Contacts of the helix formed by residues 107 - 123 (chain X) in PDB entry 1ZV4
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 107 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102X LEU* 3.0 34.6 + - - +
105X GLU* 4.0 14.0 + - - +
106X TYR* 1.3 77.3 - - - +
108X GLU* 1.3 64.5 + - - +
109X GLU* 3.1 12.6 + - - -
110X ASN* 3.2 30.9 + - - +
186X SER* 4.2 6.7 + - - -
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Residues in contact with GLU 108 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99X ARG* 2.8 42.4 + - + +
102X LEU* 3.7 14.2 + - - -
103X ARG* 3.1 47.6 + - + +
106X TYR 3.6 1.6 - - - -
107X SER* 1.3 76.3 - - - +
109X GLU* 1.3 56.5 + - - +
111X LEU* 2.8 27.0 + - - +
112X LEU* 3.1 32.5 + - + +
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Residues in contact with GLU 109 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106X TYR 3.2 17.2 - - - +
107X SER* 3.1 18.3 - - - -
108X GLU* 1.3 73.7 + - - +
110X ASN* 1.3 65.7 + - - +
112X LEU* 3.7 12.8 - - + +
113X PHE* 2.8 32.4 + - - +
140X TYR* 4.1 6.1 - - + -
147X LYS* 4.2 18.2 - - + +
148X GLU 3.9 22.7 - - - +
149X VAL* 3.9 11.4 - - + +
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Residues in contact with ASN 110 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102X LEU* 6.2 0.2 - - + -
107X SER* 3.2 24.7 + - - +
108X GLU 3.1 0.2 + - - -
109X GLU* 1.3 85.7 + - - +
111X LEU* 1.3 57.7 + - - +
113X PHE* 3.7 0.9 + - - +
114X TRP* 3.1 22.9 + - - +
149X VAL* 3.7 23.4 - - - +
150X SER 5.0 1.0 + - - -
178X ILE* 3.4 33.4 - - + +
181X LEU* 3.4 27.6 - - - +
182X MET* 4.0 17.2 - - + +
186X SER* 5.6 2.0 + - - -
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Residues in contact with LEU 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89X MET* 3.3 39.5 - - + -
95X ARG* 3.5 23.6 - - + +
98X PHE* 4.1 5.2 - - + -
99X ARG* 3.5 42.4 - - + +
102X LEU* 3.4 20.9 - - + -
107X SER 4.2 0.4 + - - -
108X GLU* 2.8 9.8 + - - +
110X ASN* 1.3 74.1 - - - +
112X LEU* 1.3 63.4 + - + +
114X TRP* 3.1 9.6 + - + +
115X LEU* 2.8 38.1 + - + +
182X MET* 3.9 6.7 - - - -
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Residues in contact with LEU 112 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99X ARG* 3.6 45.1 - - + +
108X GLU* 3.1 37.3 + - + +
109X GLU* 3.7 12.6 - - + +
111X LEU* 1.3 79.1 - - + +
113X PHE* 1.3 56.4 + - - +
115X LEU* 3.6 11.4 - - + +
116X ALA* 2.9 29.8 + - - +
140X TYR* 3.6 22.9 + - + +
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Residues in contact with PHE 113 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109X GLU 2.8 20.8 + - - +
110X ASN 3.7 2.0 - - - +
112X LEU* 1.3 71.6 - - - +
114X TRP* 1.3 66.4 + - - +
116X ALA* 3.2 2.6 + - - +
117X CYS* 3.0 46.7 + - - -
136X ILE* 3.8 10.3 - - + -
140X TYR* 3.5 39.6 - + + -
141X ILE* 3.7 22.2 - - + -
149X VAL* 3.9 12.8 - - + -
171X TYR* 4.5 3.4 - + + -
174X ALA* 3.7 45.8 - - + -
175X GLN* 3.8 6.3 - - - -
178X ILE* 3.8 24.9 - - + -
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Residues in contact with TRP 114 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89X MET* 3.6 53.8 - - + -
90X LYS* 5.5 5.2 - - + -
95X ARG* 4.1 12.6 - - - -
110X ASN 3.1 11.9 + - - +
111X LEU* 3.1 12.5 + - + +
113X PHE* 1.3 83.2 - - + +
115X LEU* 1.3 66.0 + - + +
117X CYS 3.3 1.2 + - - -
118X GLU* 3.1 54.7 + - + -
175X GLN* 3.2 56.2 + - + +
178X ILE* 5.0 2.2 - - + -
179X TYR* 3.6 31.6 - + + +
182X MET* 4.0 11.2 - - + -
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Residues in contact with LEU 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95X ARG* 3.5 46.9 - - + +
