Contacts of the helix formed by residues 146 - 156 (chain A) in PDB entry 1NPR
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 ASN 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LEU* 5.3 0.2 - - - +
42A LEU* 3.3 28.3 - - - +
144A HIS* 4.1 8.6 + - + +
145A MET* 1.3 83.2 - - - +
147A ASP* 1.3 64.5 + - - +
148A LYS* 4.1 10.8 - - - +
149A LEU* 2.7 44.0 + - - +
150A LEU* 3.1 25.9 + - - +
168A LYS* 5.6 4.9 - - - +
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Residues in contact with ASP 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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146A ASN* 1.3 73.6 - - - +
148A LYS* 1.3 66.4 + - + +
150A LEU* 3.3 10.6 + - - +
151A MET* 3.0 42.6 + - + +
168A LYS* 4.1 18.1 + - - -
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Residues in contact with LYS 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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37A GLU* 3.8 29.2 + - - -
39A LEU* 4.2 25.5 - - + +
146A ASN* 3.4 10.3 + - - +
147A ASP* 1.3 74.1 - - + +
149A LEU* 1.3 66.9 + - - +
151A MET* 3.1 19.2 + - + +
152A ALA* 2.9 24.3 + - - +
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Residues in contact with LEU 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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30A LEU* 5.8 0.2 - - + -
34A LEU* 3.8 29.2 - - + -
39A LEU* 4.1 13.8 - - + +
42A LEU* 4.5 6.7 - - + -
43A VAL* 4.0 10.8 - - + -
141A ILE* 5.0 1.8 - - + -
143A ALA* 3.8 23.1 - - + -
144A HIS 3.5 21.8 - - - +
145A MET* 3.9 18.8 - - + -
146A ASN* 2.7 22.9 + - - +
148A LYS* 1.3 76.5 - - - +
150A LEU* 1.3 57.2 - - - +
152A ALA* 3.1 4.1 + - + +
153A ILE* 2.8 50.0 + - + +
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Residues in contact with LEU 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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145A MET* 4.1 8.3 - - + -
146A ASN 3.1 18.0 + - - +
147A ASP* 3.4 11.4 - - - +
148A LYS 3.1 0.2 - - - -
149A LEU* 1.3 77.7 - - - +
151A MET* 1.3 64.2 + - + +
153A ILE* 3.1 8.7 + - - +
154A GLU* 2.9 48.9 + - - +
162A PRO* 3.8 14.4 - - + -
164A MET* 3.6 17.9 - - + -
168A LYS* 5.0 10.8 - - + +
169A PRO* 3.8 32.8 - - + -
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Residues in contact with MET 151 (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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147A ASP* 3.0 45.7 + - + +
148A LYS* 3.1 20.8 + - + +
150A LEU* 1.3 76.9 - - + +
152A ALA* 1.3 56.0 + - - +
154A GLU* 3.5 8.6 + - - +
155A LYS* 2.9 35.5 + - + +
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Residues in contact with ALA 152 (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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30A LEU* 5.1 0.7 - - + -
33A VAL* 3.8 17.9 - - + +
34A LEU* 5.3 2.9 - - + -
37A GLU* 4.4 4.0 - - + +
39A LEU* 3.6 22.9 - - + -
148A LYS 2.9 12.6 + - - +
149A LEU* 3.4 10.8 - - + +
151A MET* 1.3 76.0 - - - +
153A ILE* 1.3 57.4 + - - +
155A LYS* 2.9 27.7 - - + +
156A THR* 2.7 24.8 + - - -
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Residues in contact with ILE 153 (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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16A LEU* 3.3 30.1 - - + -
30A LEU* 4.3 15.7 - - + +
141A ILE* 4.1 14.4 - - + -
145A MET* 4.0 20.2 - - + -
149A LEU* 2.8 47.9 + - + +
150A LEU* 3.4 9.2 - - - +
152A ALA* 1.3 72.7 - - - +
154A GLU* 1.3 61.1 + - - +
156A THR* 3.1 23.5 + - - -
159A VAL* 3.5 20.0 - - + +
161A ARG* 4.7 0.2 - - - -
162A PRO* 4.2 19.3 - - + -
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Residues in contact with GLU 154 (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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150A LEU* 2.9 39.7 + - + +
151A MET* 3.8 7.0 - - - +
153A ILE* 1.3 78.9 - - - +
155A LYS* 1.3 57.6 + - - +
156A THR 3.2 1.3 + - - +
159A VAL 4.0 10.6 - - - +
160A PHE 3.7 22.1 - - - +
161A ARG* 3.6 36.1 + - + +
162A PRO* 4.8 0.2 - - + -
164A MET* 4.2 5.2 - - - +
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Residues in contact with LYS 155 (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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33A VAL* 4.7 8.5 - - + +
37A GLU* 3.5 32.1 - - - +
151A MET* 2.9 23.8 + - + +
152A ALA* 2.9 32.8 - - + +
154A GLU* 1.3 76.2 - - - +
156A THR* 1.3 62.4 + - - +
157A PRO* 3.5 7.1 - - - +
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Residues in contact with THR 156 (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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29A ASN* 3.5 15.5 - - + +
30A LEU* 3.5 42.7 - - + +
33A VAL* 3.6 13.5 - - + +
152A ALA 2.7 19.6 + - - -
153A ILE 3.1 11.7 + - - -
154A GLU 4.2 0.5 - - - +
155A LYS* 1.3 78.3 - - - +
157A PRO* 1.3 71.3 - - + +
158A HIS 3.3 0.3 + - - -
159A VAL* 3.2 37.9 + - + +
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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