Contacts of the helix formed by residues 125 - 139 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E TRP* 2.7 43.9 + - + +
124E ASN* 1.3 81.4 - - - +
126E THR* 1.3 64.9 + - - +
127E SER 3.4 1.8 - - - -
128E MET* 3.3 7.8 - - - +
129E LEU* 3.0 25.8 + - - +
170E GLY* 3.5 29.4 - - - +
173E ALA* 3.6 20.0 - - + -
174E ARG* 3.9 8.5 - - + +
177E LEU* 4.6 5.0 - - + +
121F TRP* 3.6 44.2 - - + +
125F LEU* 4.0 10.1 - - + -
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Residues in contact with THR 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E LEU* 4.8 2.2 - - + -
121E TRP 3.0 4.3 + - - -
122E ALA* 3.5 8.7 - - + +
125E LEU* 1.3 75.8 - - - +
127E SER* 1.3 60.9 + - - +
129E LEU* 3.3 1.9 + - - +
130E CYS* 2.9 31.6 + - - -
114F SER* 3.7 37.5 - - - +
117F VAL* 3.5 18.0 - - + +
118F ASN* 2.7 29.9 + - - +
121F TRP* 3.0 21.3 + - - -
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Residues in contact with SER 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E LEU* 3.5 45.8 - - - +
73E LEU* 3.9 21.2 - - - +
98E ALA* 6.0 0.2 - - - +
122E ALA 3.1 6.2 + - - -
123E LEU* 2.6 25.3 + - - +
126E THR* 1.3 76.8 - - - +
128E MET* 1.3 59.0 + - - +
131E LEU* 2.9 36.3 + - - +
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Residues in contact with MET 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E ASN* 3.8 22.8 - - + +
124E ASN 3.6 7.2 - - - +
125E LEU 3.3 13.2 - - - +
127E SER* 1.3 83.0 + - - +
129E LEU* 1.3 58.7 + - - +
131E LEU* 3.7 2.5 - - - +
132E THR* 2.6 37.4 + - - -
151E ASN* 3.6 32.5 - - + +
174E ARG* 3.5 42.4 - - + +
177E LEU* 4.1 16.2 - - - -
178E PHE* 3.7 32.8 - - + -
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Residues in contact with LEU 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E LEU 3.0 17.7 + - - +
126E THR 3.7 3.4 - - - +
128E MET* 1.3 79.7 - - - +
130E CYS* 1.3 61.0 + - - +
132E THR* 3.2 4.3 + - - -
133E SER* 2.9 28.5 + - - -
177E LEU* 4.1 23.3 - - + -
108F PHE* 3.3 38.8 - - + +
111F LEU* 4.2 24.9 - - + +
117F VAL* 4.0 20.6 - - + -
121F TRP* 4.5 2.9 - - + -
166F LEU* 3.7 29.8 - - + -
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Residues in contact with CYS 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E LEU* 4.4 12.3 - - + -
77E LEU* 4.0 8.5 - - + +
126E THR* 2.9 27.2 + - - +
127E SER 4.2 1.6 - - - +
129E LEU* 1.3 70.1 - - - +
131E LEU* 1.3 63.7 + - - +
133E SER* 3.3 1.6 + - - -
134E SER* 2.8 31.6 + - - -
111F LEU 3.7 22.2 - - - +
112F SER* 4.0 11.1 - - - +
113F ASP 4.3 0.9 - - - -
114F SER* 3.8 36.6 - - - -
117F VAL* 4.6 5.8 - - - -
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Residues in contact with LEU 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E LEU* 4.2 13.0 - - + -
10E THR* 3.6 30.5 - - + -
67E LEU* 4.9 6.3 - - + -
73E LEU* 5.3 2.0 - - + -
76E LEU* 3.8 22.2 - - + -
77E LEU* 4.1 12.0 - - + +
80E LEU* 5.0 6.3 - - + -
94E LEU* 4.1 12.6 - - + -
96E ASN* 3.8 14.6 - - - +
127E SER* 2.9 22.9 + - - +
128E MET* 3.7 4.9 - - - +
130E CYS* 1.3 78.0 - - - +
132E THR* 1.3 61.3 + - - +
134E SER* 3.5 1.4 + - - -
135E VAL* 3.0 46.3 + - + +
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Residues in contact with THR 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E LEU* 3.6 15.5 - - + -
96E ASN* 3.1 21.1 + - - -
