Contacts of the helix formed by residues 140 - 146 (chain B) in PDB entry 1NRX
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 THR 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B GLY 4.1 0.4 + - - -
114B GLY* 3.4 11.5 - - - -
139B THR* 1.3 81.3 + - - +
141B LEU* 1.3 69.3 + - + +
142B LEU* 3.4 18.4 - - + +
143B ALA* 3.1 7.7 + - - +
144B MET* 2.9 26.4 + - - +
183B LEU* 4.4 9.3 - - + +
187B GLU* 4.4 16.6 - - - +
190B ASN* 5.7 0.4 - - - +
401B NAD 3.1 51.7 + - - +
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Residues in contact with LEU 141 (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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140B THR* 1.3 73.2 - - - +
142B LEU* 1.3 64.5 + - - +
144B MET* 3.0 16.4 + - - +
145B VAL* 3.1 15.0 + - + +
180B LEU* 3.8 23.5 - - + +
183B LEU* 3.8 8.0 - - + +
187B GLU 4.8 0.4 - - - +
188B PHE* 3.2 48.2 - - + +
191B GLY* 3.7 9.9 - - - -
192B MET* 3.4 23.1 - - + +
195B VAL* 4.2 10.3 - - + -
243B ILE* 3.3 43.5 - - + -
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Residues in contact with LEU 142 (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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140B THR* 3.2 9.9 - - + +
141B LEU* 1.3 79.1 - - - +
143B ALA* 1.3 71.8 + - - +
145B VAL* 3.0 10.4 + - - +
146B ASP* 2.8 34.9 + - + +
147B SER* 3.4 25.6 - - - +
190B ASN* 4.4 11.9 - - - +
191B GLY* 3.8 20.5 - - - +
194B GLU* 4.3 20.4 - - + -
287B HIS* 4.4 22.9 - - + -
288B GLY* 5.3 1.3 - - - +
401B NAD 3.8 39.7 - - + +
1601B ZN 4.6 2.2 - - - -
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Residues in contact with ALA 143 (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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113B GLY 4.2 0.2 - - - +
114B GLY* 3.9 6.1 - - - -
115B GLY 3.7 17.7 - - - +
136B GLN* 6.1 0.2 - - - +
138B PRO* 3.5 14.8 - - + -
140B THR* 3.1 18.5 + - - +
142B LEU* 1.3 79.7 - - - +
144B MET* 1.3 53.5 + - - +
146B ASP 3.8 0.7 + - - -
147B SER* 3.3 25.8 - - - +
148B SER* 2.5 40.1 + - - +
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Residues in contact with MET 144 (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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138B PRO* 3.7 35.0 - - + +
139B THR* 5.1 0.2 - - - -
140B THR 2.9 26.5 + - - +
141B LEU* 3.0 9.6 + - - +
143B ALA* 1.3 78.0 - - - +
145B VAL* 1.3 64.3 - - + +
148B SER* 4.0 1.7 + - - -
149B ILE* 3.7 16.1 - - - +
175B ILE* 3.7 37.1 - - + +
176B ASP 3.1 36.3 - - - +
177B LEU* 3.9 9.4 - - - -
179B PHE* 4.6 4.3 - - + -
180B LEU* 4.0 32.8 - - + -
243B ILE* 4.8 3.8 - - + -
247B ALA* 4.0 1.9 - - - +
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Residues in contact with VAL 145 (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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141B LEU* 3.3 18.2 - - + +
142B LEU* 3.4 11.4 - - - +
144B MET* 1.3 78.9 - - - +
146B ASP* 1.3 58.4 + - - +
149B ILE* 4.5 5.6 - - - -
194B GLU* 4.3 13.2 - - + +
195B VAL* 4.1 19.5 - - + -
198B THR* 5.2 0.7 + - - -
243B ILE* 3.2 49.1 - - + +
246B SER* 3.7 22.9 + - - +
247B ALA* 4.1 7.8 - - + +
250B LYS* 4.0 16.8 - - - +
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Residues in contact with ASP 146 (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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142B LEU* 2.8 13.9 + - + +
144B MET 3.4 2.8 + - - -
145B VAL* 1.3 80.6 - - - +
147B SER* 1.3 52.9 + - - +
148B SER 2.5 18.9 + - - -
149B ILE* 2.6 17.8 + - - +
194B GLU* 4.4 23.9 - - + +
197B LYS* 4.7 5.7 + - - -
250B LYS* 2.7 44.5 + - - +
267B LEU* 5.6 0.3 - - - +
401B NAD 3.3 31.3 + - - -
1601B ZN 4.0 11.8 - - - -
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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