Contacts of the helix formed by residues 120 - 134 (chain A) in PDB entry 1WZN
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 ASP 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A TYR 4.2 0.2 + - - -
119A PHE* 1.3 70.4 - - - +
121A GLU* 1.3 60.3 + - - +
122A GLU* 3.3 12.7 + - - +
123A ASP* 3.0 31.6 + - - +
124A LEU* 2.8 24.9 + - - +
182A LYS* 4.2 11.8 + - - +
208A ASN* 3.5 20.4 - - - +
210A TYR* 2.9 10.6 + - - -
1007A MG 2.4 29.1 - - - -
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Residues in contact with GLU 121 (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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120A ASP* 1.3 74.7 - - - +
122A GLU* 1.3 81.5 + - - +
124A LEU* 3.3 4.4 + - - +
125A ARG* 3.0 42.9 + - - +
210A TYR* 3.0 15.2 + - + +
218A LEU* 3.9 32.5 - - + +
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Residues in contact with GLU 122 (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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120A ASP* 3.5 19.1 - - - +
121A GLU* 1.3 98.1 + - - +
123A ASP* 1.3 66.4 + - - +
125A ARG* 3.3 10.3 + - - +
126A LYS* 3.1 21.1 + - - +
1007A MG 4.1 8.0 - - - -
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Residues in contact with ASP 123 (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* 3.4 37.1 - - + +
119A PHE* 3.9 19.8 - - + -
120A ASP* 3.0 26.5 + - - +
122A GLU* 1.3 76.9 - - - +
124A LEU* 1.3 60.8 + - - +
126A LYS* 3.3 11.5 + - - +
127A LEU* 2.9 23.4 + - - +
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Residues in contact with LEU 124 (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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116A ILE* 3.8 35.7 - - + +
119A PHE* 4.0 5.6 - - + +
120A ASP 2.8 16.8 + - - +
121A GLU* 3.6 4.7 - - - +
122A GLU 3.2 0.2 - - - -
123A ASP* 1.3 74.0 - - - +
125A ARG* 1.3 67.0 + - - +
127A LEU* 3.2 14.7 + - + +
128A PHE* 2.9 63.3 + - + -
210A TYR* 3.5 39.5 - - + +
215A VAL* 5.2 3.1 - - + -
218A LEU* 4.0 15.5 - - + -
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Residues in contact with ARG 125 (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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121A GLU* 3.0 34.2 + - - +
122A GLU* 3.7 9.9 - - - +
123A ASP 3.3 0.2 - - - -
124A LEU* 1.3 76.1 - - - +
126A LYS* 1.3 64.3 + - - +
128A PHE* 3.4 2.8 + - - -
129A SER* 3.0 24.3 + - - -
218A LEU* 3.5 29.6 - - + +
221A LYS* 3.6 32.1 - - - +
222A TYR* 3.4 35.5 + - + +
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Residues in contact with LYS 126 (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* 3.2 45.2 + - + +
99A GLU* 5.2 5.7 - - - +
122A GLU 3.1 13.4 + - - +
123A ASP* 3.5 15.9 - - - +
125A ARG* 1.3 78.0 - - - +
127A LEU* 1.3 60.8 + - - +
129A SER* 3.3 6.7 + - - -
130A LYS* 3.0 42.6 + - + +
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Residues in contact with LEU 127 (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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48A LEU* 4.2 8.5 - - + -
97A VAL* 4.0 35.9 - - + +
98A LEU* 3.9 8.7 - - + +
100A ILE* 5.6 0.4 - - + -
111A MET* 3.9 27.8 - - + -
116A ILE* 4.8 3.1 - - + -
119A PHE* 4.2 11.4 - - + -
123A ASP 2.9 14.3 + - - +
124A LEU* 3.2 26.9 + - + +
126A LYS* 1.3 77.2 - - - +
128A PHE* 1.3 64.6 + - + +
130A LYS* 3.1 6.5 + - + +
131A VAL* 2.9 47.8 + - + +
141A PHE* 5.2 3.1 - - + -
