Contacts of the strand formed by residues 152 - 161 (chain A) in PDB entry 4U7B
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 ILE 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A PHE* 3.4 7.3 + - + +
149A LEU* 3.0 36.5 + - + +
150A HIS 4.4 1.4 - - - +
151A ARG* 1.3 81.4 - - - +
153A VAL* 1.3 66.5 + - - +
154A THR* 4.6 2.5 - - - +
198A ASP* 3.2 19.2 - - - +
237A TYR* 4.7 0.2 + - - -
245A ILE* 3.9 24.8 - - + +
247A LEU* 3.6 41.5 - - + +
271A LEU* 4.4 9.0 - - + -
282A PRO* 6.1 0.2 - - + -
326A ILE* 3.6 36.1 - - + -
329A LEU* 4.8 4.9 - - + -
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Residues in contact with VAL 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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151A ARG 3.9 4.0 - - - +
152A ILE* 1.3 76.9 - - - +
154A THR* 1.3 63.0 + - - +
196A TRP* 4.7 7.2 - - + -
197A TRP 3.4 22.9 - - - +
198A ASP* 4.2 5.4 - - + +
203A ILE* 4.6 7.9 - - + -
226A LEU* 5.2 3.6 - - + -
230A LEU* 4.5 22.7 - - + -
237A TYR* 4.8 4.5 - - + +
244A VAL* 3.6 22.2 - - + -
245A ILE 3.0 20.5 + - - +
246A PHE* 3.2 27.4 - - + -
247A LEU 3.4 8.2 + - - -
268A TRP* 6.2 0.7 - - + -
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Residues in contact with THR 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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152A ILE* 4.2 4.3 - - - +
153A VAL* 1.3 76.0 - - - +
155A GLY* 1.3 59.2 + - - +
196A TRP* 3.2 11.3 - - - +
197A TRP* 3.1 55.0 + - + +
246A PHE* 5.0 0.4 - - - -
247A LEU* 2.7 44.5 + - - +
281A ALA* 5.5 0.9 - - - +
282A PRO* 4.0 15.0 - - + +
283A SER* 3.2 20.2 + - - +
326A ILE* 4.5 6.1 - - + -
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Residues in contact with GLY 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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154A THR* 1.3 83.9 + - - +
156A ASP* 1.3 62.8 + - - +
157A GLU* 5.1 0.3 - - - +
195A VAL 3.2 16.2 - - - -
196A TRP* 3.4 17.6 + - - -
197A TRP* 4.8 0.4 - - - -
219A TYR* 5.2 0.7 + - - -
247A LEU 3.3 3.4 + - - +
248A HIS* 3.9 23.4 - - - +
249A ALA 4.5 1.0 + - - -
254A HIS* 5.5 0.9 - - - -
283A SER* 3.4 7.2 - - - -
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Residues in contact with ASP 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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155A GLY* 1.3 74.9 - - - +
157A GLU* 1.3 101.3 + - - +
194A CYS* 3.8 1.2 - - - +
195A VAL* 3.2 28.6 + - - +
196A TRP* 5.3 2.7 - - - -
249A ALA* 3.6 27.5 + - - +
281A ALA* 5.2 6.9 - - - +
283A SER* 3.6 23.7 + - - -
284A ASP* 4.1 18.7 - - - +
288A PHE* 3.9 9.2 - - + -
57F T 4.2 12.7 + - - +
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Residues in contact with GLU 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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155A GLY 5.1 0.2 - - - +
156A ASP* 1.3 103.6 + - - +
158A LYS* 1.3 63.7 + - - +
192A MET* 3.7 24.9 - - + -
193A LEU 3.1 13.0 - - - +
194A CYS* 3.5 26.2 - - - +
196A TRP* 5.2 1.7 - - - -
214A VAL* 3.8 13.7 - - - +
219A TYR* 4.4 10.1 - - - -
254A HIS* 3.1 37.3 + - - -
284A ASP* 5.2 0.7 - - - +
288A PHE* 4.0 4.8 - - - -
56F A 4.6 3.1 + - - -
57F T 4.6 6.8 + - - -
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Residues in contact with LYS 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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157A GLU* 1.3 76.0 - - - +
159A TRP* 1.3 83.2 + - - +
160A ILE* 4.0 1.8 - - + +
192A MET* 4.5 4.4 - - - +
193A LEU* 2.9 39.6 + - + +
288A PHE* 3.4 47.1 - - + -
291A MET* 4.1 13.5 - - + -
295A LEU* 3.8 29.1 - - - +
55F G 4.3 13.1 + - - -
56F A 2.6 41.0 + - - +
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Residues in contact with TRP 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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158A LYS* 1.3 102.9 + - - +
160A ILE* 1.3 58.0 + - - +
161A PHE* 4.0 23.0 + + + -
190A LYS* 3.3 48.4 - - + +
191A THR 3.9 2.5 - - - -
192A MET* 3.6 49.4 - - + +
211A GLY* 5.2 8.7 - - - -
212A GLU 4.1 17.7 - - - -
213A THR* 5.5 5.6 - - - -
56F A 5.1 1.0 + - - -
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Residues in contact with ILE 160 (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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158A LYS* 4.0 11.4 - - - +
159A TRP* 1.3 77.2 - - - +
161A PHE* 1.3 71.5 - - - +
162A PHE* 3.6 2.1 + - - -
164A ASN* 5.3 1.6 - - - +
190A LYS* 3.7 1.1 - - - -
191A THR* 3.0 38.1 + - - +
193A LEU* 3.9 19.7 - - + -
207A LEU* 4.4 5.6 - - + -
291A MET* 3.8 24.5 - - + -
295A LEU* 4.1 16.2 - - + -
300A PHE* 4.1 19.7 - - + -
306A VAL* 4.2 8.7 - - + +
310A LEU* 3.8 27.8 - - + -
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Residues in contact with PHE 161 (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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159A TRP* 4.3 23.6 - + + -
160A ILE* 1.3 83.7 - - - +
162A PHE* 1.3 63.0 + - - +
163A VAL* 3.3 23.1 - - + +
164A ASN* 3.6 23.3 + - - +
184A PRO* 6.0 5.4 - - + -
185A ASN 4.3 11.0 - - - -
186A ARG* 3.7 35.0 - - - -
188A GLY 5.2 2.5 - - - -
189A LYS 3.8 11.2 - - - -
190A LYS* 4.2 23.6 - - + -
300A PHE* 3.9 3.6 - - - -
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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