Contacts of the strand formed by residues 183 - 190 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LEU* 3.4 39.3 - - + +
18B ILE* 3.7 22.4 - - + -
19B ALA* 4.2 12.1 - - + +
22B ILE* 5.0 0.2 - - + -
143B ASP 3.0 11.3 + - - +
144B PHE* 3.1 13.2 - - + +
145B ALA 2.8 25.6 + - - -
182B ILE* 1.3 69.4 - - - +
184B PRO* 1.3 73.4 - - - +
185B ILE* 5.3 0.2 - - + -
225B GLY 3.7 14.8 - - - +
226B THR* 4.3 5.6 - - - -
227B LEU* 4.4 13.5 - - + -
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Residues in contact with PRO 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ALA 4.1 0.4 - - - +
173B TYR* 3.5 20.9 - - + +
174B ALA* 3.7 42.8 - - + +
177B CYS* 4.0 9.0 - - + -
178B GLN* 3.8 11.9 - - + -
182B ILE 3.2 10.1 - - - +
183B VAL* 1.3 83.4 - - - +
185B ILE* 1.3 62.1 + - - +
186B VAL* 3.7 1.8 + - + +
225B GLY 3.4 13.5 - - - +
226B THR* 3.6 12.3 - - + -
227B LEU 3.3 21.7 + - - +
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Residues in contact with ILE 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ILE* 3.7 21.1 - - + -
77B ILE* 4.5 10.3 - - + -
144B PHE* 3.5 35.7 - - + -
145B ALA 2.9 20.4 + - - +
146B LYS* 4.7 5.2 - - + -
147B TRP 3.9 8.3 + - - -
173B TYR* 2.9 18.7 + - - -
183B VAL 4.7 1.3 - - - +
184B PRO* 1.3 73.4 - - - +
186B VAL* 1.3 61.1 + - - +
187B GLU* 3.6 4.9 + - + +
227B LEU* 3.5 24.2 - - + +
228B LEU 4.5 0.9 - - - -
229B LYS* 3.5 39.9 - - + +
268B THR* 4.2 5.8 - - - +
300B SER* 5.1 1.1 - - - +
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Residues in contact with VAL 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 4.2 24.9 - - + +
173B TYR* 4.5 4.5 - - + -
174B ALA* 4.5 21.1 - - + -
184B PRO 4.4 6.1 - - - +
185B ILE* 1.3 71.7 - - - +
187B GLU* 1.3 56.3 + - - +
188B PRO* 3.4 6.1 - - + +
212B VAL* 3.9 27.4 - - + -
213B TYR* 5.3 1.6 - - - +
216B LEU* 4.5 17.9 - - + -
226B THR* 4.8 7.9 - - - -
227B LEU 2.9 14.6 + - - +
228B LEU* 3.5 12.8 - - + +
229B LYS 2.7 30.8 + - - -
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Residues in contact with GLU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LYS* 3.1 33.3 + - - +
147B TRP 3.2 15.3 + - - +
148B ARG* 3.6 29.4 + - + +
149B CYS* 2.9 28.4 + - - +
170B LEU* 3.9 6.2 - - - +
185B ILE* 3.6 5.3 + - + +
186B VAL* 1.3 74.1 - - - +
188B PRO* 1.3 60.1 - - - +
189B GLU* 4.4 3.4 - - - +
229B LYS* 3.4 45.2 - - + +
270B LEU* 4.0 14.0 - - + +
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Residues in contact with PRO 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B CYS* 3.9 6.3 - - + +
151B LEU* 5.0 6.1 - - + -
166B ASN* 6.5 0.4 - - + -
170B LEU* 3.8 18.2 - - + -
186B VAL* 3.4 10.3 - - + +
187B GLU* 1.3 84.3 - - - +
189B GLU* 1.3 62.3 + - - +
190B VAL* 3.4 8.0 + - - +
208B VAL* 4.0 21.2 - - + +
209B LEU* 4.2 11.3 - - + +
212B VAL* 4.1 16.4 - - + -
228B LEU* 3.8 18.6 - - + -
229B LYS 3.7 9.2 - - - +
230B PRO* 4.7 5.5 - - + +
231B ASN* 3.7 7.1 - - - +
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Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ARG* 3.0 38.6 + - - +
149B CYS 2.8 18.7 + - - +
150B VAL* 3.5 4.4 - - - +
151B LEU* 2.8 32.8 + - - +
187B GLU* 3.4 6.7 + - - +
188B PRO* 1.3 70.9 - - - +
190B VAL* 1.3 66.9 + - - +
191B LEU* 3.6 14.2 + - + +
192B PRO* 4.2 11.4 - - - +
231B ASN* 4.1 2.7 - - + -
270B LEU* 3.7 42.2 - - + +
272B GLY* 4.3 8.1 - - - -
361B HIS* 5.8 0.5 - - - -
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Residues in contact with VAL 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B LEU* 3.4 13.7 - - + +
153B ILE* 3.6 36.3 - - + -
188B PRO 3.4 6.0 + - - +
189B GLU* 1.3 73.9 - - - +
191B LEU* 1.3 66.7 + - - +
192B PRO* 3.7 2.4 - - - +
201B ALA* 5.3 1.8 - - + +
204B VAL* 3.9 9.6 - - + -
205B THR* 4.1 15.0 - - + +
208B VAL* 4.1 29.2 - - + -
231B ASN* 2.9 44.8 + - - +
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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