.0 - - - +
118C LYS* 1.3 68.9 + - - +
121C ASN 3.4 2.8 + - - -
122C ASN* 2.8 60.3 + - + +
123C PRO* 3.4 13.4 - - + +
135C LEU* 4.5 11.9 - - + -
138C LEU* 3.9 22.0 - - + -
140C VAL* 4.3 18.8 - - + -
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Residues in contact with LYS 118 (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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114C ARG* 3.3 17.5 - - - +
115C ARG* 3.6 31.0 - - - +
117C VAL* 1.3 88.7 - - - +
119C VAL* 1.3 64.8 + - + +
121C ASN* 3.0 21.3 + - - +
122C ASN* 4.2 22.4 + - - +
140C VAL* 5.5 7.9 - - - +
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Residues in contact with VAL 119 (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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85C LEU* 5.7 0.4 - - + -
89C VAL* 5.1 6.3 - - + -
115C ARG* 3.0 29.3 + - - +
116C LEU* 4.2 11.9 - - + +
118C LYS* 1.3 79.7 - - + +
120C LEU* 1.3 69.6 + - + +
121C ASN* 3.3 8.0 + - - +
89D VAL* 3.5 38.6 - - + +
90D ILE* 3.6 15.0 - - - +
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Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C LEU* 4.1 8.7 - - + +
84C ARG* 3.8 25.3 - - + +
85C LEU* 3.8 17.9 - - + +
88C ASP* 4.2 20.8 - - + +
89C VAL* 4.0 27.8 - - + -
116C LEU* 2.8 44.8 + - + +
119C VAL* 1.3 76.8 - - + +
121C ASN* 1.3 73.2 + - - +
122C ASN 3.8 0.2 - - - -
123C PRO* 3.8 22.8 - - + +
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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