Contacts of the strand formed by residues 145 - 152 (chain A) in PDB entry 2NSQ
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 PHE 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A GLY* 3.5 2.6 - - - -
30A ILE* 2.8 54.0 + - + +
31A ASP* 5.7 2.2 - - + -
130A ASP* 3.6 40.6 - - + -
131A PHE 3.1 11.9 - - - +
132A LEU* 3.6 31.2 - - + -
133A LEU* 4.0 10.1 - - - +
144A GLY* 1.3 83.1 - - - -
146A LEU* 1.3 61.4 + - - +
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Residues in contact with LEU 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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26A VAL* 4.3 8.5 - - + -
28A SER 3.5 15.5 - - - +
29A GLY* 4.7 1.6 - - - -
45A VAL* 4.0 15.0 - - + -
74A TRP* 3.7 21.8 - - + -
91A PHE* 3.5 33.7 - - + -
93A VAL* 4.5 5.8 - - + -
108A VAL* 4.1 11.4 - - + -
129A LYS 3.6 1.2 - - - +
130A ASP* 4.4 0.9 - - - -
131A PHE* 2.7 40.1 + - - +
133A LEU* 4.0 19.3 - - + +
145A PHE* 1.3 73.8 - - - +
147A ARG* 1.3 59.4 + - - +
148A LEU* 3.7 24.4 + - + -
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Residues in contact with ARG 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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27A VAL* 2.9 50.4 + - + +
28A SER* 2.9 34.4 + - - +
30A ILE* 3.8 14.7 - - + +
128A PHE* 3.3 51.8 - - + -
129A LYS 3.4 4.0 - - - -
130A ASP* 2.6 40.3 + - - +
145A PHE 4.2 0.6 - - - -
146A LEU* 1.3 70.2 - - - +
148A LEU* 1.3 61.7 + - - +
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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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24A VAL* 5.1 0.2 - - + -
25A LYS 3.4 4.3 - - - +
26A VAL* 3.9 19.5 - - + -
27A VAL* 4.7 0.9 - - - +
91A PHE* 3.8 52.0 - - + -
108A VAL* 4.7 3.6 - - + -
128A PHE* 3.3 5.1 - - - -
129A LYS 2.9 31.7 + - - +
131A PHE* 3.7 31.4 - - + -
146A LEU* 3.8 26.0 - - + -
147A ARG* 1.3 83.3 - - - +
149A LYS* 1.3 59.5 + - - +
150A MET* 4.2 12.3 - - + -
155A EDO 3.5 4.6 - - - -
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Residues in contact with LYS 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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23A ARG* 3.8 33.3 + - - +
24A VAL* 3.4 1.2 - - - -
25A LYS* 2.8 46.1 + - + +
27A VAL* 4.7 4.9 - - + +
118A GLU* 2.6 37.7 + - - -
127A THR* 3.3 28.7 + - - +
128A PHE* 4.3 8.7 - - + +
148A LEU* 1.3 73.9 - - - +
150A MET* 1.3 68.4 + - - +
151A ALA* 4.4 15.9 - - - +
155A EDO 3.3 10.6 + - - +
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Residues in contact with MET 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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22A LEU* 4.4 4.3 - - + -
23A ARG 3.3 7.6 - - - +
24A VAL* 4.1 20.4 - - + -
89A LEU* 5.0 2.0 - - - -
91A PHE* 4.0 20.2 - - - -
110A VAL* 3.9 29.6 - - + -
115A LEU* 4.4 19.7 - - + -
116A PRO* 3.6 11.0 - - - +
131A PHE* 3.4 36.3 - - + -
148A LEU* 4.2 11.7 - - + -
149A LYS* 1.3 84.0 + - - +
151A ALA* 1.3 63.4 + - - +
155A EDO 3.0 37.0 + - - +
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Residues in contact with ALA 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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22A LEU* 3.6 8.6 - - - +
23A ARG* 3.0 35.8 + - + +
115A LEU* 5.1 0.2 - - - -
116A PRO* 3.2 20.2 - - + +
118A GLU* 3.8 29.5 - - + +
149A LYS* 4.4 15.4 - - - +
150A MET* 1.3 75.5 - - - +
152A TYR* 1.3 63.1 + - - +
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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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20A ARG* 3.6 43.7 - - + +
21A ILE 3.5 15.9 - - - -
22A LEU* 3.9 13.5 - - + -
82A VAL* 3.5 24.7 - - + +
84A PRO* 3.3 19.7 - - + +
112A LEU* 2.7 44.0 + - + +
113A SER 5.6 1.3 - - - -
115A LEU* 3.9 23.6 - - + -
116A PRO 2.8 16.7 + - - -
117A THR* 3.6 11.6 - - - +
118A GLU 2.9 31.0 + - - +
151A ALA* 1.3 72.5 - - - +
153A MET* 1.3 61.0 + - - +
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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