Contacts of the helix formed by residues 125 - 139 (chain C) in PDB entry 1Z6Z
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 LEU 125 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C TRP* 2.7 46.0 + - + +
124C ASN* 1.3 81.2 - - + +
126C THR* 1.3 65.7 + - - +
127C SER 3.4 1.1 - - - -
128C MET* 3.3 7.6 - - - +
129C LEU* 3.0 24.7 + - - +
170C GLY* 3.5 28.9 - - - +
173C ALA* 3.5 20.2 - - + -
174C ARG* 3.9 8.1 - - + +
177C LEU* 4.7 6.5 - - + +
121D TRP* 3.6 41.1 - - + +
125D LEU* 3.9 9.6 - - + -
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Residues in contact with THR 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C LEU* 4.8 2.7 - - + -
121C TRP 3.0 4.3 + - - -
122C ALA 3.5 9.2 - - - -
125C LEU* 1.3 76.4 - - - +
127C SER* 1.3 60.0 + - - +
129C LEU* 3.2 1.8 + - - +
130C CYS* 2.9 31.8 + - - +
114D SER* 3.7 36.1 - - - +
117D VAL* 3.7 15.6 - - + +
118D ASN* 2.6 30.3 + - - +
121D TRP* 3.0 22.8 + - - +
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Residues in contact with SER 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU* 3.5 46.3 - - - +
73C LEU* 3.9 22.3 - - - +
98C ALA* 6.0 0.5 - - - +
122C ALA 3.1 8.5 + - - -
123C LEU* 2.7 23.7 + - - +
126C THR* 1.3 75.0 - - - +
128C MET* 1.3 58.4 + - - +
131C LEU* 2.9 35.5 + - - +
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Residues in contact with MET 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ASN* 3.8 24.2 - - + +
98C ALA 6.0 0.2 - - - +
123C LEU 4.5 0.4 + - - +
124C ASN 3.6 6.7 - - - +
125C LEU 3.3 10.4 + - - +
127C SER* 1.3 82.2 + - - +
129C LEU* 1.3 58.7 + - - +
131C LEU* 3.7 2.9 - - - +
132C THR* 2.6 37.4 + - - -
151C ASN* 3.6 32.5 - - + +
174C ARG* 3.6 40.8 - - + +
177C LEU* 4.1 17.0 - - - -
178C PHE* 3.7 33.0 - - + -
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Residues in contact with LEU 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C LEU 3.0 17.5 + - - +
126C THR 3.6 2.7 - - - +
128C MET* 1.3 79.7 - - - +
130C CYS* 1.3 62.3 + - - +
132C THR* 3.3 3.6 + - - -
133C SER* 3.0 28.6 + - - -
177C LEU* 4.1 21.8 - - + -
108D PHE* 3.4 40.2 - - + -
111D LEU* 4.4 21.1 - - + +
117D VAL* 3.9 22.4 - - + -
121D TRP* 4.5 4.5 - - + -
166D LEU* 3.8 29.4 - - + -
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Residues in contact with CYS 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C LEU* 4.4 12.6 - - + -
77C LEU* 4.0 10.0 - - + +
126C THR* 2.9 26.0 + - - +
127C SER 4.3 1.6 - - - +
129C LEU* 1.3 70.8 - - - +
131C LEU* 1.3 58.7 + - - +
133C SER* 3.2 8.7 + - - -
134C SER* 2.8 36.0 + - - -
111D LEU 3.8 13.9 - - - -
112D SER* 3.9 13.4 - - - +
113D ASP 4.4 1.1 - - - -
114D SER* 3.8 33.4 - - - -
117D VAL* 4.6 7.2 - - - -
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Residues in contact with LEU 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LEU* 4.2 10.3 - - + -
10C THR* 3.6 30.3 - - + -
67C LEU* 4.9 6.1 - - + -
73C LEU* 5.0 2.9 - - + +
76C LEU* 3.8 19.1 - - + -
77C LEU* 4.1 11.4 - - + +
80C LEU* 3.9 22.2 - - + -
94C LEU* 4.1 13.5 - - + -
96C ASN* 3.8 13.7 - - - +
127C SER* 2.9 23.2 + - - +
128C MET* 3.7 4.7 - - - +
130C CYS* 1.3 77.9 - - - +
132C THR* 1.3 61.9 - - - +
134C SER* 3.6 0.9 + - - -
135C VAL* 3.0 38.1 + - + +
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Residues in contact with THR 132 (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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94C LEU* 3.6 8.3 - - + -
96C ASN* 3.0 21.5 + - - -
128C MET 2.6 23.7 + - - -
129C LEU 3.3 3.3 + - - -
