Contacts of the helix formed by residues 107 - 118 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ASN* 3.8 6.2 + - - +
103A ASP* 2.5 23.7 - - - +
105A LYS* 4.1 9.6 - - - +
106A ILE* 1.3 82.0 - - - +
108A ALA* 1.3 67.5 + - - +
109A SER* 3.2 3.8 - - - +
110A GLU* 2.9 29.1 + - - +
111A ILE* 3.4 4.0 + - - +
131A LEU* 3.7 3.4 - - - -
141A THR* 5.0 13.5 - - + -
1003A CA 2.3 26.5 - - - -
1007A SO4 3.3 34.3 - - - +
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLU* 1.3 73.0 - - - +
109A SER* 1.3 56.8 + - - +
111A ILE* 3.0 3.9 + - - +
112A VAL* 2.9 29.6 + - - +
124A GLU* 3.0 20.4 - - - +
127A ALA* 3.3 24.3 - - + +
128A GLU* 3.8 23.8 - - + +
131A LEU* 3.3 18.2 - - + +
141A THR* 5.8 0.2 - - - +
1007A SO4 3.3 3.7 + - - +
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Residues in contact with SER 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLU* 4.0 2.8 - - - +
108A ALA* 1.3 76.8 - - - +
110A GLU* 1.3 61.8 + - - +
112A VAL* 3.2 6.6 + - - +
113A GLN* 2.9 45.9 + - - +
124A GLU* 3.3 15.6 + - - -
1007A SO4 2.4 37.4 + - - -
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Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 3.3 17.0 - - - +
99A ASP* 3.6 0.3 - - - +
100A LYS* 3.0 31.4 + - + +
101A ASN* 2.7 17.8 + - - +
105A LYS 3.3 1.0 - - - +
106A ILE* 3.3 9.7 - - + -
107A GLU* 2.9 30.3 + - + +
109A SER* 1.3 81.6 + - - +
111A ILE* 1.3 58.7 + - - +
113A GLN* 3.4 12.8 + - - +
114A SER* 2.9 34.8 + - - -
1003A CA 2.3 30.9 - - - -
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Residues in contact with ILE 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 4.6 11.7 - - + -
106A ILE* 3.9 18.2 - - + -
107A GLU 3.4 3.1 + - - +
108A ALA 3.0 9.0 + - - +
110A GLU* 1.3 73.7 - - - +
112A VAL* 1.3 67.5 + - - +
114A SER* 3.4 4.4 + - - -
115A LEU* 2.9 38.7 + - + +
122A ILE* 4.1 11.2 - - + -
127A ALA* 4.0 15.7 - - + +
130A ILE* 4.0 29.2 - - + -
131A LEU* 3.6 34.3 - - + -
147A TRP* 6.0 0.4 - - + -
166A TRP* 4.3 12.8 - - + -
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ALA 2.9 19.4 + - - +
109A SER* 3.3 8.7 - - - +
111A ILE* 1.3 76.0 - - - +
113A GLN* 1.3 59.3 + - + +
115A LEU* 3.8 1.7 - - - +
116A GLN* 2.9 40.4 + - + +
120A LEU 4.5 1.4 - - - +
121A THR* 6.3 0.7 - - + -
122A ILE* 3.7 29.5 - - + +
123A SER 3.8 15.7 - - - +
124A GLU* 4.1 16.2 - - - +
127A ALA* 3.8 15.0 - - + -
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Residues in contact with GLN 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LYS* 4.0 25.5 - - - +
109A SER* 2.9 37.7 + - - +
110A GLU* 3.7 13.3 - - - +
112A VAL* 1.3 76.7 - - + +
114A SER* 1.3 62.5 + - - +
116A GLN* 3.0 12.7 + - - +
117A THR* 2.9 29.3 + - + +
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Residues in contact with SER 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A SER 4.0 0.6 + - - -
98A LEU* 3.3 35.0 - - - +
100A LYS* 3.4 25.1 + - - +
110A GLU 2.9 21.3 + - - -
111A ILE 3.8 3.1 - - - -
113A GLN* 1.3 76.1 - - - +
115A LEU* 1.3 64.5 + - - +
117A THR* 2.6 25.5 + - - -
118A LEU* 3.4 14.0 + - - +
159A ILE* 5.9 1.1 - - - -
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 5.5 1.1 - - + -
111A ILE* 2.9 30.2 + - + +
112A VAL 4.0 2.2 - - - +
114A SER* 1.3 82.8 - - - +
116A GLN* 1.3 61.2 + - - +
118A LEU* 3.1 14.3 + - + +
119A GLY 3.2 0.5 + - - -
120A LEU* 2.8 43.8 + - + +
122A ILE* 3.7 35.9 - - + -
130A ILE* 4.8 1.8 - - + -
159A ILE* 5.3 4.3 - - + -
163A ILE* 3.9 30.5 - - + -
166A TRP* 4.4 9.0 - - + -
174A ILE* 4.2 24.2 - - + -
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Residues in contact with GLN 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A VAL* 2.9 24.9 + - - +
113A GLN* 3.0 15.0 + - - +
115A LEU* 1.3 78.4 - - - +
117A THR* 1.3 60.0 + - - +
119A GLY* 3.2 12.8 + - - -
120A LEU 3.2 10.9 + - - +
121A THR* 3.7 29.7 + - - +
93C LEU* 3.9 37.5 - - + +
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Residues in contact with THR 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LYS* 5.3 8.8 + - - +
113A GLN* 2.9 19.1 + - + +
114A SER* 2.6 23.6 + - - -
116A GLN* 1.3 76.1 - - - +
118A LEU* 1.3 63.8 + - - +
119A GLY 3.3 1.6 + - - -
93C LEU* 4.5 23.2 - - + +
94C ALA* 5.3 4.9 + - - +
97C SER* 3.8 32.8 + - - -
158C ASP* 4.7 1.9 - - - +
159C ILE* 3.8 21.8 + - - +
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A SER* 3.5 15.7 - - - +
115A LEU* 3.1 10.8 + - + +
117A THR* 1.3 83.9 - - - +
119A GLY* 1.3 58.8 + - - +
120A LEU* 3.4 9.0 + - + +
159A ILE* 4.0 25.1 - - + -
160A GLU* 5.4 3.4 - - + +
163A ILE* 3.7 29.2 - - + -
118C LEU* 3.9 19.1 - - + -
158C ASP* 3.7 4.3 - - - +
159C ILE* 3.8 17.9 - - + -
160C GLU* 3.3 39.1 - - - +
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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