Contacts of the strand formed by residues 184 - 189 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A GLY 4.9 0.9 - - - +
183A PRO* 1.3 69.9 - - - +
185A ARG* 1.3 63.6 + - - +
186A VAL* 3.4 5.4 + - + +
212A SER 3.1 12.9 + - - +
213A VAL* 3.3 12.7 - - + +
214A THR 3.0 21.9 + - - +
256A ASP* 3.6 21.1 - - + -
257A VAL* 3.9 17.5 - - + -
319A LEU* 6.0 2.5 - - + +
322A TRP 4.7 9.0 - - - +
323A SER* 6.1 0.2 - - - -
324A ARG* 4.0 16.2 - - + +
327A LEU* 3.7 25.6 - - + -
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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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180A ARG* 3.3 35.4 - - - +
181A GLU 5.0 5.7 + - - -
183A PRO 3.9 5.3 + - - +
184A VAL* 1.3 70.8 - - - +
186A VAL* 1.3 61.7 + - - +
187A LEU 3.9 0.8 + - - -
214A THR* 3.4 22.4 - - + -
254A TRP* 2.9 66.8 + - + +
255A ALA 3.9 0.3 - - - -
256A ASP* 2.8 48.1 + - - +
257A VAL* 3.1 10.7 + - - +
324A ARG* 4.8 2.4 - - - +
183B PRO* 5.9 3.6 - - - +
211B ASP* 3.3 41.4 + - - +
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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
----------------------------------------------------------
184A VAL* 3.9 13.2 - - + +
185A ARG* 1.3 74.1 - - - +
187A LEU* 1.3 61.2 + - - +
188A VAL* 4.2 12.6 - - + -
202A MET* 4.3 10.1 - - + -
213A VAL* 4.1 21.8 - - + -
214A THR 2.9 11.9 + - - +
215A ILE* 3.4 12.2 - - + +
216A TRP 3.1 24.6 + - - -
254A TRP* 3.9 2.9 - - - -
257A VAL* 3.6 19.5 - - + -
259A VAL* 3.8 28.7 - - + -
319A LEU* 4.4 12.8 - - + -
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Residues in contact with LEU 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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185A ARG 3.9 0.8 + - - -
186A VAL* 1.3 73.6 - - - +
188A VAL* 1.3 66.9 + - - +
189A VAL* 3.3 24.7 - - + -
216A TRP* 3.6 12.6 - - + +
245A ILE* 3.9 16.4 - - + -
248A MET* 4.9 0.9 - - - -
251A ALA* 3.8 27.6 - - + +
252A TYR* 3.7 36.1 - - + -
254A TRP* 4.2 7.6 - - + -
255A ALA* 3.8 17.7 - - + -
257A VAL 2.9 9.4 + - - +
258A VAL* 3.3 10.8 - - + +
259A VAL 2.9 24.8 + - - -
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Residues in contact with VAL 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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186A VAL* 4.2 5.4 - - + -
187A LEU* 1.3 75.8 - - - +
189A VAL* 1.3 63.0 + - - +
190A GLY 4.2 0.2 - - - -
198A LEU* 3.9 23.6 - - + -
202A MET* 3.8 34.1 - - + -
215A ILE* 3.9 23.3 - - + -
216A TRP 3.0 6.5 + - - -
217A HIS* 3.8 34.8 - - + +
218A GLN* 2.9 32.6 + - - +
259A VAL* 3.5 7.9 - - + +
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Residues in contact with VAL 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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187A LEU* 3.3 35.4 - - + -
188A VAL* 1.3 72.1 - - - +
190A GLY* 1.3 60.0 + - - +
191A GLY* 3.8 8.7 - - - +
198A LEU* 3.6 8.1 - - - +
218A GLN* 3.6 13.9 - - - +
245A ILE* 5.0 0.4 - - + -
248A MET* 4.0 24.9 - - + -
252A TYR* 5.1 5.2 - - + +
258A VAL* 4.1 11.2 - - + -
259A VAL 3.0 7.7 + - - -
260A CYS* 3.4 33.2 - - + +
261A ARG* 4.3 2.8 + - - +
266A THR* 6.4 2.0 - - + -
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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