131C LEU* 1.3 77.0 - - - +
133C SER* 1.3 62.6 + - - +
135C VAL* 3.7 1.9 - - - +
136C LEU* 3.1 25.4 + - + +
149C VAL* 4.0 16.8 - - + -
178C PHE* 3.5 19.0 - - + -
181C LEU* 3.9 28.7 - - + -
108D PHE* 4.0 6.7 - - + -
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Residues in contact with SER 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C LEU 3.0 12.1 + - - -
130C CYS* 3.2 8.8 + - - -
132C THR* 1.3 77.1 - - - +
134C SER* 1.3 59.2 + - - +
136C LEU* 3.5 5.8 + - - +
137C LYS* 3.1 26.0 + - - +
108D PHE* 3.3 37.0 - - - -
109D VAL* 3.6 16.3 + - - +
111D LEU* 3.1 24.8 + - - -
112D SER* 4.0 4.2 - - - -
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Residues in contact with SER 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU* 3.2 24.9 - - - +
80C LEU* 4.3 7.3 - - - +
81C ARG* 6.1 4.5 - - - -
130C CYS 2.8 20.5 + - - -
131C LEU 3.6 2.1 + - - -
133C SER* 1.3 78.9 + - - +
135C VAL* 1.3 62.2 + - - +
137C LYS* 3.8 7.4 - - - +
138C ALA* 3.0 29.1 + - - +
109D VAL 5.3 0.4 - - - -
112D SER* 4.8 13.2 - - - -
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Residues in contact with VAL 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LEU* 3.9 12.1 - - + -
80C LEU* 3.4 35.7 - - + -
92C LEU* 3.9 31.4 - - + -
94C LEU* 4.6 20.4 - - + -
131C LEU* 3.0 28.9 + - + +
132C THR 3.7 4.0 - - - +
134C SER* 1.3 78.9 - - - +
136C LEU* 1.3 61.7 + - + +
138C ALA* 3.4 4.0 + - - -
139C PHE* 2.9 32.5 + - + +
149C VAL* 5.6 0.7 - - + -
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Residues in contact with LEU 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LEU* 4.3 16.2 - - + -
132C THR* 3.1 25.5 + - + +
133C SER* 3.9 4.0 - - - +
135C VAL* 1.3 75.7 - - + +
137C LYS* 1.3 63.2 + - - +
139C PHE 3.2 16.4 - - - +
140C PRO* 3.8 3.8 - - - +
147C ARG* 3.2 29.2 + - + +
149C VAL* 4.0 21.1 - - + -
181C LEU* 3.9 39.3 - - + -
185C GLU* 5.2 0.9 - - + -
188C VAL* 4.1 20.0 - - + -
108D PHE* 5.0 2.2 - - + -
109D VAL* 4.5 17.2 - - + +
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Residues in contact with LYS 137 (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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133C SER 3.1 15.5 + - - +
134C SER* 4.0 7.9 - - - +
135C VAL 3.3 0.2 - - - -
136C LEU* 1.3 77.2 - - - +
138C ALA* 1.3 63.5 + - - +
140C PRO* 4.0 11.8 - - - +
109D VAL* 3.4 33.1 - - + +
110D ASP* 3.4 22.7 - - - +
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Residues in contact with ALA 138 (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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80C LEU* 4.8 13.2 - - + +
81C ARG* 5.3 10.8 - - + -
134C SER 3.0 19.0 + - - +
135C VAL* 3.8 4.7 - - - +
137C LYS* 1.3 78.7 - - - +
139C PHE* 1.3 78.1 + - + +
140C PRO* 3.3 9.2 - - - +
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Residues in contact with PHE 139 (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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6C VAL* 3.9 34.3 - - + -
8C LEU* 5.6 0.2 - - + -
80C LEU* 4.7 11.9 - - + -
83C LEU* 4.4 26.9 - - + -
84C PRO 4.7 1.8 - - - -
85C ARG* 4.4 32.3 - - + +
89C LEU* 4.4 13.2 - - + -
92C LEU* 3.6 33.8 - - + +
135C VAL* 2.9 21.1 + - + +
136C LEU* 3.2 6.2 - - - +
138C ALA* 1.3 91.6 - - + +
140C PRO* 1.3 64.4 - - - +
145C LEU* 5.1 2.0 - - + -
147C ARG* 2.8 25.7 + - - -
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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
------------------------------------------------------------
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