128E MET 2.6 23.0 + - - -
129E LEU 3.6 3.4 - - - -
131E LEU* 1.3 75.6 - - - +
133E SER* 1.3 64.7 + - - +
135E VAL* 3.3 2.8 + - - +
136E LEU* 3.1 30.5 + - + +
149E VAL* 4.1 4.7 - - + -
178E PHE* 3.6 17.3 - - + -
181E LEU* 3.9 17.7 - - + -
108F PHE* 3.8 19.5 - - + -
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Residues in contact with SER 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E LEU 2.9 12.5 + - - -
130E CYS 3.3 6.9 + - - -
132E THR* 1.3 76.8 - - - +
134E SER* 1.3 59.7 + - - +
136E LEU* 3.6 4.6 + - - +
137E LYS* 3.1 20.4 + - - +
108F PHE* 3.1 37.0 - - - -
109F VAL* 3.3 24.9 + - - +
111F LEU* 3.0 26.5 + - - -
112F SER* 3.9 3.5 + - - -
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Residues in contact with SER 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E LEU* 3.2 24.7 - - - +
80E LEU* 3.7 11.1 - - - +
130E CYS 2.8 22.1 + - - -
131E LEU 3.5 2.1 + - - -
133E SER* 1.3 76.5 + - - +
135E VAL* 1.3 60.4 + - - +
137E LYS* 3.8 8.0 - - - +
138E ALA* 3.0 28.2 + - - +
109F VAL 5.0 0.7 - - - -
112F SER* 4.6 14.8 - - - -
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Residues in contact with VAL 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E LEU* 4.0 11.0 - - + -
80E LEU* 3.7 31.4 - - + -
92E LEU* 3.9 31.0 - - + -
94E LEU* 4.5 20.4 - - + -
131E LEU* 3.0 34.0 + - + +
132E THR 3.3 3.8 + - - +
134E SER* 1.3 76.0 - - - +
136E LEU* 1.3 63.7 + - + +
138E ALA* 3.3 2.8 + - - -
139E PHE* 2.9 34.0 + - + +
149E VAL* 5.6 0.4 - - + -
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Residues in contact with LEU 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E LEU* 4.3 15.5 - - + -
132E THR* 3.1 26.2 + - + +
133E SER 4.0 4.5 - - - +
134E SER 3.3 0.2 - - - -
135E VAL* 1.3 76.7 - - + +
137E LYS* 1.3 60.7 + - - +
139E PHE 3.2 17.0 - - - +
140E PRO* 3.8 3.6 - - - +
147E ARG* 3.3 29.4 + - + +
149E VAL* 4.0 20.2 - - + -
181E LEU* 3.8 39.7 - - + -
185E GLU* 5.3 0.7 - - + -
188E VAL* 4.1 19.5 - - + -
108F PHE* 5.0 2.0 - - + -
109F VAL* 4.2 18.6 - - + +
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Residues in contact with LYS 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E SER 3.1 16.6 + - - +
134E SER* 4.0 7.4 - - - +
135E VAL 3.3 0.2 - - - -
136E LEU* 1.3 76.9 - - - +
138E ALA* 1.3 62.9 + - - +
139E PHE 3.6 0.2 + - - -
140E PRO* 4.1 11.3 - - - +
109F VAL* 3.6 31.1 - - + +
110F ASP* 3.7 17.3 - - - +
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Residues in contact with ALA 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E LEU* 5.1 15.0 - - + +
81E ARG* 6.2 1.3 - - - -
134E SER 3.0 18.9 + - - +
135E VAL* 3.7 5.4 - - - +
137E LYS* 1.3 78.0 - - - +
139E PHE* 1.3 76.3 + - + +
140E PRO* 3.3 8.7 - - - +
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Residues in contact with PHE 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E VAL* 3.9 34.3 - - + -
8E LEU* 5.6 0.9 - - + -
80E LEU* 5.4 9.0 - - + -
83E LEU* 4.9 22.2 - - + -
85E ARG* 4.0 24.9 - - + -
89E LEU* 4.1 17.0 - - + -
92E LEU* 3.6 34.3 - - + +
135E VAL* 2.9 19.8 + - + +
136E LEU* 3.2 6.7 - - - +
138E ALA* 1.3 91.9 - - + +
140E PRO* 1.3 65.6 - - - +
145E LEU* 5.1 5.2 - - + -
147E ARG* 2.8 25.2 + - - -
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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