Contacts of the strand formed by residues 182 - 189 (chain A) in PDB entry 1F7U
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 GLU 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A ASN* 3.2 32.5 + - - +
143A LYS 2.8 14.8 + - - +
144A LYS* 3.4 31.7 + - + +
145A VAL* 2.9 27.9 + - - +
180A GLY 4.0 0.4 + - - -
181A TRP* 1.3 71.9 - - - +
183A VAL* 1.3 62.8 + - - +
184A ILE* 4.4 11.8 - - + +
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Residues in contact with VAL 183 (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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145A VAL* 3.4 20.6 - - + +
147A ILE* 3.9 21.3 - - + -
173A ALA* 3.8 17.9 - - + +
176A TYR* 3.6 19.3 - - + -
177A GLU* 3.5 39.2 + - + +
181A TRP 3.7 3.2 + - - +
182A GLU* 1.3 79.9 - - - +
184A ILE* 1.3 79.8 + - - +
185A ARG* 4.2 7.5 + - + +
289A ASP* 3.5 10.2 - - - +
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Residues in contact with ILE 184 (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 LYS* 4.4 12.6 - - + -
145A VAL 2.9 11.4 + - - +
146A ILE* 3.6 30.5 - - + +
147A ILE* 3.0 24.9 + - - +
182A GLU* 4.4 15.9 - - + +
183A VAL* 1.3 81.8 - - - +
185A ARG* 1.3 65.4 + - - +
186A MET* 3.4 7.9 + - + -
289A ASP* 3.5 19.5 - - + +
290A VAL* 4.8 2.0 - - + -
362A TYR* 4.3 40.4 - - + +
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Residues in contact with ARG 185 (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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147A ILE 3.8 4.9 - - - -
149A PHE* 3.9 19.9 - - + -
170A GLY* 5.1 2.2 + - - -
173A ALA* 3.3 32.3 - - + +
174A ASN* 3.0 24.9 + - - -
177A GLU* 2.8 43.6 + - - -
183A VAL* 4.2 10.6 + - + +
184A ILE* 1.3 70.1 - - - +
186A MET* 1.3 60.6 + - - +
286A ILE* 4.9 3.3 - - - +
287A LYS 3.5 26.3 - - - +
288A TYR* 3.6 10.6 - - + -
289A ASP* 2.7 49.4 + - - +
290A VAL 3.3 6.1 + - - -
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Residues in contact with MET 186 (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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146A ILE* 4.2 21.5 - - + -
147A ILE 3.1 11.6 + - - +
148A GLU* 3.2 7.9 - - + +
149A PHE 3.1 24.9 + - - -
184A ILE* 3.4 6.4 + - + +
185A ARG* 1.3 74.3 - - - +
187A ASN* 1.3 65.0 + - - +
188A TYR 4.4 0.9 - - - +
288A TYR* 3.6 6.3 - - - -
290A VAL* 3.5 13.2 - - + +
292A SER* 3.9 26.9 - - - -
358A ARG* 3.5 46.9 - - + +
362A TYR* 4.0 31.9 - - + +
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Residues in contact with ASN 187 (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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149A PHE 4.0 2.7 - - - -
151A SER* 3.0 31.1 - - - -
152A PRO* 3.5 0.2 - - - +
186A MET* 1.3 72.3 - - - +
188A TYR* 1.3 57.8 + - - +
189A LEU* 3.2 22.7 + - - +
281A TYR* 3.2 31.3 + - - -
288A TYR* 3.3 33.9 + - + -
290A VAL 3.0 8.9 + - - +
291A TYR* 3.5 18.3 - - + -
292A SER 2.8 27.1 + - - +
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Residues in contact with TYR 188 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A GLU* 3.2 23.1 - - + +
151A SER* 2.9 27.0 + - - +
186A MET 3.9 2.4 - - - -
187A ASN* 1.3 68.0 - - - +
189A LEU* 1.3 65.6 + - - +
190A GLY 3.5 0.9 + - - -
292A SER* 4.1 8.1 - - - -
293A GLY 3.5 29.8 - - - -
294A GLU* 3.4 34.8 - - + +
297A VAL* 5.8 0.7 - - + +
347A TYR* 4.9 1.7 + + - -
350A ARG* 3.6 27.2 + - - +
351A ASP* 3.7 8.6 + - - -
354A ALA* 3.8 15.7 - - + +
358A ARG* 3.1 20.6 - - - +
800A ARG* 3.2 41.1 + - + -
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Residues in contact with LEU 189 (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 PRO* 3.6 15.3 - - + +
154A ILE* 4.1 18.6 - - + -
187A ASN* 3.2 32.0 + - - +
188A TYR* 1.3 72.7 - - - +
190A GLY* 1.3 60.5 + - - +
191A ASP* 3.1 3.3 + - - -
270A ARG* 3.2 28.9 - - + +
274A ILE* 3.9 27.6 - - + -
277A TYR* 4.0 22.2 - - + -
291A TYR* 4.3 5.6 - - + -
292A SER 3.4 15.3 + - - +
293A GLY* 4.3 0.2 - - - -
294A GLU* 3.1 27.7 + - - +
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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