Contacts of the helix formed by residues 125 - 141 (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 ASN 125 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123X GLU* 4.2 5.9 + - - +
124X GLN* 1.3 77.7 - - - +
126X LYS* 1.3 65.4 + - - +
127X LYS 3.4 2.1 + - - +
128X VAL* 3.4 20.6 + - + +
129X ILE* 3.2 23.3 + - - +
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Residues in contact with LYS 126 (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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124X GLN 3.5 3.2 + - - -
125X ASN* 1.3 71.7 - - - +
127X LYS* 1.3 63.7 + - - +
129X ILE* 3.2 16.2 + - - +
130X GLU* 3.1 21.5 + - - +
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Residues in contact with LYS 127 (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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125X ASN* 3.4 2.0 - - - +
126X LYS* 1.3 78.7 - - - +
128X VAL* 1.3 58.4 + - - +
130X GLU* 3.3 9.0 + - - +
131X GLU* 3.1 25.5 + - - +
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Residues in contact with VAL 128 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123X GLU* 3.4 26.5 - - - +
125X ASN* 3.4 15.1 + - + +
126X LYS 3.3 0.2 - - - -
127X LYS* 1.3 73.9 - - - +
129X ILE* 1.3 59.5 + - - +
131X GLU* 3.8 8.5 - - + +
132X LYS* 2.9 48.8 + - + +
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Residues in contact with ILE 129 (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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120X LEU* 3.6 15.3 - - + +
123X GLU* 4.1 20.8 + - + +
124X GLN* 3.8 19.1 - - - +
125X ASN 3.2 19.6 + - - +
126X LYS* 3.3 11.9 - - - +
128X VAL* 1.3 77.6 - - - +
130X GLU* 1.3 57.5 + - - +
133X ALA* 2.9 28.3 + - + +
166X PRO* 4.5 9.4 - - + +
167X ASN* 4.0 31.2 - - - +
168X PRO* 3.8 23.3 - - + -
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Residues in contact with GLU 130 (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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126X LYS 3.1 8.9 + - - +
127X LYS* 3.5 10.5 - - - +
128X VAL 3.3 0.2 - - - -
129X ILE* 1.3 77.4 - - + +
131X GLU* 1.3 61.0 + - - +
133X ALA* 3.5 5.0 + - - +
134X ARG* 3.0 30.1 + - - +
166X PRO* 4.8 15.5 - - + +
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Residues in contact with GLU 131 (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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127X LYS 3.1 16.1 + - - +
128X VAL* 3.8 11.7 - - + +
130X GLU* 1.3 75.7 - - - +
132X LYS* 1.3 57.9 + - + +
134X ARG* 3.4 7.3 + - - +
135X MET* 3.1 26.9 + - - +
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Residues in contact with LYS 132 (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* 2.5 36.0 + - - +
120X LEU* 3.9 18.4 - - + -
123X GLU* 3.5 35.4 - - + -
128X VAL* 2.9 31.3 + - + +
131X GLU* 1.3 74.7 - - + +
133X ALA* 1.3 59.2 + - - +
135X MET* 3.3 8.0 + - + +
136X ILE* 3.0 36.6 + - + +
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Residues in contact with ALA 133 (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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120X LEU* 4.2 7.1 - - + +
129X ILE* 2.9 20.0 + - + +
130X GLU 3.9 3.4 - - - +
132X LYS* 1.3 72.4 - - - +
134X ARG* 1.3 65.1 + - - +
136X ILE 3.6 0.3 + - - -
137X TYR* 3.1 9.2 + - - +
163X LEU* 5.4 1.2 - - - +
166X PRO* 4.0 11.9 - - + -
170X MET* 3.5 32.3 - - + -
171X TYR* 2.6 32.0 + - + +
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Residues in contact with ARG 134 (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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130X GLU 3.0 17.9 + - - +
131X GLU* 3.5 6.7 - - - +
133X ALA* 1.3 76.1 - - - +
135X MET* 1.3 63.5 + - - +
137X TYR* 3.0 8.6 + - - +
138X GLU* 3.0 24.6 + - - +
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Residues in contact with MET 135 (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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131X GLU 3.1 14.3 + - - +
132X LYS* 3.3 11.4 + - - +
134X ARG* 1.3 76.3 - - - +
136X ILE* 1.3 63.4 + - + +
138X GLU* 5.0 3.1 - - - -
139X ASP* 3.0 39.3 + - - +
140X TYR* 5.5 0.2 - - - -
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Residues in contact with ILE 136 (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* 3.8 29.6 - - + -
116X ALA* 3.6 42.2 - - + +
117X CYS* 4.2 2.5 - - - +
120X LEU* 3.8 29.6 - - + -
132X LYS* 3.0 22.0 + - + +
135X MET* 1.3 75.7 - - + +
137X TYR* 1.3 58.8 + - - +
140X TYR* 2.8 41.7 + - + +
141X ILE* 3.6 1.6 + - + -
171X TYR* 3.8 27.1 - - + -
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Residues in contact with TYR 137 (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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133X ALA 3.1 7.0 + - - +
134X ARG* 3.0 11.9 + - - +
136X ILE* 1.3 76.5 - - - +
138X GLU* 1.3 59.3 + - + +
141X ILE* 2.9 42.7 + - + -
142X SER* 2.6 57.4 + - - -
156X ARG* 5.1 4.4 + - - -
159X ILE* 4.3 5.2 - - + -
160X ASN* 4.0 14.9 + - - -
163X LEU* 3.7 40.4 - - + +
171X TYR* 3.6 11.2 + - - +
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Residues in contact with GLU 138 (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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134X ARG 3.0 14.5 + - - +
135X MET* 4.3 4.0 - - - +
137X TYR* 1.3 80.1 - - + +
139X ASP* 1.3 64.7 + - - +
142X SER* 4.0 14.8 - - - -
144X LEU 4.5 0.7 - - - +
146X PRO* 3.4 22.5 - - - +
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Residues in contact with ASP 139 (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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135X MET* 3.0 26.0 + - - +
138X GLU* 1.3 86.4 - - - +
140X TYR* 1.3 85.4 + - + +
146X PRO* 3.1 21.9 - - - +
147X LYS* 3.2 16.6 - - + +
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Residues in contact with TYR 140 (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* 4.1 9.9 - - + -
112X LEU* 3.6 29.3 + - + +
113X PHE* 3.5 57.0 - + + -
116X ALA* 4.0 19.8 - - + +
135X MET 5.0 0.4 - - - -
136X ILE* 2.8 30.5 + - + +
139X ASP* 1.3 98.1 + - + +
141X ILE* 1.3 58.1 + - + +
142X SER 3.9 0.9 - - - -
147X LYS* 4.1 12.3 - - + -
148X GLU* 3.6 8.8 - - - +
149X VAL* 3.2 34.4 + - + +
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Residues in contact with ILE 141 (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* 3.7 22.4 - - + -
136X ILE* 3.9 12.6 - - + +
137X TYR* 2.9 37.4 + - + +
140X TYR* 1.3 84.1 - - + +
142X SER* 1.3 65.2 + - - +
149X VAL* 4.5 0.7 - - + -
151X LEU* 3.6 24.7 - - + -
156X ARG* 2.6 48.7 + - + +
159X ILE* 4.0 22.4 - - + -
160X ASN* 5.6 0.4 - - - +
171X TYR* 4.1 13.7 - - + -
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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