Contacts of the helix formed by residues 125 - 139 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A TRP* 3.7 42.6 - - + +
125A LEU* 3.9 10.3 - - + -
121B TRP* 2.7 45.0 + - + +
124B ASN* 1.3 80.3 - - - +
126B THR* 1.3 64.2 + - - +
127B SER 3.4 1.3 - - - -
128B MET* 3.3 8.3 - - - +
129B LEU* 3.0 25.5 + - - +
170B GLY* 3.4 30.3 - - - +
173B ALA* 3.6 19.5 - - + -
174B ARG* 3.9 7.9 - - + +
177B LEU* 4.6 5.2 - - + +
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Residues in contact with THR 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A SER* 3.7 36.1 - - - +
117A VAL* 3.6 15.3 - - + +
118A ASN* 2.7 31.1 + - - +
121A TRP* 2.9 25.0 + - - +
73B LEU* 4.7 2.5 - - + -
121B TRP 3.0 3.9 + - - -
122B ALA* 3.5 9.2 - - + +
125B LEU* 1.3 76.2 - - - +
127B SER* 1.3 58.5 + - - +
129B LEU* 3.3 2.3 + - - +
130B CYS* 2.9 31.7 + - - -
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Residues in contact with SER 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 3.5 45.3 - - - +
73B LEU* 3.9 22.2 - - - +
98B ALA* 6.1 0.5 - - - +
122B ALA 3.1 8.3 + - - -
123B LEU* 2.7 22.3 + - - +
126B THR* 1.3 76.0 - - - +
128B MET* 1.3 58.4 + - - +
131B LEU* 2.9 35.9 + - - +
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Residues in contact with MET 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ASN* 3.6 25.3 - - + +
98B ALA 6.0 0.2 - - - +
123B LEU 5.4 0.2 - - - +
124B ASN 3.6 5.8 - - - +
125B LEU 3.3 13.2 + - - +
127B SER* 1.3 82.8 + - - +
129B LEU* 1.3 58.0 + - - +
131B LEU* 3.7 2.7 - - - +
132B THR* 2.6 37.6 + - - -
151B ASN* 3.5 33.4 - - + +
174B ARG* 3.5 42.0 - - + +
177B LEU* 4.1 16.2 - - - -
178B PHE* 3.7 31.4 - - + -
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 3.4 38.6 - - + -
111A LEU* 4.1 26.0 - - + +
117A VAL* 3.9 20.4 - - + -
121A TRP* 4.4 4.7 - - + -
166A LEU* 3.6 30.3 - - + -
125B LEU 3.0 17.3 + - - +
126B THR 3.3 3.8 + - - +
128B MET* 1.3 80.0 - - - +
130B CYS* 1.3 59.3 + - - +
132B THR* 3.2 4.6 + - - -
133B SER* 2.9 27.0 + - - -
177B LEU* 4.1 20.6 - - + -
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Residues in contact with CYS 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU 3.7 20.6 - - - +
112A SER* 4.1 10.3 - - - +
113A ASP 4.4 1.1 - - - -
114A SER* 3.9 36.3 - - - -
117A VAL* 4.6 6.5 - - - -
73B LEU* 4.4 12.8 - - + -
77B LEU* 4.3 8.5 - - + -
126B THR* 2.9 27.2 + - - +
127B SER 4.1 1.3 - - - +
129B LEU* 1.3 71.2 - - - +
131B LEU* 1.3 62.8 + - - +
133B SER* 3.3 1.4 + - - -
134B SER* 2.9 31.2 + - - -
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 4.2 9.9 - - + -
10B THR* 3.6 31.0 - - + +
67B LEU* 5.0 5.6 - - + -
73B LEU* 5.0 2.6 - - + +
76B LEU* 3.9 18.8 - - + -
77B LEU* 4.1 11.6 - - + +
80B LEU* 4.1 11.7 - - + -
94B LEU* 4.0 13.2 - - + -
96B ASN* 3.8 15.5 - - - +
127B SER* 2.9 21.8 + - - +
128B MET* 3.7 5.2 - - - +
130B CYS* 1.3 78.2 - - - +
132B THR* 1.3 62.2 + - - +
134B SER* 3.6 1.0 + - - -
135B VAL* 3.0 46.6 + - + +
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Residues in contact with THR 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A PHE* 3.7 20.9 - - + -
94B LEU* 3.6 15.0 - - + -
96B ASN* 3.1 20.8 + - - -