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Residues in contact with PHE 128 (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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116A ILE* 4.8 6.5 - - + -
124A LEU* 2.9 51.9 + - + +
125A ARG* 3.8 0.4 - - - +
127A LEU* 1.3 81.8 - - + +
129A SER* 1.3 58.9 + - - +
131A VAL* 3.4 6.2 + - + +
132A ALA* 3.0 29.3 + - - +
141A PHE* 3.5 39.3 - + - -
143A THR* 5.6 0.2 - - + -
215A VAL* 4.0 22.2 - - + -
218A LEU* 3.8 27.8 - - + -
219A ALA* 3.8 23.1 - - + -
222A TYR* 3.5 22.6 - + + +
223A PHE* 4.0 11.2 - + + -
245A ILE* 5.7 0.7 - - + -
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Residues in contact with SER 129 (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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125A ARG 3.0 18.1 + - - -
126A LYS* 3.5 8.1 - - - -
128A PHE* 1.3 78.1 - - - +
130A LYS* 1.3 64.9 + - - +
132A ALA* 3.4 4.2 + - - +
133A GLU* 3.1 35.7 + - - +
222A TYR* 3.6 27.0 - - - -
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Residues in contact with LYS 130 (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 VAL 4.7 1.8 - - - +
98A LEU 3.5 27.5 + - - +
99A GLU* 4.5 4.0 - - - +
100A ILE* 3.0 47.9 + - + +
101A ALA* 5.0 3.8 - - - +
102A PHE 4.8 1.0 - - - +
126A LYS* 3.0 30.9 + - + +
127A LEU* 3.1 7.8 + - - +
129A SER* 1.3 75.4 - - - +
131A VAL* 1.3 64.9 + - - +
133A GLU* 3.3 22.0 + - - +
134A ALA* 3.1 21.8 + - - +
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Residues in contact with VAL 131 (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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48A LEU* 3.8 28.3 - - + -
100A ILE* 4.7 2.7 - - + -
109A VAL* 3.9 15.0 - - + -
127A LEU* 2.9 29.7 + - + +
128A PHE* 3.6 7.6 - - - +
130A LYS* 1.3 74.3 - - - +
132A ALA* 1.3 66.4 + - - +
134A ALA* 3.0 17.0 + - - +
135A LEU* 3.2 14.2 + - + +
141A PHE* 3.6 45.3 - - + -
223A PHE* 3.9 6.5 - - + -
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Residues in contact with ALA 132 (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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104A ASN* 4.4 2.9 + - - -
128A PHE 3.0 17.6 + - - +
129A SER* 3.6 5.8 - - - +
131A VAL* 1.3 76.8 - - - +
133A GLU* 1.3 64.1 + - + +
135A LEU* 3.3 21.7 + - - +
222A TYR* 3.5 30.1 - - + +
223A PHE* 4.2 12.5 - - + -
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Residues in contact with GLU 133 (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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102A PHE 3.3 10.0 - - - +
103A LYS* 3.4 19.7 - - + +
104A ASN* 2.7 39.7 + - - +
129A SER* 3.1 22.3 + - - +
130A LYS* 3.6 29.5 + - - +
131A VAL 3.2 0.2 - - - -
132A ALA* 1.3 77.4 - - + +
134A ALA* 1.3 49.2 + - - +
135A LEU 3.4 0.2 - - - -
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Residues in contact with ALA 134 (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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46A LEU* 4.6 1.8 - - + -
100A ILE* 4.6 9.6 - - + -
102A PHE* 3.5 28.2 + - + +
104A ASN 3.7 2.5 - - - +
105A GLU* 2.9 22.3 + - - +
106A PHE* 3.1 17.2 + - + +
109A VAL* 4.4 12.1 - - + -
130A LYS 3.1 11.5 + - - +
131A VAL* 3.0 12.8 + - - +
133A GLU* 1.3 79.4 - - - +
135A LEU* 1.3 57.4 + - - +
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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