Contacts of the strand formed by residues 146 - 156 (chain A) in PDB entry 4COF
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 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A ASP 4.4 4.0 - - - +
140A LEU* 4.2 2.3 - - - +
142A ARG* 4.0 10.8 - - + +
143A TYR* 3.4 22.7 - - - +
144A PRO 3.3 11.4 + - - -
145A LEU* 1.3 73.6 - - - +
147A GLU* 1.4 63.8 + - - +
148A GLN* 2.8 31.5 + - - +
186A PHE* 5.3 0.9 - - - -
215A LYS* 4.1 3.0 - - - +
216A ARG* 2.8 66.6 + - - +
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Residues in contact with GLU 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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139A ASP 5.1 0.2 - - - +
146A ASP* 1.4 73.5 - - - +
148A GLN* 1.3 72.6 + - - +
189A VAL* 3.8 16.0 - - - +
213A ARG* 3.2 41.7 + - - -
214A LEU 3.2 13.2 - - - +
215A LYS* 4.0 26.4 - - + +
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Residues in contact with GLN 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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136A CYS* 4.8 0.7 - - - -
137A MET 4.3 2.3 - - - +
138A MET* 3.3 37.9 - - + +
139A ASP* 2.7 44.9 + - - +
140A LEU* 4.3 2.0 - - - +
146A ASP* 2.8 26.7 + - - +
147A GLU* 1.3 83.1 + - - +
149A ASN* 1.3 61.1 + - - +
150A CYS* 4.0 11.1 + - - -
186A PHE* 5.1 5.8 - - + -
212A PHE 3.7 0.5 - - - +
213A ARG* 3.4 6.0 - - - +
214A LEU* 2.8 45.9 + - + +
216A ARG* 4.6 5.6 - - - +
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Residues in contact with ASN 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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136A CYS* 3.6 9.5 - - - -
137A MET 4.9 4.2 - - - +
148A GLN* 1.3 75.3 + - - +
150A CYS* 1.3 58.5 + - - +
151A THR* 3.4 23.8 + - - +
192A ARG* 6.1 0.8 - - - +
211A SER* 4.6 10.9 - - - -
212A PHE 3.2 11.9 + - - +
213A ARG* 4.6 14.0 - - + +
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Residues in contact with CYS 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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57A TYR* 3.7 25.1 - - + -
136A CYS* 2.1 46.7 - - - -
138A MET* 4.3 6.3 - - - -
148A GLN* 4.0 4.1 + - - -
149A ASN* 1.3 73.7 - - - +
151A THR* 1.3 63.0 + - - +
211A SER* 3.5 0.9 - - - -
212A PHE* 2.8 46.5 + - + +
214A LEU* 3.6 29.8 - - + +
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Residues in contact with THR 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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57A TYR* 2.6 24.6 + - - -
100A ASN* 2.7 27.6 + - - +
135A ALA 5.1 2.1 + - - -
149A ASN* 3.4 23.8 + - - +
150A CYS* 1.3 76.2 - - - +
152A LEU* 1.3 53.1 + - - +
153A GLU* 3.0 28.7 + - - +
209A SER* 4.8 1.6 - - - +
210A LEU 3.1 7.6 - - - +
211A SER* 3.9 18.8 - - - +
212A PHE* 5.2 0.7 - - - -
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Residues in contact with LEU 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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42A ILE* 4.6 6.7 - - + -
57A TYR* 3.9 14.1 - - - +
59A LEU* 4.6 12.3 - - + -
61A MET* 3.9 32.1 - - + -
98A PHE* 4.1 29.4 - - + -
100A ASN* 3.7 1.8 - - - +
132A THR* 4.0 27.6 - - + -
134A ALA* 4.2 9.6 - - + -
151A THR* 1.3 71.6 - - - +
153A GLU* 1.3 61.7 + - - +
154A ILE* 3.7 12.8 + - + +
208A LEU 3.9 0.2 - - - +
209A SER* 3.6 4.3 - - - -
210A LEU* 2.7 48.7 + - + +
212A PHE* 5.6 0.4 - - + -
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Residues in contact with GLU 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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98A PHE* 3.1 7.1 - - - -
99A LEU* 2.7 54.3 + - + -
100A ASN* 2.8 24.8 + - + +
151A THR* 3.0 29.3 + - - +
152A LEU* 1.3 70.5 - - - +
154A ILE* 1.3 59.6 + - - +
196A ARG* 4.1 5.2 + - - -
207A ARG* 3.3 36.8 + - - +
208A LEU 3.9 1.1 - - - -
209A SER* 3.1 27.2 + - - -
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Residues in contact with ILE 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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40A MET* 3.8 18.2 - - - -
42A ILE* 3.9 17.3 - - + -
63A PHE* 4.3 4.5 - - + -
96A THR* 3.6 27.1 - - + -
97A TYR 3.6 3.8 - - - +
98A PHE* 3.7 22.7 - - + -
152A LEU* 4.1 14.8 - - + +
153A GLU* 1.3 71.0 - - - +
155A GLU* 1.3 62.4 + - - +
166A PHE* 3.9 8.0 - - + -
168A TRP* 3.6 32.1 - - + -
207A ARG* 3.3 8.0 - - - +
208A LEU* 2.8 46.3 + - + +
210A LEU* 5.0 0.7 - - + +
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Residues in contact with GLU 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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96A THR* 3.4 4.3 - - - -
97A TYR* 2.9 60.0 + - + +
99A LEU* 3.7 13.8 - - + +
153A GLU 4.1 0.2 + - - -
154A ILE* 1.3 74.5 - - - +
156A SER* 1.4 70.1 + - - +
166A PHE* 3.5 7.6 - - - -
198A VAL* 4.3 3.6 - - - +
200A PHE* 3.8 16.1 - - - -
205A TYR* 3.8 23.7 - - + +
206A PRO 3.2 22.2 - - - +
207A ARG* 3.0 37.4 + - + -
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Residues in contact with SER 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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95A ASP* 2.7 26.3 + - - -
97A TYR* 3.5 7.6 - - - -
155A GLU* 1.4 78.5 - - - +
157A TYR* 1.3 62.7 + - - +
159A TYR* 3.0 35.0 + - - +
164A ILE* 4.4 3.2 - - - +
166A PHE* 3.6 20.6 - - - -
205A TYR* 3.6 13.7 - - - -
206A PRO* 3.9 15.1 + - - -
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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