Contacts of the strand formed by residues 148 - 154 (chain A) in PDB entry 2NS2
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 ASP 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A CYS* 5.4 0.2 - - - -
126A TRP* 3.5 24.5 - - + -
144A THR* 3.7 0.2 + - - -
145A TYR* 3.1 21.1 + - - +
147A LYS* 1.3 81.6 - - - +
149A PRO* 1.3 63.7 - - - +
150A VAL* 2.9 32.8 + - - +
152A TYR* 2.6 29.3 + - + +
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Residues in contact with PRO 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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144A THR* 3.3 15.3 - - + +
145A TYR 3.1 8.0 - - - +
146A GLU* 4.2 7.4 - - - +
147A LYS 4.0 3.4 - - - -
148A ASP* 1.3 85.8 - - - +
150A VAL* 1.3 57.7 - - + +
229A TYR* 3.4 12.3 - - + +
230A VAL 2.8 37.0 + - - +
231A TYR* 3.8 23.1 - - + +
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Residues in contact with VAL 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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71A CYS* 4.1 15.0 - - - -
144A THR* 2.9 19.3 + - - -
148A ASP* 2.9 26.4 + - - +
149A PRO* 1.3 77.5 - - - +
151A LEU* 1.3 61.9 + - - +
152A TYR* 3.4 36.5 - - + -
227A HIS* 3.9 22.7 - - + -
228A ILE 3.0 10.8 - - - +
229A TYR* 3.8 32.3 - - + +
230A VAL* 4.0 2.0 - - - -
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Residues in contact with LEU 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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63A LEU* 4.9 2.5 - - + -
71A CYS* 3.4 7.6 - - - +
72A VAL* 2.8 58.9 + - + +
131A LEU* 3.8 19.3 - - + -
142A TYR* 3.6 41.7 - - + +
143A ILE 4.1 0.9 - - - +
150A VAL* 1.3 70.5 - - - +
152A TYR* 1.3 64.9 + - - +
219A PHE* 3.5 31.2 - - + -
228A ILE* 2.6 30.5 + - + +
230A VAL* 4.2 6.3 - - + -
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Residues in contact with TYR 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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70A ASP* 3.4 20.6 - - + -
71A CYS* 3.7 18.6 - - - -
72A VAL* 4.7 1.1 - - - -
126A TRP* 4.4 7.3 - + - -
142A TYR* 3.4 6.6 - - - -
143A ILE* 2.8 46.2 + - + +
145A TYR* 3.7 28.5 - + + -
148A ASP* 2.6 29.2 + - + +
150A VAL* 3.4 32.1 - - + -
151A LEU* 1.3 79.1 - - - +
153A MET* 1.3 62.5 + - - +
154A TYR* 3.5 28.9 - + + -
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Residues in contact with MET 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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52A LEU* 3.6 30.5 - - + -
65A LYS* 3.8 27.6 - - + -
70A ASP* 3.0 15.0 + - - +
72A VAL* 3.7 10.8 - - + -
134A ALA* 3.6 13.0 - - + -
137A MET* 3.8 28.0 - - + -
140A TRP* 3.6 37.6 - - + -
141A PHE 3.2 12.8 - - - +
142A TYR* 3.7 20.9 - - + -
152A TYR* 1.3 73.2 - - - +
154A TYR* 1.3 73.7 + - - +
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Residues in contact with TYR 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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70A ASP* 3.1 43.8 + - + +
114A HIS* 4.0 8.7 - - - -
116A PHE* 3.4 29.6 - + - -
140A TRP* 3.6 14.1 - + - -
141A PHE 2.9 26.1 + - - +
143A ILE* 3.8 10.5 - - + +
145A TYR* 3.4 26.2 - - - -
152A TYR* 3.5 25.6 - + + -
153A MET* 1.3 77.7 - - - +
155A GLN* 1.3 61.4 + - - +
156A LEU* 2.9 26.9 + - + +
159A ASP* 4.5 8.3 - - - +
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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