Contacts of the helix formed by residues 150 - 162 (chain D) in PDB entry 1NBI
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 GLN 150 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145D ASP* 3.8 7.0 + - - +
148D GLY 5.6 0.2 - - - +
149D ASP* 1.3 68.6 - - - +
151D SER* 1.3 56.8 - - - -
152D GLU 3.4 2.2 - - - -
153D HIS* 2.7 47.5 + - + +
154D ARG* 2.9 63.4 + - + +
243D TYR* 2.7 30.4 + - - -
245D HIS* 4.3 1.2 + - - -
249D SER* 4.4 10.6 + - - -
253D LEU* 4.6 11.5 - - + +
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Residues in contact with SER 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D LYS* 3.0 33.5 + - - +
149D ASP* 2.4 55.0 + - - +
150D GLN* 1.3 66.3 - - - +
152D GLU* 1.3 55.4 + - - -
154D ARG* 3.9 7.5 - - - +
155D LEU* 3.0 27.5 + - - +
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Residues in contact with GLU 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D LEU* 3.6 19.6 - - + +
143D LEU* 4.2 8.7 - - + +
144D PRO* 3.1 21.0 - - - +
145D ASP* 2.5 11.6 - - - +
146D SER* 2.2 48.8 + - - -
147D LYS* 2.4 17.1 + - + -
149D ASP 4.4 1.1 - - - +
151D SER* 1.3 74.2 - - - +
153D HIS* 1.3 58.3 + - + +
155D LEU* 3.1 9.3 + - + +
156D ALA* 2.7 36.4 + - - +
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Residues in contact with HIS 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D PHE* 3.9 19.4 - + + -
143D LEU* 2.7 34.8 + - + -
144D PRO 3.2 22.5 - - - -
145D ASP* 3.3 6.6 + - - -
150D GLN* 2.7 36.5 + - + +
152D GLU* 1.3 72.3 - - + +
154D ARG* 1.3 56.1 + - - +
155D LEU 2.6 15.8 + - - -
156D ALA 2.8 12.6 + - - -
157D LEU* 2.8 14.7 + - - +
243D TYR* 3.4 31.4 - + - -
245D HIS* 3.1 22.7 + + - +
253D LEU* 4.7 4.7 - - + -
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Residues in contact with ARG 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D ASP* 5.1 4.0 - - - +
150D GLN* 2.9 54.7 + - - +
151D SER* 3.9 6.0 - - - +
153D HIS* 1.3 76.4 - - - +
155D LEU* 1.3 61.8 + - - +
157D LEU* 4.1 6.0 - - - +
158D LYS* 3.4 18.7 + - - +
252D GLU* 5.0 9.1 + - - -
253D LEU* 3.2 39.2 - - + +
256D GLU* 3.4 25.3 + - + +
257D ALA* 5.5 2.1 - - - +
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Residues in contact with LEU 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D LEU* 3.4 50.0 - - + +
151D SER 3.0 15.6 + - - +
152D GLU* 3.1 10.1 - - - +
153D HIS 2.6 4.9 + - - -
154D ARG* 1.3 70.9 - - - +
156D ALA* 1.3 56.4 + - - +
158D LYS* 2.8 39.8 + - + +
159D ASN* 3.1 19.0 + - - +
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Residues in contact with ALA 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D TRP* 3.5 32.0 - - + +
118D LEU* 3.6 5.2 - - + -
140D PHE* 3.8 6.7 - - + -
143D LEU* 3.4 33.9 - - + -
152D GLU 2.7 11.5 + - - +
153D HIS 3.6 0.9 - - - +
155D LEU* 1.3 73.0 - - - +
157D LEU* 1.3 65.0 + - - +
158D LYS 3.1 0.2 + - - -
159D ASN* 3.4 1.9 + - - +
160D ILE* 3.1 28.3 + - - +
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Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D PHE* 3.5 33.8 - - + -
153D HIS 2.8 11.8 + - - +
154D ARG* 4.1 6.1 - - - +
156D ALA* 1.3 78.4 - - - +
158D LYS* 1.3 55.8 + - - +
160D ILE* 3.5 9.2 - - + +
161D ALA* 3.0 26.5 + - - +
170D LEU* 5.4 5.0 - - + +
172D ILE* 3.4 32.5 - - + -
250D PHE* 4.4 9.0 - - + -
253D LEU* 4.0 36.8 - - + +
254D VAL* 4.3 19.5 - - + +
257D ALA* 3.7 9.4 - - + +
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Residues in contact with LYS 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D ARG 3.4 12.1 + - - +
155D LEU* 2.8 30.1 + - + +
157D LEU* 1.3 69.1 - - - +
159D ASN* 1.3 76.4 + - - +
160D ILE 3.0 1.1 - - - -
161D ALA* 2.8 15.3 + - - +
162D SER* 2.9 15.7 + - - -
257D ALA* 4.1 25.1 - - - +
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Residues in contact with ASN 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D TRP 2.7 29.4 + - - +
118D LEU* 2.9 20.6 + - - +
119D THR* 3.5 3.2 - - - +
120D LEU* 3.0 21.3 - - + +
121D ASP* 3.1 31.2 + - - +
155D LEU* 3.1 14.6 + - - +
156D ALA 3.8 3.1 - - - +
158D LYS* 1.3 85.8 - - - +
160D ILE* 1.3 63.4 + - - +
162D SER* 2.8 25.7 + - - -
163D MET* 3.6 9.5 + - - +
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Residues in contact with ILE 160 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63D VAL* 4.3 13.9 - - + -
117D TRP* 4.3 21.5 - - + +
120D LEU* 3.7 20.9 - - + -
133D VAL* 3.9 24.0 - - + -
135D CYS* 5.1 2.5 - - + -
140D PHE* 4.4 9.4 - - + -
156D ALA 3.1 19.2 + - - +
157D LEU* 3.5 26.7 - - + +
158D LYS 3.0 0.8 - - - -
159D ASN* 1.3 76.0 - - - +
161D ALA* 1.3 54.1 + - - +
163D MET* 2.6 36.7 + - - +
164D VAL* 3.9 2.7 + - + +
170D LEU* 4.2 19.7 - - + -
172D ILE* 4.7 6.1 - - + -
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Residues in contact with ALA 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D LEU 3.0 11.0 + - - +
158D LYS 2.8 12.8 + - - +
160D ILE* 1.3 76.7 - - - +
162D SER* 1.3 56.3 + - - +
164D VAL* 2.9 24.5 + - - +
170D LEU* 4.7 1.5 - - + +
257D ALA* 3.8 22.4 - - + +
258D PHE* 3.5 35.8 - - + -
290D LYS* 3.2 16.0 + - - +
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Residues in contact with SER 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ASP* 5.0 6.2 - - - +
126D ALA* 4.1 9.7 - - - +
129D GLY* 5.5 0.7 - - - -
158D LYS* 2.9 14.7 + - - -
159D ASN* 2.8 21.0 + - - -
160D ILE 2.9 0.4 + - - -
161D ALA* 1.3 75.1 - - - +
163D MET* 1.3 68.5 + - - +
164D VAL 3.2 4.6 - - - +
290D LYS* 4.3 7.2 - - - +
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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