Contacts of the strand formed by residues 142 - 148 (chain A) in PDB entry 1NOZ
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 ARG 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A TYR* 3.3 3.4 - - - -
137A ASP 3.2 23.3 + - - -
140A ASP* 3.6 25.1 + - + +
141A ASP* 1.3 96.7 + - - +
143A PHE* 1.3 63.7 + - - +
144A TYR* 3.4 19.8 - - + +
181A ASP 5.0 3.7 + - - -
182A ARG* 3.2 40.4 - - - +
184A ILE* 3.4 31.8 - - + +
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Residues in contact with PHE 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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134A THR* 4.0 13.9 - - + -
135A HIS 4.0 4.3 - - - -
136A TYR* 3.6 33.2 - + + -
142A ARG* 1.3 70.5 - - - +
144A TYR* 1.3 61.3 + - - +
145A VAL* 3.1 7.7 + - - +
179A ILE* 3.9 17.3 - - + -
182A ARG* 2.8 57.7 + - + +
183A VAL* 3.4 13.4 - - + -
184A ILE* 2.9 22.5 + - - -
322A ILE* 4.7 6.3 - - + -
325A VAL* 4.2 13.2 - - + -
326A GLU* 3.7 46.4 - - + -
329A GLN* 5.3 2.9 - - + -
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Residues in contact with TYR 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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134A THR* 3.3 0.2 - - - -
135A HIS* 2.9 37.1 + - - +
137A ASP* 4.1 11.2 - - + -
140A ASP* 2.5 35.3 + - - +
142A ARG* 3.4 26.2 - - + +
143A PHE* 1.3 68.0 - - - +
145A VAL* 1.3 60.9 + - - +
146A PHE* 3.3 26.0 - - + -
184A ILE* 3.9 38.2 - - + +
186A MET* 4.4 10.3 - - - -
201A LEU* 4.1 24.9 - - + -
205A LYS* 3.5 15.7 + - + -
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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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133A ILE 3.7 2.7 - - - -
134A THR* 3.5 27.8 - - + +
143A PHE 3.1 14.9 + - - +
144A TYR* 1.3 73.4 - - - +
146A PHE* 1.3 69.3 + - - +
147A ASP 4.0 0.4 - - - -
159A TRP* 5.5 0.7 - - + -
183A VAL* 3.6 25.6 - - + -
184A ILE 3.3 6.6 + - - +
185A TYR* 4.2 17.5 - - + -
186A MET* 3.0 27.6 + - - +
318A ILE* 3.8 31.0 - - + -
321A ASN* 5.0 0.9 - - - +
322A ILE* 4.1 10.8 - - + -
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Residues in contact with PHE 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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132A ALA* 3.5 8.0 - - - -
133A ILE* 2.8 51.6 + - + +
135A HIS* 4.6 1.1 - - + -
144A TYR* 3.3 29.6 - - + -
145A VAL* 1.3 76.5 - - - +
147A ASP* 1.3 60.8 + - - +
186A MET* 3.4 32.1 - - + -
188A PHE* 3.9 17.0 - + - -
194A MET* 3.5 28.3 - - + +
197A GLU* 4.2 3.4 - - + -
198A TYR* 3.8 33.2 - + + -
201A LEU* 3.5 30.1 - - + -
318A ILE* 5.1 0.2 - - - +
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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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131A ASP 4.0 2.9 - - - +
145A VAL* 4.0 1.1 - - + -
146A PHE* 1.3 72.0 - - - +
148A LEU* 1.3 63.7 + - - +
149A LEU* 3.4 5.5 + - - +
159A TRP* 3.8 0.3 - - - +
185A TYR* 2.7 40.1 + - + +
186A MET 2.9 10.5 + - - -
187A PRO* 3.0 6.3 - - + +
188A PHE 2.6 33.5 + - - -
194A MET* 4.1 2.5 - - - -
314A HIS* 2.7 43.1 + - - -
318A ILE* 3.3 21.9 - - + +
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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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129A GLU* 4.6 1.8 - - + -
130A ILE 3.3 22.4 - - - +
131A ASP* 3.5 23.3 + - + +
147A ASP* 1.3 78.5 + - - +
149A LEU* 1.3 56.5 + - - +
150A ASN 3.4 14.1 - - - +
151A SER* 3.4 30.5 - - - +
156A VAL* 4.4 0.2 - - - +
188A PHE* 3.5 15.9 - - + +
190A ASN* 3.4 30.7 - - - +
191A GLU* 4.0 15.7 - - + -
194A MET* 3.5 15.9 - - + -
310A ARG* 3.1 21.3 + - - -
314A HIS* 4.5 0.3 + - - -
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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