Contacts of the strand formed by residues 230 - 238 (chain A) in PDB entry 5F2R
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 PHE 230 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A PHE* 3.6 33.7 - + - -
224A ASP 3.5 9.2 - - - -
225A LEU* 3.8 16.6 - - + -
229A THR* 1.3 74.2 - - - +
231A ASP* 1.3 73.2 + - - +
232A VAL* 3.3 25.4 - - + -
249A GLY* 3.2 13.6 - - - -
250A ASP* 2.8 40.9 + - + +
251A THR* 5.1 0.3 - - - -
253A LEU* 3.1 22.2 + - + +
338A THR* 3.2 44.6 - - + -
341A PRO* 3.8 15.9 - - + -
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Residues in contact with ASP 231 (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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173A PRO* 5.5 4.4 - - - +
175A TYR* 3.3 32.5 + - - -
201A GLU* 5.4 2.1 - - - +
222A VAL 3.7 1.0 - - - +
224A ASP* 2.8 57.1 + - + +
229A THR* 3.8 20.3 + - - -
230A PHE* 1.3 82.4 - - - +
232A VAL* 1.3 63.9 + - - +
233A SER* 4.8 8.5 - - - +
248A ASN 3.6 7.5 - - - +
251A THR* 6.1 1.2 - - - +
501A ACP 3.9 7.3 + - - -
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A LEU* 3.5 33.2 - - + -
222A VAL 3.3 7.2 - - - +
223A PHE* 4.9 1.6 - - + -
230A PHE* 3.3 38.4 - - + -
231A ASP* 1.3 72.0 - - - +
233A SER* 1.3 66.0 + - - +
247A THR* 3.2 4.0 - - - -
248A ASN 2.8 36.8 + - - +
249A GLY* 4.4 1.1 - - - -
341A PRO* 4.1 11.9 - - + +
342A VAL* 4.0 15.5 - - + -
345A VAL* 3.6 22.0 - - + +
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Residues in contact with SER 233 (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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174A ALA* 4.3 6.8 - - - +
202A PRO* 3.5 37.9 - - - +
220A ILE 3.5 2.8 - - - +
221A LEU* 3.6 5.5 - - - +
222A VAL* 2.9 36.0 + - - +
231A ASP* 4.8 6.8 - - - +
232A VAL* 1.3 78.7 + - - +
234A LEU* 1.3 59.7 + - - +
235A LEU* 3.8 8.9 + - - -
244A VAL* 5.1 0.2 - - - -
246A ALA 3.5 7.2 - - - -
247A THR* 4.3 8.4 - - - +
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Residues in contact with LEU 234 (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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219A ASN* 4.9 2.0 - - + +
220A ILE 3.5 8.3 - - - +
221A LEU* 4.5 6.7 - - + +
232A VAL 4.3 0.2 - - - -
233A SER* 1.3 71.9 - - - +
235A LEU* 1.3 65.3 + - - +
236A THR* 4.8 4.0 - - + -
244A VAL 3.7 1.6 - - - -
245A VAL* 2.8 56.8 + - + +
246A ALA* 2.8 18.8 + - + +
345A VAL* 4.8 9.7 - - + +
346A LEU* 4.2 11.2 - - + -
349A SER* 3.8 22.0 - - - +
351A LEU* 3.5 33.0 - - + -
356A ILE* 3.7 20.6 - - + -
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Residues in contact with LEU 235 (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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202A PRO* 3.8 24.0 - - + +
203A THR* 3.6 24.5 - - - +
206A ALA* 4.6 5.4 - - + -
219A ASN* 3.7 3.1 - - - -
220A ILE* 2.8 44.7 + - + +
222A VAL* 4.3 13.0 - - + -
233A SER* 4.3 11.4 - - - +
234A LEU* 1.3 83.2 - - - +
236A THR* 1.3 68.1 + - - +
242A PHE* 4.2 16.2 - - + -
243A GLU 3.2 7.4 - - - +
244A VAL* 3.7 34.8 - - + -
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Residues in contact with THR 236 (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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217A GLU* 4.3 19.9 + - - +
218A LYS 3.2 5.8 - - - +
219A ASN* 3.3 24.7 - - - +
220A ILE* 5.2 0.2 - - - -
234A LEU* 4.8 2.2 - - + -
235A LEU* 1.3 78.1 - - - +
237A ILE* 1.3 63.6 + - - +
238A ASP* 4.2 1.0 - - - +
241A VAL 3.7 1.0 + - - +
242A PHE* 3.3 6.7 - - - +
243A GLU* 2.9 55.1 + - - +
245A VAL* 3.9 15.9 - - + +
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Residues in contact with ILE 237 (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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211A LEU* 3.8 19.1 - - + +
212A ASP* 4.0 7.6 - - - +
214A ARG* 5.5 6.3 - - + +
216A GLY 3.7 3.8 - - - +
217A GLU* 3.3 4.4 - - - +
218A LYS* 3.0 56.0 + - + +
220A ILE* 3.8 14.8 - - + +
236A THR* 1.3 75.1 - - - +
238A ASP* 1.3 72.1 + - - +
239A ASN 5.0 0.2 - - - +
240A GLY* 3.6 13.7 - - - +
241A VAL 3.6 27.6 - - - +
242A PHE* 3.8 30.1 - - + -
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Residues in contact with ASP 238 (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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216A GLY* 3.8 17.0 - - - +
217A GLU* 3.9 29.6 + - + +
236A THR* 6.0 1.1 - - - +
237A ILE* 1.3 77.0 - - - +
239A ASN* 1.3 101.8 + - - +
240A GLY 3.2 1.1 - - - -
241A VAL* 2.8 26.3 + - - +
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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