Contacts of the strand formed by residues 149 - 154 (chain B) in PDB entry 1NRJ
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 ILE 149 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B LEU* 3.2 29.6 - - + +
114B PHE* 4.4 13.0 - - + -
132B LEU* 4.8 8.7 - - + -
135B ILE* 5.1 2.7 - - + -
136B LEU* 4.0 27.1 - - + -
139B THR* 4.7 8.7 - - + +
147B ILE* 3.3 22.9 - - + +
148B ASP* 1.4 73.3 - - - +
150B LEU* 1.3 71.7 + - - +
151B ILE* 4.3 13.5 - - + -
219B ALA* 5.3 0.9 - - + -
220B SER 3.0 12.1 + - - +
221B VAL* 3.4 16.1 - - + -
222B VAL* 3.1 28.9 + - - +
239B TRP* 4.0 5.5 + - - -
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Residues in contact with LEU 150 (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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112B LEU 3.0 7.2 + - - +
113B ILE* 3.4 20.3 - - + -
114B PHE 2.8 27.5 + - - -
149B ILE* 1.3 74.7 - - - +
151B ILE* 1.3 67.2 + - - +
152B ALA* 3.4 8.9 + - + +
222B VAL* 3.5 13.0 - - + +
224B PHE* 3.7 30.1 - - + +
236B TRP* 4.0 36.6 - - + -
239B TRP* 3.5 45.9 - - + +
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Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PHE* 3.4 17.0 - - + +
116B VAL* 4.5 9.0 - - + -
132B LEU* 4.5 7.4 - - + -
149B ILE* 4.3 9.0 - - + -
150B LEU* 1.3 72.0 - - - +
152B ALA* 1.3 57.3 + - - +
153B CYS* 3.5 21.0 + - - -
167B ILE* 4.9 2.2 - - + -
168B LYS* 4.2 17.7 - - + -
171B LEU* 4.3 25.4 - - + -
214B PHE* 4.2 19.7 - - + -
221B VAL* 3.8 27.6 - - + -
222B VAL 2.7 12.7 + - - +
223B ALA* 3.4 8.4 - - + -
224B PHE 3.2 24.8 + - - -
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Residues in contact with ALA 152 (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 ILE* 3.8 26.7 - - + -
114B PHE 3.0 8.7 + - - -
115B MET* 3.5 13.7 - - + +
116B VAL 3.1 23.4 + - - +
150B LEU* 3.4 3.9 + - + -
151B ILE* 1.3 69.5 - - - +
153B CYS* 1.3 60.8 + - - +
154B ASN* 3.3 4.8 + - - +
236B TRP* 3.5 36.7 - - + +
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Residues in contact with CYS 153 (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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116B VAL* 3.9 9.4 - - - -
118B SER* 3.0 22.3 + - - +
151B ILE* 3.8 28.9 - - - -
152B ALA* 1.3 68.4 - - - +
154B ASN* 1.4 56.5 + - - +
156B SER* 4.6 1.2 - - - -
162B ARG 5.3 0.7 - - - +
164B PRO* 3.9 24.9 - - + -
167B ILE* 3.7 27.1 - - + -
223B ALA* 4.6 1.3 - - - -
224B PHE 3.0 14.1 + - - +
225B GLU* 3.4 9.5 - - + +
226B GLY 3.0 23.0 + - - +
236B TRP* 3.8 2.4 - - - -
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Residues in contact with ASN 154 (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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49B SER 2.9 24.0 + - - +
50B GLY* 3.9 0.8 - - - -
115B MET* 3.7 19.0 - - + +
116B VAL 2.9 17.8 + - - +
118B SER* 2.8 36.4 + - - -
152B ALA 3.3 1.4 + - - +
153B CYS* 1.4 71.3 - - - +
155B LYS* 1.3 77.6 + - + +
156B SER 3.4 1.3 - - - -
226B GLY 3.4 3.7 - - - +
228B ILE* 3.4 35.0 + - - +
236B TRP* 3.5 9.3 - - + -
1001B GTP 3.2 28.6 + - - +
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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