Contacts of the strand formed by residues 231 - 238 (chain A) in PDB entry 2F24
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 231 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ALA 3.8 0.2 - - - +
223A GLU* 3.3 6.0 - - - +
224A VAL* 2.7 46.3 + - + +
229A GLN* 4.2 12.3 - - + +
230A ARG* 1.3 78.6 - - - +
232A VAL* 1.3 68.8 + - - +
233A THR 3.9 0.5 + - - -
247A GLN* 3.4 43.5 - - + +
248A SER 3.2 16.2 - - - +
249A THR* 4.3 15.9 - - + -
316A PRO* 4.9 6.3 - - + -
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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
----------------------------------------------------------
165A LEU* 4.4 4.0 - - + -
167A LEU* 4.0 26.9 - - + -
175A VAL* 4.8 6.5 - - + -
221A VAL* 3.8 32.5 - - + -
222A ALA 3.4 5.4 - - - +
223A GLU* 5.3 0.7 - - + +
231A VAL* 1.3 79.7 - - - +
233A THR* 1.3 62.8 + - - +
247A GLN* 3.3 4.7 - - - -
248A SER* 2.9 33.7 + - - +
251A ASP* 3.9 30.1 - - - +
252A GLY* 4.4 6.3 - - - +
255A PHE* 3.7 11.6 - - + -
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Residues in contact with THR 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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220A GLN 3.9 0.2 - - - +
221A VAL* 3.2 5.7 - - - +
222A ALA* 2.8 49.8 + - + +
224A VAL* 5.0 5.6 - - + -
231A VAL 3.9 1.0 + - - -
232A VAL* 1.3 76.5 - - - +
234A LEU* 1.3 62.2 + - - +
235A ASN* 4.2 1.7 + - + +
245A GLN* 3.7 23.7 + - - +
246A ALA 3.5 4.6 + - - -
247A GLN* 4.5 1.5 - - - +
276A VAL* 5.2 6.0 - - + +
293A LEU* 4.2 21.7 - - + +
316A PRO* 3.8 25.4 - - + +
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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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194A ALA* 4.3 5.6 - - + -
195A PHE 4.3 9.0 - - - +
196A CYS* 3.9 15.7 - - - -
212A VAL* 4.3 18.2 - - + -
219A CYS* 3.8 36.6 - - + -
220A GLN 3.5 3.4 - - - -
221A VAL* 3.8 7.0 - - + -
232A VAL 4.1 0.4 + - - -
233A THR* 1.3 74.2 + - - +
235A ASN* 1.3 62.4 + - - +
236A ALA* 3.8 15.7 - - + -
244A VAL* 5.0 2.0 - - + +
245A GLN* 3.2 7.8 - - - +
246A ALA* 2.8 33.1 + - + +
255A PHE* 3.7 36.6 - - + -
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Residues in contact with ASN 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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219A CYS* 3.3 3.9 - - - -
220A GLN* 3.0 27.3 + - - +
233A THR* 4.1 2.9 - - + +
234A LEU* 1.3 71.8 - - - +
236A ALA* 1.3 59.0 + - - +
243A ARG* 2.8 49.6 + - - +
244A VAL 3.6 5.4 - - - -
245A GLN* 4.4 16.0 + - + +
264A LEU* 3.8 25.5 - - - +
274A GLY 5.3 0.2 - - - +
276A VAL* 4.1 22.8 - - + +
295A TYR* 3.7 15.1 - - - -
321A TRP* 4.5 7.5 - - - -
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Residues in contact with ALA 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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194A ALA* 4.5 0.7 - - + -
216A THR* 4.1 22.9 - - + -
217A LEU 4.2 2.2 - - - +
218A GLU 3.6 4.3 - - - +
219A CYS* 3.6 16.4 - - + -
234A LEU* 3.8 11.9 - - + -
235A ASN* 1.3 73.8 + - - +
237A ARG* 1.3 71.1 + - - +
238A SER 3.7 0.5 + - - -
243A ARG* 3.4 14.6 + - - -
244A VAL* 2.8 36.5 + - + +
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Residues in contact with ARG 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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216A THR* 3.4 6.1 - - - -
217A LEU* 3.0 48.4 + - + +
218A GLU* 2.8 61.7 + - - +
236A ALA* 1.3 74.5 - - - +
238A SER* 1.3 66.4 + - - +
239A HIS* 5.1 2.2 - - - -
243A ARG* 3.3 10.8 - - - +
266A GLU* 3.3 8.3 - - - +
270A GLN* 2.8 33.5 + - - +
271A GLY 3.5 3.4 + - - -
272A CYS* 3.7 22.4 - - - +
273A GLN* 4.6 0.9 - - - -
304A ARG* 3.3 23.9 - - - +
334A TYR* 3.0 15.8 + - - -
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Residues in contact with SER 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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215A ASP 3.9 11.0 - - - -
217A LEU* 4.4 1.1 - - - -
236A ALA 4.7 0.7 - - - -
237A ARG* 1.3 77.1 - - - +
239A HIS* 1.3 64.2 + - - +
240A LEU* 3.1 17.9 + - - +
242A ALA 2.8 23.7 + - - -
244A VAL* 3.8 26.5 - - - -
266A GLU* 3.2 24.0 + - - +
270A GLN 3.7 3.5 - - - +
271A GLY* 3.6 12.6 - - - -
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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