Contacts of the strand formed by residues 183 - 190 (chain A) in PDB entry 1FBA
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 VAL 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A LEU* 3.3 41.0 - - + +
18A ILE* 3.7 20.0 - - + -
19A ALA* 4.2 13.5 - - + +
22A ILE* 4.9 0.9 - - + -
143A ASP 3.0 13.3 + - - +
144A PHE* 3.0 14.0 - - + +
145A ALA 2.8 26.0 + - - -
182A ILE* 1.3 71.2 - - - +
184A PRO* 1.3 75.2 - - - +
185A ILE* 3.6 0.4 + - + -
225A GLY 3.6 15.0 - - - +
226A THR* 4.2 7.9 - - - -
227A LEU* 4.5 10.1 - - + -
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Residues in contact with PRO 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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145A ALA 4.0 1.1 - - - +
173A TYR* 3.5 21.3 - - + +
174A ALA* 3.7 43.5 - - + +
177A CYS* 4.0 7.6 - - + -
178A GLN* 3.8 7.6 - - + -
182A ILE 3.2 11.0 - - - +
183A VAL* 1.3 85.9 - - - +
185A ILE* 1.3 62.0 - - - +
186A VAL* 3.8 1.9 + - + -
225A GLY 3.5 13.7 - - - +
226A THR* 3.6 14.7 - - + -
227A LEU 3.3 21.7 + - - +
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Residues in contact with ILE 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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29A ILE* 3.7 21.1 - - + -
77A ILE* 4.7 10.8 - - + -
144A PHE* 3.5 35.7 - - + -
145A ALA 2.9 19.1 + - - +
146A LYS* 4.3 5.1 - - + -
147A TRP 4.0 8.3 + - - +
173A TYR* 2.9 18.3 + - - -
183A VAL* 4.8 1.3 - - + +
184A PRO* 1.3 73.0 - - - +
186A VAL* 1.3 62.4 + - - +
187A GLU* 3.6 5.0 + - + +
227A LEU* 3.5 25.1 - - + +
228A LEU 4.5 0.4 - - - -
229A LYS* 3.4 39.7 - - + +
268A THR* 4.2 7.2 - - - +
300A SER* 5.1 1.1 - - - +
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Residues in contact with VAL 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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170A LEU* 4.0 25.8 - - + +
173A TYR* 4.5 3.6 - - + -
174A ALA* 4.4 22.4 - - + -
184A PRO 4.4 6.1 - - - +
185A ILE* 1.3 72.1 - - - +
187A GLU* 1.3 56.6 + - - +
188A PRO* 3.4 5.2 - - + +
212A VAL* 4.0 28.0 - - + -
213A TYR* 5.4 1.6 - - - +
216A LEU* 4.6 18.2 - - + -
226A THR* 4.7 7.6 - - - -
227A LEU 2.8 18.5 + - - +
228A LEU* 3.4 12.5 - - + +
229A LYS 2.8 30.3 + - - -
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Residues in contact with GLU 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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146A LYS* 3.3 33.1 + - + +
147A TRP 3.3 16.1 + - - +
148A ARG* 3.6 29.3 + - + +
149A CYS* 2.9 27.9 + - - +
170A LEU* 4.0 5.9 - - - +
185A ILE* 3.6 6.0 + - + +
186A VAL* 1.3 73.7 - - - +
188A PRO* 1.3 60.0 - - - +
189A GLU* 4.2 2.7 - - - +
229A LYS* 3.3 42.3 + - + +
270A LEU* 3.7 18.6 - - + +
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Residues in contact with PRO 188 (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 CYS* 4.1 6.5 - - + +
151A LEU* 4.7 8.1 - - + -
166A ASN* 6.5 0.2 - - + -
170A LEU* 3.8 18.2 - - + -
186A VAL* 3.4 10.5 - - + +
187A GLU* 1.3 83.4 - - - +
189A GLU* 1.3 62.8 + - - +
190A VAL* 3.4 8.5 + - - +
208A VAL* 4.2 12.4 - - + +
209A LEU* 4.0 25.3 - - + +
212A VAL* 4.1 17.3 - - + -
228A LEU* 3.9 11.0 - - + -
229A LYS 3.7 10.5 - - - +
230A PRO* 4.6 3.9 - - + +
231A ASN* 3.5 9.4 - - - +
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Residues in contact with GLU 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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148A ARG* 2.9 37.6 + - - +
149A CYS 2.9 18.2 + - - +
150A VAL* 3.5 3.6 - - - +
151A LEU* 2.8 27.5 + - - +
187A GLU* 3.5 6.4 + - - +
188A PRO* 1.3 70.4 - - - +
190A VAL* 1.3 72.9 + - - +
191A LEU* 3.6 14.0 + - + +
192A PRO* 4.1 12.1 - - - +
231A ASN* 4.1 2.9 - - + -
270A LEU* 3.8 43.0 - - + +
272A GLY* 4.3 7.4 - - - -
361A HIS* 4.9 4.3 + - - -
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Residues in contact with VAL 190 (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 LEU* 3.5 12.8 - - + +
153A ILE* 3.6 37.2 - - + -
188A PRO 4.2 5.6 - - - +
189A GLU* 1.3 76.7 - - - +
191A LEU* 1.3 63.3 + - - +
192A PRO* 3.8 2.8 - - - +
201A ALA* 5.5 1.1 - - + +
204A VAL* 3.9 9.9 - - + -
205A THR* 4.3 13.9 - - + +
208A VAL* 4.2 28.9 - - + -
231A ASN* 3.1 42.5 + - - +
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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