128B MET 2.6 25.1 + - - -
129B LEU 3.6 3.4 - - - -
131B LEU* 1.3 75.1 - - - +
133B SER* 1.3 63.3 + - - +
135B VAL* 3.3 2.6 + - - +
136B LEU* 3.1 26.0 + - + +
149B VAL* 4.0 9.6 - - + -
178B PHE* 3.6 22.0 - - + -
181B LEU* 4.0 11.7 - - + -
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Residues in contact with SER 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 3.0 36.3 - - - -
109A VAL* 3.2 23.8 + - - +
111A LEU* 2.9 27.8 + - - -
112A SER* 3.8 3.5 + - - -
129B LEU* 2.9 12.4 + - - -
130B CYS* 3.3 6.4 + - - -
132B THR* 1.3 77.5 - - - +
134B SER* 1.3 59.6 + - - +
136B LEU* 3.5 4.0 + - - +
137B LYS* 3.1 21.0 + - - +
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Residues in contact with SER 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A VAL 4.9 0.4 - - - -
112A SER* 4.5 17.0 - - - -
77B LEU* 3.2 24.9 - - - +
80B LEU* 4.3 7.4 - - - +
130B CYS 2.9 18.8 + - - -
131B LEU 3.6 1.7 + - - -
133B SER* 1.3 78.9 + - - +
135B VAL* 1.3 60.9 + - - +
137B LYS* 3.8 8.2 - - - +
138B ALA* 3.0 27.7 + - - +
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Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 4.0 17.0 - - + -
80B LEU* 3.4 25.4 - - + -
92B LEU* 3.9 31.2 - - + -
94B LEU* 4.5 20.6 - - + -
131B LEU* 3.0 32.4 + - + +
132B THR 3.3 4.5 + - - +
134B SER* 1.3 77.0 - - - +
136B LEU* 1.3 60.9 + - + +
138B ALA* 3.4 3.7 + - - -
139B PHE* 2.9 35.5 + - + +
149B VAL* 5.7 0.7 - - + -
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 4.9 1.8 - - + -
109A VAL* 4.0 20.5 - - + +
92B LEU* 4.3 15.3 - - + -
132B THR* 3.1 26.1 + - + +
133B SER* 3.9 4.7 - - - +
135B VAL* 1.3 74.3 - - + +
137B LYS* 1.3 61.0 + - - +
139B PHE 3.2 17.2 - - - +
140B PRO* 3.8 3.8 - - - +
147B ARG* 3.3 28.8 + - + +
149B VAL* 4.0 20.2 - - + -
181B LEU* 3.9 38.6 - - + -
185B GLU* 5.3 0.4 - - + -
188B VAL* 4.1 20.9 - - + -
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Residues in contact with LYS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A VAL* 3.8 22.6 - - + +
110A ASP* 3.3 28.3 - - - +
133B SER 3.1 17.0 + - - +
134B SER* 4.1 7.6 - - - +
135B VAL 3.3 0.2 - - - -
136B LEU* 1.3 75.7 - - - +
138B ALA* 1.3 65.1 + - - +
140B PRO* 4.0 10.8 - - - +
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B LEU* 5.2 14.6 - - + +
81B ARG* 5.9 2.5 - - - +
134B SER 3.0 19.5 + - - +
135B VAL* 3.8 4.9 - - - +
137B LYS* 1.3 77.8 - - - +
139B PHE* 1.3 77.7 + - + +
140B PRO* 3.3 8.9 - - - +
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Residues in contact with PHE 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 3.9 32.1 - - + -
8B LEU* 5.6 1.1 - - + -
80B LEU* 5.1 4.9 - - + -
83B LEU* 4.1 29.8 - - + -
84B PRO 4.5 4.5 - - - -
85B ARG* 4.9 16.6 - - + -
89B LEU* 4.2 15.0 - - + -
92B LEU* 3.6 37.2 - - + +
135B VAL* 2.9 21.2 + - + -
136B LEU* 3.2 6.8 - - - +
138B ALA* 1.3 91.4 - - + +
140B PRO* 1.3 64.7 - - - +
145B LEU* 5.1 5.6 - - + -
147B ARG* 2.8 25.4 + - - -
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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
------------------------------------------------------------
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