Contacts of the helix formed by residues 107 - 118 (chain C) in PDB entry 4ZCU
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 GLU 107 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101C ASN* 4.0 3.5 + - - +
103C ASP* 2.7 21.9 - - - +
105C LYS* 3.9 12.7 - - - +
106C ILE* 1.3 82.0 - - - +
108C ALA* 1.3 65.7 + - - +
109C SER* 3.2 6.3 - - - +
110C GLU* 2.8 28.2 + - + +
111C ILE* 3.3 8.3 + - - +
131C LEU* 3.5 3.1 - - - -
141C THR* 4.9 10.2 - - - +
1003C CA 2.4 25.4 - - - -
1005C SO4 3.1 32.8 - - - +
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Residues in contact with ALA 108 (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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107C GLU* 1.3 72.0 - - - +
109C SER* 1.3 55.4 + - - +
111C ILE* 3.1 7.3 + - - +
112C VAL* 2.9 29.7 + - - +
124C GLU* 3.0 23.3 - - - +
127C ALA* 3.4 20.7 - - + +
128C GLU* 3.9 18.4 - - + +
131C LEU* 3.2 21.6 - - + +
1005C SO4 3.4 7.3 + - - +
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Residues in contact with SER 109 (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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107C GLU* 3.7 4.3 - - - +
108C ALA* 1.3 80.3 - - - +
110C GLU* 1.3 60.5 + - - +
112C VAL* 3.3 6.0 + - - +
113C GLN* 2.9 44.3 + - - +
124C GLU* 3.5 14.2 + - - -
1005C SO4 2.6 31.7 + - - -
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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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98C LEU* 3.5 15.0 - - - +
99C ASP* 3.1 8.4 - - - +
100C LYS* 3.3 22.9 + - + +
101C ASN* 2.6 18.7 + - - +
105C LYS 3.2 6.4 - - - +
106C ILE* 3.2 6.2 - - + -
107C GLU* 2.8 33.3 + - + +
109C SER* 1.3 77.1 + - - +
111C ILE* 1.3 59.2 + - - +
113C GLN* 3.6 10.3 + - - +
114C SER* 2.7 38.1 + - - -
1003C CA 2.4 31.7 - - - -
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Residues in contact with ILE 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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98C LEU* 4.7 12.3 - - + -
106C ILE* 4.0 11.7 - - + -
107C GLU 3.3 9.1 + - - +
108C ALA 3.1 9.2 + - - +
110C GLU* 1.3 75.1 - - - +
112C VAL* 1.3 59.8 + - - +
114C SER* 4.4 3.8 - - - -
115C LEU* 2.9 46.5 + - + +
122C ILE* 4.0 17.7 - - + -
127C ALA* 4.1 8.5 - - + +
130C ILE* 3.8 28.3 - - + -
131C LEU* 3.6 33.2 - - + -
147C TRP* 6.2 0.7 - - + -
166C TRP* 4.2 11.7 - - + -
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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
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108C ALA 2.9 21.9 + - - +
109C SER* 3.3 11.2 + - - +
111C ILE* 1.3 77.0 - - - +
113C GLN* 1.3 60.0 + - + +
115C LEU* 3.5 1.7 + - - +
116C GLN* 2.9 34.7 + - + +
120C LEU 4.4 1.7 - - - +
122C ILE* 3.7 28.9 - - + +
123C SER 3.7 26.2 - - - +
124C GLU* 4.3 8.5 - - - +
127C ALA* 3.7 7.9 - - + -
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Residues in contact with GLN 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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93A LEU* 5.5 1.0 - - + +
100C LYS* 5.0 19.8 - - - +
109C SER* 2.9 33.4 + - - +
110C GLU* 3.9 12.7 + - - +
112C VAL* 1.3 78.6 - - + +
114C SER* 1.3 64.1 + - - +
116C GLN* 3.0 9.1 + - - +
117C THR* 2.9 29.6 + - + +
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Residues in contact with SER 114 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97C SER 5.1 0.2 - - - -
98C LEU* 3.6 31.1 + - - +
100C LYS* 2.3 37.3 + - - +
110C GLU 2.7 18.9 + - - -
111C ILE 3.8 2.5 - - - -
113C GLN* 1.3 76.2 - - - +
115C LEU* 1.3 63.9 + - - +
117C THR* 2.5 27.0 + - - -
118C LEU* 3.3 14.0 + - - +
159C ILE* 6.1 0.2 - - - -
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Residues in contact with LEU 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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98C LEU* 5.3 4.7 - - + -
111C ILE* 2.9 30.9 + - + +
112C VAL 3.9 2.7 - - - +
114C SER* 1.3 80.5 - - - +
116C GLN* 1.3 55.2 + - - +
118C LEU* 3.0 18.4 + - + +
119C GLY 3.1 0.5 + - - -
120C LEU* 2.7 48.5 + - + +
122C ILE* 3.7 37.2 - - + -
130C ILE* 4.8 1.1 - - + -
159C ILE* 5.5 1.1 - - + -
163C ILE* 4.0 29.2 - - + -
166C TRP* 4.3 8.5 - - + -
174C ILE* 4.3 21.8 - - + -
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Residues in contact with GLN 116 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A LEU* 3.8 21.2 - - + +
158A ASP* 5.3 0.9 - - - +
112C VAL* 2.9 21.4 + - + +
113C GLN* 3.0 13.2 + - - +
115C LEU* 1.3 75.4 - - - +
117C THR* 1.3 63.7 + - - +
119C GLY* 3.1 13.3 + - - -
120C LEU 3.3 8.1 + - - +
121C THR* 3.2 43.1 + - - +
122C ILE 5.0 0.4 - - - +
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Residues in contact with THR 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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93A LEU* 3.8 35.0 - - + -
94A ALA* 6.1 1.3 - - - +
97A SER* 4.4 21.8 - - - -
158A ASP* 3.7 10.4 - - - +
159A ILE* 3.5 21.6 + - - +
100C LYS* 5.5 8.0 - - - -
113C GLN* 2.9 19.7 + - + +
114C SER* 2.5 24.3 + - - -
116C GLN* 1.3 76.9 - - - +
118C LEU* 1.3 63.1 + - - +
119C GLY 3.3 1.0 + - - -
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Residues in contact with LEU 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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118A LEU* 3.9 18.6 - - + -
158A ASP* 3.3 3.6 - - - +
159A ILE* 3.7 17.3 - - + -
160A GLU* 3.0 44.5 - - - +
114C SER* 3.4 17.0 - - - +
115C LEU* 3.0 12.3 + - + +
117C THR* 1.3 82.0 - - - +
119C GLY* 1.3 57.6 - - - -
120C LEU* 3.4 7.7 - - + +
159C ILE* 4.2 24.0 - - + -
160C GLU* 5.3 3.8 - - + -
163C ILE* 3.6 30.3 - - + -
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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
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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