Contacts of the helix formed by residues 110 - 121 (chain C) in PDB entry 4I7C
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 PRO 110 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94C VAL 4.6 5.6 - - - +
95C LEU* 3.7 22.9 - - + -
108C THR 4.8 0.4 - - - +
109C LEU* 1.4 98.3 - - + +
111C HIS* 1.3 66.4 + - - +
112C THR* 3.2 6.3 - - - +
113C GLU* 3.1 38.0 + - + +
114C LYS* 3.2 8.7 + - - +
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Residues in contact with HIS 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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96C PHE* 4.1 31.0 - + + -
109C LEU 3.8 0.6 + - - -
110C PRO* 1.3 72.4 - - - +
112C THR* 1.3 63.2 + - - +
114C LYS* 3.4 32.2 - - + +
115C ALA 4.5 1.9 + - - -
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Residues in contact with THR 112 (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 PRO* 3.2 4.7 + - - +
111C HIS* 1.3 80.0 + - - +
113C GLU* 1.3 66.0 + - - +
114C LYS 3.3 0.6 + - - -
115C ALA* 4.5 6.9 + - - +
116C ASP* 3.9 11.4 - - - +
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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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109C LEU* 3.8 25.0 - - + +
110C PRO* 3.1 29.2 + - + +
112C THR* 1.3 83.2 - - - +
114C LYS* 1.3 64.7 + - - +
115C ALA 3.4 1.3 - - - -
116C ASP* 3.5 14.3 + - + +
117C HIS* 3.2 23.2 + - - +
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Residues in contact with LYS 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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96C PHE* 4.5 21.1 - - + +
97C PRO* 3.3 25.1 - - - +
98C CYS* 5.3 1.3 - - - -
99C LYS* 4.8 7.9 - - - +
109C LEU* 4.5 11.7 - - + -
110C PRO 3.2 9.7 + - - +
111C HIS* 3.4 33.0 - - + +
112C THR 3.3 1.0 - - - -
113C GLU* 1.3 78.8 - - - +
115C ALA* 1.3 64.9 + - - +
117C HIS* 3.4 2.8 + - + +
118C GLU* 3.2 53.5 + - + +
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Residues in contact with ALA 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 HIS 4.5 1.4 + - - +
112C THR 4.5 6.6 + - - +
113C GLU 3.4 0.4 - - - -
114C LYS* 1.3 78.1 - - - +
116C ASP* 1.3 66.2 + - - +
118C GLU* 3.1 21.9 + - - +
119C GLU* 3.5 10.9 + - - +
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Residues in contact with ASP 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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112C THR 3.9 14.5 - - - +
113C GLU* 3.5 12.1 + - + +
114C LYS 3.3 0.6 - - - -
115C ALA* 1.3 79.3 - - - +
117C HIS* 1.3 60.8 + - - +
119C GLU* 3.9 3.2 + - - +
120C LEU* 3.9 25.9 + - + +
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Residues in contact with HIS 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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98C CYS* 3.5 19.4 - - + +
105C CYS* 3.3 4.1 - - - -
107C ILE* 3.8 25.7 - - + +
109C LEU* 3.3 33.5 - - + +
113C GLU 3.2 4.0 + - - +
114C LYS* 3.7 3.8 - - + +
115C ALA 3.3 0.2 - - - -
116C ASP* 1.3 77.5 - - - +
118C GLU* 1.3 63.0 + - + +
120C LEU* 3.3 6.4 + - - +
121C CYS* 2.8 39.6 + - + +
602C ZN 2.0 36.5 - - - -
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Residues in contact with GLU 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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98C CYS* 4.0 9.1 - - - -
99C LYS* 3.1 56.2 + - + +
100C TYR* 3.3 21.5 + - - -
114C LYS* 3.2 48.9 + - + +
115C ALA* 3.1 14.1 + - - +
117C HIS* 1.3 79.1 - - + +
119C GLU* 1.3 64.0 + - - +
121C CYS* 4.0 5.9 + - - +
124C ARG* 3.9 4.7 - - - -
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Residues in contact with GLU 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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115C ALA 3.5 8.2 + - - +
116C ASP* 4.4 6.1 - - - +
117C HIS 3.3 0.4 - - - -
118C GLU* 1.3 78.3 - - - +
120C LEU* 1.3 71.1 + - + +
121C CYS 3.3 2.3 + - - +
124C ARG* 3.1 40.4 + - - +
215C ARG* 3.9 15.1 + - - +
244C HIS* 4.2 0.2 - - - -
245C GLU* 6.1 1.4 - - - +
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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
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116C ASP* 3.9 15.0 + - + +
117C HIS* 3.3 8.1 + - - +
119C GLU* 1.3 88.3 - - + +
121C CYS* 1.3 64.5 + - - +
122C GLU* 3.4 11.8 + - - +
215C ARG* 3.7 36.7 + - - +
244C HIS* 4.5 3.7 - - - -
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Residues in contact with CYS 121 (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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98C CYS* 3.9 2.7 - - - -
100C TYR* 4.3 7.9 - - + -
105C CYS* 3.6 8.7 - - - -
117C HIS* 2.8 28.3 + - + +
118C GLU 4.1 8.3 - - - +
119C GLU 3.2 2.0 - - - -
120C LEU* 1.3 72.5 - - - +
122C GLU* 1.3 64.4 + - - +
123C PHE* 3.3 28.1 + - - -
124C ARG* 3.4 9.4 + - - +
244C HIS* 3.2 17.0 + - - -
602C ZN 2.3 36.8 - - - -
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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