Contacts of the strand formed by residues 229 - 235 (chain B) in PDB entry 4FK8
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 ASP 229 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B THR* 3.7 13.5 + - - -
126B TRP* 2.9 33.5 + - + +
221B MET* 5.4 1.0 - - - +
222B PRO* 4.5 8.9 - - - +
223B PRO 3.9 4.3 - - - +
224B PHE* 3.4 22.2 - - + -
225B SER* 2.9 36.5 + - - +
228B GLN* 1.3 85.0 - - - +
230B ARG* 1.3 80.7 + - - +
231B VAL* 4.7 2.0 - - + -
252B LEU* 4.1 9.9 - - + +
262B HIS 3.9 4.3 - - - +
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Residues in contact with ARG 230 (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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119B LEU* 4.1 14.1 - - + -
120B LEU* 2.8 34.2 + - - +
121B PRO 2.9 20.4 + - - -
122B GLY* 4.2 5.2 - - - -
124B THR 2.8 12.6 + - - +
125B LEU* 3.4 4.1 - - + +
126B TRP* 2.8 27.2 + - - -
150B PHE* 3.7 31.0 - - + -
226B PRO 2.8 26.4 + - - -
227B GLU* 3.0 22.6 + - - +
229B ASP* 1.3 100.5 + - - +
231B VAL* 1.3 64.0 + - - +
261B GLY 4.0 10.3 - - - -
262B HIS* 3.1 29.0 - - - +
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Residues in contact with VAL 231 (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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119B LEU* 4.1 2.4 - - - +
125B LEU* 4.5 0.2 - - - +
126B TRP* 3.3 18.4 - - + +
128B LEU* 3.8 17.7 - - + -
224B PHE* 4.3 12.8 - - + -
229B ASP 4.7 0.4 - - - -
230B ARG* 1.3 81.2 - - - +
232B MET* 1.3 65.0 + - - +
233B LEU* 3.2 29.6 - - + -
247B LEU* 4.0 11.4 - - + -
252B LEU* 3.7 25.8 - - + -
262B HIS 3.0 6.5 + - - -
263B TYR* 3.1 16.0 - - + +
264B VAL 3.0 23.4 + - - -
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Residues in contact with MET 232 (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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114B LEU* 4.1 11.7 - - + +
115B VAL 4.5 2.7 - - - -
116B ALA* 3.8 29.6 - - + +
119B LEU* 3.6 26.0 - - + -
125B LEU* 4.1 27.1 - - + -
126B TRP 2.7 12.6 + - - +
127B MET* 3.5 2.8 - - - -
128B LEU 2.9 26.0 + - - +
137B PHE* 3.6 18.6 - - + -
140B ILE* 3.9 33.4 - - + -
231B VAL* 1.3 75.7 - - - +
233B LEU* 1.3 63.6 + - - +
264B VAL* 3.4 19.7 - - + -
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Residues in contact with LEU 233 (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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114B LEU* 3.7 3.9 - - - +
128B LEU* 3.5 23.8 - - + +
231B VAL* 3.2 35.7 - - + -
232B MET* 1.3 75.1 - - - +
234B CYS* 1.3 61.8 + - - +
239B MET* 4.4 3.8 - - + -
240B LEU* 3.5 21.5 - - + +
243B THR* 3.6 29.6 - - + -
244B THR* 3.8 23.1 - - + +
247B LEU* 4.0 9.4 - - + -
263B TYR* 5.2 0.4 - - + -
264B VAL 2.9 10.6 + - - +
265B ILE* 3.3 15.1 - - + -
266B GLU 2.8 27.7 + - - +
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Residues in contact with CYS 234 (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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69B SER* 5.2 1.6 - - - -
114B LEU* 4.1 11.2 - - + -
128B LEU 3.0 11.1 + - - -
129B SER* 3.1 22.7 - - - -
130B THR 3.2 2.9 + - - -
133B GLY* 3.5 38.2 - - - +
136B PRO* 3.7 15.5 - - - -
137B PHE* 3.7 13.9 - - + -
233B LEU* 1.3 74.9 - - - +
235B GLY* 1.3 59.4 + - - +
239B MET* 4.9 0.4 - - - -
240B LEU* 4.2 0.4 - - - +
266B GLU* 3.2 17.3 - - - +
267B ARG 4.4 2.5 - - - -
268B ALA* 4.0 12.3 - - - -
301B FAD 6.2 0.7 - - - -
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Residues in contact with GLY 235 (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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130B THR* 3.2 15.5 - - - -
234B CYS* 1.3 75.3 - - - +
236B SER* 1.3 67.5 + - - +
239B MET* 4.1 10.3 - - - -
240B LEU* 3.8 6.6 - - - +
266B GLU 3.5 4.6 + - - -
267B ARG* 3.5 7.4 - - - +
268B ALA* 2.8 32.8 + - - +
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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