96X ASN* 6.1 2.7 - - - +
99X ARG* 4.6 18.6 - - - +
111X LEU* 2.8 34.3 + - + +
112X LEU* 3.6 12.6 - - + +
114X TRP* 1.3 79.6 - - + +
116X ALA* 1.3 60.3 + - - +
118X GLU* 3.2 8.5 + - + +
119X ASP* 2.9 27.9 + - - +
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Residues in contact with ALA 116 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112X LEU 2.9 17.2 + - - +
113X PHE 3.6 4.5 - - - +
115X LEU* 1.3 77.4 - - - +
117X CYS* 1.3 57.4 + - - +
119X ASP* 3.3 8.3 + - - +
120X LEU 3.0 23.2 + - - -
136X ILE* 3.6 30.6 - - + +
140X TYR* 4.0 14.8 - - + +
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Residues in contact with CYS 117 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113X PHE* 3.0 54.9 + - - -
114X TRP 3.6 2.5 - - - +
116X ALA* 1.3 74.9 - - - +
118X GLU* 1.3 60.5 + - - +
120X LEU* 3.5 4.6 + - - +
121X LYS* 3.2 27.4 + - - +
136X ILE* 4.3 7.2 - - - -
168X PRO 4.7 1.0 - - - +
171X TYR* 3.5 26.0 - - + -
175X GLN* 3.6 30.1 - - + +
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Residues in contact with GLU 118 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95X ARG* 6.0 1.1 - - - +
114X TRP* 3.1 44.8 + - + +
115X LEU* 3.2 13.7 + - + +
117X CYS* 1.3 76.4 - - - +
119X ASP* 1.3 60.9 + - - +
121X LYS* 3.1 37.6 + - - +
122X LYS* 3.6 12.3 + - - +
175X GLN* 2.7 26.9 + - - +
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Residues in contact with ASP 119 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115X LEU 2.9 13.0 + - - +
116X ALA* 3.3 12.3 + - - +
118X GLU* 1.3 72.8 - - - +
120X LEU* 1.3 64.8 + - - +
122X LYS* 3.6 13.6 + - - +
123X GLU* 3.6 14.1 + - - +
132X LYS* 2.5 43.9 + - - +
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Residues in contact with LEU 120 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116X ALA 3.0 15.6 + - - +
117X CYS* 3.8 5.6 - - - +
118X GLU 3.3 0.2 - - - -
119X ASP* 1.3 75.0 + - - +
121X LYS* 1.3 64.7 + - - +
123X GLU* 3.2 12.7 + - + +
129X ILE* 3.6 41.3 - - + +
132X LYS* 3.9 21.1 - - + -
133X ALA* 4.3 6.3 - - + -
136X ILE* 3.8 9.4 - - + -
167X ASN 4.0 10.5 - - - +
168X PRO* 3.5 26.0 - - + +
170X MET* 5.0 0.2 - - + -
171X TYR* 3.6 36.6 - - + -
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Residues in contact with LYS 121 (chain X).
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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117X CYS 3.2 12.9 + - - +
118X GLU* 3.1 40.4 + - - +
119X ASP 3.4 0.2 - - - -
120X LEU* 1.3 78.0 - - - +
122X LYS* 1.3 59.9 + - - +
123X GLU 3.5 5.0 + - - +
168X PRO* 3.7 25.2 + - - +
169X HIS* 3.6 35.5 + - + +
172X GLU* 5.7 6.3 - - + +
175X GLN* 3.4 18.1 + - - +
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Residues in contact with LYS 122 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118X GLU 3.6 9.4 + - - +
119X ASP* 4.0 9.4 - - - +
120X LEU 3.3 0.8 - - - -
121X LYS* 1.3 77.2 - - - +
123X GLU* 1.3 65.8 + - + +
124X GLN* 3.6 5.0 + - - +
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Residues in contact with GLU 123 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119X ASP* 3.6 6.7 + - - +
120X LEU 3.2 15.7 + - - +
121X LYS 3.8 6.8 - - - +
122X LYS* 1.3 82.3 - - + +
124X GLN* 1.3 63.2 + - - +
125X ASN* 4.2 7.6 + - - +
128X VAL* 3.4 31.1 - - + +
129X ILE* 4.1 15.0 - - + +
132X LYS* 3.5 32.9 - - + -
168X PRO* 4.0 13.9 - - - +
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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