Contacts of the strand formed by residues 184 - 189 (chain B) in PDB entry 1F0K
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 184 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B GLY 3.6 1.7 + - - +
183B PRO* 1.3 69.2 - - - +
185B ARG* 1.3 62.0 + - - +
186B VAL* 3.5 5.1 + - + -
212B SER 3.1 13.9 + - - +
213B VAL* 3.2 14.3 - - + +
214B THR 3.0 21.5 + - - +
256B ASP* 3.5 12.3 - - + +
257B VAL* 3.9 18.4 - - + -
319B LEU* 5.8 7.0 - - + +
322B TRP 4.3 11.2 - - - +
324B ARG* 4.0 15.3 - - + +
327B LEU* 3.8 33.4 - - + -
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Residues in contact with ARG 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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183A PRO* 6.0 2.6 - - - +
211A ASP* 3.1 43.6 + - - +
238A GLN* 6.0 1.4 - - - +
180B ARG* 3.3 33.1 - - - +
181B GLU 5.4 3.6 + - - -
183B PRO 3.7 6.1 + - - +
184B VAL* 1.3 68.5 - - - +
186B VAL* 1.3 61.5 + - - +
187B LEU 3.9 0.2 + - - -
214B THR* 3.3 23.5 - - + +
254B TRP* 2.9 67.2 + - + +
255B ALA* 3.9 0.7 - - - -
256B ASP* 2.8 50.1 + - - +
257B VAL* 3.2 9.7 + - - +
324B ARG* 5.0 1.0 - - - +
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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
----------------------------------------------------------
184B VAL* 3.8 13.7 - - + +
185B ARG* 1.3 75.1 - - - +
187B LEU* 1.3 60.5 + - - +
188B VAL* 4.3 11.2 - - + -
202B MET* 4.6 5.4 - - + -
213B VAL* 3.9 23.6 - - + -
214B THR 2.8 8.5 + - - -
215B ILE* 3.3 15.0 - - + +
216B TRP 3.0 25.6 + - - +
254B TRP* 3.8 2.7 - - - -
257B VAL* 3.6 19.7 - - + -
259B VAL* 3.8 29.6 - - + -
319B LEU* 4.6 16.2 - - + -
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Residues in contact with LEU 187 (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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185B ARG 3.9 0.6 + - - -
186B VAL* 1.3 72.7 - - - +
188B VAL* 1.3 59.8 + - - +
189B VAL* 3.7 15.3 - - + -
216B TRP* 3.5 27.1 - - + +
245B ILE* 3.8 26.2 - - + -
248B MET* 4.8 1.1 - - - -
251B ALA* 3.9 26.9 - - + +
252B TYR* 3.7 34.8 - - + -
254B TRP* 4.1 3.1 - - + -
255B ALA* 3.7 17.7 - - + -
257B VAL 3.0 9.6 + - - +
258B VAL* 3.3 9.6 - - + +
259B VAL 2.8 26.3 + - - -
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Residues in contact with VAL 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B VAL* 4.3 6.3 - - + -
187B LEU* 1.3 75.0 - - - +
189B VAL* 1.3 61.7 + - - +
190B GLY 4.2 0.2 - - - -
198B LEU* 4.0 23.6 - - + -
202B MET* 3.8 40.6 - - + -
215B ILE* 3.9 24.5 - - + -
216B TRP 2.9 8.2 + - - +
217B HIS* 3.7 27.5 - - + +
218B GLN* 2.8 32.8 + - - +
259B VAL* 3.5 8.5 - - + +
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Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LEU* 3.7 29.6 - - + -
188B VAL* 1.3 75.3 - - - +
190B GLY* 1.3 60.5 + - - +
191B GLY* 4.0 8.1 - - - +
195B ALA* 4.8 0.3 - - - +
198B LEU* 3.7 8.2 - - - +
218B GLN* 3.5 13.5 - - - +
245B ILE* 5.1 0.9 - - + -
248B MET* 3.8 26.5 - - + -
252B TYR* 5.0 5.6 - - + +
258B VAL* 4.0 12.1 - - + -
259B VAL 3.0 7.1 + - - -
260B CYS* 3.5 30.3 - - + +
261B ARG* 4.4 3.3 + - - +
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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