Contacts of the strand formed by residues 150 - 159 (chain A) in PDB entry 1NSX
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 LYS 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A SER* 3.7 1.4 + - - +
145A PHE* 3.5 6.4 - - - -
146A ASP* 2.9 45.5 + - - +
148A ASP* 4.0 21.9 + - - +
149A ASN* 1.4 77.5 - - - +
151A TRP* 1.3 59.7 + - - +
152A LYS* 3.8 3.9 + - + +
333A ILE* 4.6 17.0 - - + -
334A TYR 3.8 3.1 - - - -
335A SER* 3.9 22.2 - - - +
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Residues in contact with TRP 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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25A ILE* 3.6 24.0 - - + -
27A PHE* 3.8 7.9 - + - -
34A ILE* 3.7 44.9 - - + -
37A TRP* 3.5 30.1 - + + -
143A HIS* 3.2 26.3 + + - -
144A SER 3.3 13.7 - - - +
145A PHE* 4.1 4.5 - - + -
149A ASN 3.8 1.2 + - - -
150A LYS* 1.3 71.7 - - - +
152A LYS* 1.3 66.3 + - - +
153A ILE* 3.6 25.1 - - + +
171A VAL* 3.9 23.6 - - + -
173A PHE* 4.5 1.1 - + - -
332A THR 4.0 0.5 - - - +
333A ILE* 3.4 2.1 - - - -
334A TYR* 2.7 71.3 + + - +
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Residues in contact with LYS 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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117A GLU* 4.5 16.4 + - - -
119A GLN* 5.5 2.6 - - - +
142A THR 3.4 1.4 - - - +
143A HIS* 3.3 4.0 - - - -
144A SER* 2.8 45.7 + - - +
150A LYS* 3.8 4.9 + - + +
151A TRP* 1.3 76.6 - - - +
153A ILE* 1.3 64.6 + - - +
154A HIS* 4.7 13.9 - - + +
331A THR* 4.0 18.6 - - + -
332A THR 3.5 4.0 - - - +
333A ILE* 3.5 29.6 - - + -
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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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64A THR* 5.7 0.2 - - - +
141A VAL* 3.5 30.7 - - + -
142A THR 3.3 2.5 - - - -
143A HIS* 3.9 13.2 - - + +
151A TRP* 3.6 36.8 - - + +
152A LYS* 1.3 78.1 - - - +
154A HIS* 1.3 60.1 + - - +
155A TYR* 3.6 30.7 - - + +
169A GLY* 4.9 10.1 - - - -
330A ALA 3.8 0.2 - - - +
331A THR* 3.2 5.2 - - - +
332A THR* 2.9 44.2 + - + +
334A TYR* 4.0 18.2 - - + -
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Residues in contact with HIS 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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140A SER* 4.0 1.0 + - - +
141A VAL* 3.5 1.8 - - - -
142A THR* 2.9 47.7 + - + +
152A LYS* 4.7 13.2 - - + +
153A ILE* 1.3 76.2 - - - +
155A TYR* 1.3 68.2 + - - +
156A GLU* 2.5 43.4 + - + +
329A GLN* 3.6 23.4 + - + -
330A ALA 2.9 14.3 + - - -
331A THR* 2.9 25.2 + - - +
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Residues in contact with TYR 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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64A THR* 4.2 23.1 + - + -
140A SER 3.5 4.9 - - - +
141A VAL* 4.1 19.7 - - + -
153A ILE* 3.6 32.7 - - + +
154A HIS* 1.3 74.5 - - - +
156A GLU* 1.3 72.8 + - - +
165A PHE* 5.6 1.6 - + + -
167A PRO* 3.9 26.5 - - + -
168A THR* 3.3 7.6 + - - -
169A GLY* 3.1 31.2 + - - -
305A CYS 6.1 0.4 - - - -
328A TYR* 4.0 17.9 - - + -
329A GLN* 3.2 4.0 - - - -
330A ALA* 2.8 48.2 + - + +
332A THR* 4.9 12.0 - - - -
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Residues in contact with GLU 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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121A LYS* 5.5 5.6 + - - -
138A GLU 4.1 0.4 - - - +
139A MET* 3.6 1.2 - - - +
140A SER* 3.0 45.7 + - - +
154A HIS* 2.5 31.8 + - + +
155A TYR* 1.3 83.5 - - - +
157A ALA* 1.3 63.0 + - - +
165A PHE* 5.1 0.9 - - - -
327A LYS* 2.8 36.4 + - + +
328A TYR* 3.2 11.4 - - - +
329A GLN* 3.4 15.4 - - + +
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Residues in contact with ALA 157 (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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137A ILE* 3.9 11.7 - - + -
138A GLU 3.3 12.1 - - - +
139A MET* 4.4 1.3 - - - -
156A GLU* 1.3 76.3 - - - +
158A ILE* 1.4 68.7 + - - +
165A PHE* 3.5 37.2 - - + -
322A LEU* 4.5 3.4 - - + -
326A GLU 3.6 1.0 - - - +
327A LYS* 3.5 2.4 - - - +
328A TYR* 2.8 36.3 + - + +
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Residues in contact with ILE 158 (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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136A LYS 3.8 0.9 - - - +
137A ILE* 3.3 2.8 - - - -
138A GLU* 2.7 46.5 + - + +
157A ALA* 1.4 79.7 - - - +
159A SER* 1.3 72.1 - - - +
160A ASP* 5.5 2.1 - - - +
322A LEU* 4.9 1.1 - - - -
325A GLY* 4.2 15.3 - - - +
326A GLU 4.0 15.5 - - - +
327A LYS* 4.2 25.4 - - + +
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Residues in contact with SER 159 (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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135A GLY* 3.9 7.8 - - - -
136A LYS 3.2 10.5 + - - -
137A ILE* 4.0 6.0 - - - +
158A ILE* 1.3 79.2 - - - +
160A ASP* 1.3 64.3 + - - +
161A LYS 2.6 28.8 + - - -
163A THR* 3.5 21.6 - - - +
322A LEU* 4.3 13.2 - - - +
323A LYS 5.2 0.4 + - - -
324A ALA* 3.6 2.4 - - - -
325A GLY* 3.1 26.2 + - - +
326A GLU 4.5 2.2 + - - -
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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