Contacts of the helix formed by residues 138 - 150 (chain A) in PDB entry 1NZB
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 GLU 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A ALA* 3.6 13.9 - - + +
137A PHE* 1.3 76.0 - - - +
139A ARG* 1.3 68.0 + - - +
140A THR* 3.2 14.2 - - + +
141A ASP* 2.9 23.6 + - - +
142A PHE* 3.3 8.3 + - - +
168A TYR* 4.1 2.2 - - - -
294A GLY* 3.6 23.1 - - - +
297A ARG* 2.8 32.5 + - - -
298A ASP* 3.5 13.9 - - - +
301A ARG* 3.1 28.6 + - - -
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Residues in contact with ARG 139 (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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138A GLU* 1.3 72.7 - - - +
140A THR* 1.3 65.5 + - + +
142A PHE* 3.1 8.4 + - - +
143A ASP* 3.0 50.5 + - - +
146A ARG* 5.2 4.2 - - - +
168A TYR* 3.2 22.9 + - - +
298A ASP* 2.9 20.9 + - + +
338B LEU* 3.4 26.7 + - - +
339B LEU* 3.4 45.5 + - - +
341B ASP* 5.3 4.8 - - - +
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Residues in contact with THR 140 (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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138A GLU* 4.7 13.9 - - + +
139A ARG* 1.3 82.6 - - + +
141A ASP* 1.3 66.7 + - - +
143A ASP* 3.6 10.2 + - - +
144A GLN* 3.2 37.6 + - - +
298A ASP* 5.3 2.0 - - - +
301A ARG* 6.1 1.3 - - - +
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Residues in contact with ASP 141 (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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136A ALA 4.1 7.3 - - - +
137A PHE* 4.0 10.3 - - + -
138A GLU* 2.9 23.3 + - - +
140A THR* 1.3 82.5 + - - +
142A PHE* 1.3 61.9 + - - +
144A GLN* 3.8 7.6 - - - +
145A VAL* 2.8 34.3 + - - +
272A ILE* 5.0 0.9 - - - +
273A TYR* 3.1 24.6 + - - -
286A TRP* 3.4 29.9 + - + -
5303A MG 3.8 15.6 - - - -
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Residues in contact with PHE 142 (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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137A PHE* 3.9 27.3 - + + -
138A GLU 3.3 3.9 + - - +
139A ARG* 3.1 14.5 + - - +
141A ASP* 1.3 76.7 - - - +
143A ASP* 1.3 63.5 + - - +
145A VAL* 4.5 2.0 - - + -
146A ARG* 2.8 73.0 + - + +
161A LEU* 4.1 17.5 - - + -
164A LEU* 4.6 3.4 - - + -
165A GLY* 3.5 38.4 - - - -
168A TYR* 4.5 13.2 - + + -
217A VAL* 4.4 13.7 - - + -
220A LEU* 4.5 7.4 - - + -
339B LEU* 4.5 22.4 - - + -
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Residues in contact with ASP 143 (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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139A ARG* 3.0 52.9 + - - +
140A THR* 3.8 8.7 - - - +
142A PHE* 1.3 78.4 - - - +
144A GLN* 1.3 60.9 + - + +
146A ARG* 3.9 23.1 + - - +
147A SER* 3.1 26.0 + - - -
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Residues in contact with GLN 144 (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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140A THR* 3.2 29.0 + - - +
141A ASP* 3.8 8.8 - - - +
142A PHE 3.3 0.2 - - - -
143A ASP* 1.3 76.3 - - + +
145A VAL* 1.3 64.4 + - - +
147A SER* 3.1 20.4 + - - +
148A LEU* 3.7 15.4 + - + +
272A ILE* 4.5 13.9 - - + +
273A TYR* 3.9 18.0 + - - -
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Residues in contact with VAL 145 (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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137A PHE* 4.4 3.4 - - + -
141A ASP 2.8 23.7 + - - +
142A PHE* 4.0 5.2 - - + +
144A GLN* 1.3 74.0 - - - +
146A ARG* 1.3 63.6 + - - +
148A LEU* 3.5 3.6 + - - +
149A MET* 3.3 35.0 + - + +
161A LEU* 4.7 5.8 - - + -
164A LEU* 3.7 27.6 - - + -
268A THR* 3.6 22.7 - - + -
271A LEU* 5.7 2.0 - - + +
272A ILE* 3.2 28.3 - - + -
286A TRP* 4.0 10.8 - - + -
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Residues in contact with ARG 146 (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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139A ARG* 5.2 5.5 - - - +
142A PHE* 2.8 54.6 + - + +
143A ASP* 3.9 22.0 + - - +
145A VAL* 1.3 70.4 - - - +
147A SER* 1.3 58.9 + - - +
148A LEU 3.1 5.2 - - - -
149A MET 4.0 0.4 - - - -
150A GLU* 3.0 51.9 + - + +
161A LEU* 3.8 34.3 - - + -
216A GLY* 4.5 18.4 + - - -
217A VAL* 5.9 0.6 - - - +
220A LEU* 4.4 20.4 - - + +
339B LEU* 5.4 2.4 - - - +
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Residues in contact with SER 147 (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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143A ASP 3.1 14.8 + - - -
144A GLN* 3.1 15.4 + - - +
145A VAL 3.3 0.2 - - - -
146A ARG* 1.3 77.7 - - - +
148A LEU* 1.3 64.6 + - - +
150A GLU* 4.1 17.1 - - - +
151A ASN* 3.9 13.3 + - - -
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Residues in contact with LEU 148 (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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144A GLN* 3.8 14.8 - - + +
145A VAL 3.5 6.5 + - - +
146A ARG 3.1 0.4 - - - -
147A SER* 1.3 87.8 - - - +
149A MET* 1.3 64.9 + - + +
150A GLU 3.4 1.0 + - - -
151A ASN* 4.1 14.1 + - - +
152A SER* 4.9 2.9 + - - -
271A LEU* 4.9 13.2 - - + +
272A ILE* 4.4 24.0 - - + -
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Residues in contact with MET 149 (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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145A VAL* 3.3 32.2 + - - +
148A LEU* 1.3 78.7 - - - +
150A GLU* 1.3 58.8 + - - +
151A ASN 3.0 7.4 + - - -
152A SER* 3.3 21.8 + - - +
157A ASP* 3.4 48.8 - - + +
158A ILE* 5.7 1.2 - - - +
160A ASN* 4.2 17.5 - - + +
161A LEU* 3.9 27.5 - - + +
164A LEU* 5.1 0.7 - - - -
268A THR* 4.4 14.6 - - - +
271A LEU* 4.4 24.7 - - + -
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Residues in contact with GLU 150 (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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146A ARG* 3.0 38.5 + - + +
147A SER* 4.1 17.0 - - - +
149A MET* 1.3 78.5 - - - +
151A ASN* 1.3 75.0 + - - +
152A SER 3.4 3.1 + - - +
161A LEU* 4.1 13.2 - - + +
220A LEU* 5.9 3.0 - - + +
223A ARG* 5.1 9.1 + - - +
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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