Contacts of the strand formed by residues 229 - 238 (chain A) in PDB entry 5DQE
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 GLN 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A LEU 3.9 5.4 - - - +
224A GLY* 4.6 2.9 - - - -
225A THR 2.9 29.4 + - - +
226A ALA* 3.4 15.6 + - - +
227A ARG 4.1 0.6 - - - -
228A LEU* 1.3 77.8 - - - +
230A LEU* 1.3 66.3 + - - +
231A VAL* 3.6 0.7 + - - +
333A TYR* 3.1 9.1 - - - +
334A GLU* 2.8 63.8 + - + +
335A SER* 4.9 4.2 - - - +
336A LEU 5.9 0.2 - - - +
422A LEU* 5.0 0.2 - - - -
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Residues in contact with LEU 230 (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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223A LEU* 2.9 53.7 + - + +
224A GLY* 4.5 0.2 - - - -
228A LEU 4.3 0.4 + - - -
229A GLN* 1.3 74.5 - - - +
231A VAL* 1.3 61.1 + - - +
232A GLU 3.8 17.0 - - - +
233A PHE* 4.2 21.3 - - + -
254A ILE* 4.2 19.1 - - + -
256A GLN* 3.0 25.4 - - - +
331A SER* 4.9 2.5 - - - -
332A GLN 3.6 16.2 - - - +
333A TYR* 3.8 33.4 - - + +
422A LEU* 4.7 1.6 - - + +
426A TYR* 5.0 6.3 - - - +
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Residues in contact with VAL 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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229A GLN* 3.6 3.1 + - + +
230A LEU* 1.3 78.0 - - - +
232A GLU* 1.3 64.7 + - + +
255A SER* 3.7 0.9 + - - -
256A GLN* 2.8 44.1 + - - +
332A GLN* 2.7 40.1 + - + +
333A TYR 4.5 0.7 - - - -
334A GLU* 3.1 48.2 - - + +
369A ARG* 6.3 0.4 - - - +
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Residues in contact with GLU 232 (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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230A LEU* 3.8 5.6 - - - +
231A VAL* 1.3 84.0 - - + +
233A PHE* 1.3 62.8 + - - +
234A SER* 5.7 1.6 - - - -
253A HIS* 2.9 28.0 + - + +
254A ILE 3.1 18.8 - - - +
255A SER* 3.5 17.5 + - - +
330A SER 3.9 0.4 - - - +
331A SER* 3.3 4.2 - - - -
332A GLN* 2.9 40.9 + - + +
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Residues in contact with PHE 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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230A LEU* 4.2 21.1 - - + -
232A GLU* 1.3 75.8 - - - +
234A SER* 1.3 66.5 + - - +
252A VAL* 3.9 20.4 - - + -
253A HIS* 3.2 5.4 - - - -
254A ILE* 2.7 48.6 + - + +
302A PHE* 4.3 16.8 - + - -
329A VAL* 3.6 25.8 - - + -
330A SER 3.5 10.3 - - - -
331A SER* 3.9 14.1 - - - -
333A TYR* 6.0 0.2 - - - -
410A GLN* 4.5 15.3 - - - -
426A TYR* 4.6 9.2 - - - -
501A 5E4 3.4 47.6 - + + -
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Residues in contact with SER 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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232A GLU* 5.7 2.2 - - - -
233A PHE* 1.3 83.8 - - - +
235A ALA* 1.3 60.4 + - - +
236A PHE* 3.6 17.8 - - - -
248A ARG* 4.3 5.5 + - - -
250A LEU* 4.1 13.5 - - - -
252A VAL 3.3 9.0 - - - -
253A HIS* 3.8 17.0 - - - -
329A VAL* 3.5 5.0 - - - +
330A SER* 3.0 37.2 + - - +
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Residues in contact with ALA 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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233A PHE* 4.6 1.3 - - + -
234A SER* 1.3 72.8 - - - +
236A PHE* 1.3 58.4 + - - +
250A LEU* 3.6 1.6 - - - +
251A PHE* 2.8 38.6 + - + -
252A VAL* 3.1 22.6 + - + +
328A GLY 3.5 8.5 - - - +
329A VAL* 4.2 7.2 - - + -
379A MET* 4.2 6.1 - - + -
501A 5E4 3.7 31.4 - - + -
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Residues in contact with PHE 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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234A SER* 3.6 20.2 - - - -
235A ALA* 1.3 74.1 - - - +
237A VAL* 1.3 67.1 + - - +
238A GLU* 3.9 18.8 - - + -
248A ARG* 3.5 51.1 - - - -
249A HIS 3.1 15.5 - - - +
250A LEU* 3.8 12.8 - - + -
251A PHE* 3.7 12.4 - - - -
326A PHE* 4.5 7.0 - + - -
327A TYR* 3.5 3.3 - - - -
328A GLY* 3.0 58.3 + - - +
329A VAL 4.1 1.1 - - - -
330A SER* 3.7 20.4 - - - -
376A ARG* 4.1 9.2 - - + -
379A MET* 4.2 1.2 - - - +
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Residues in contact with VAL 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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236A PHE* 1.3 75.8 - - - +
238A GLU* 1.3 76.4 + - - +
239A PRO* 4.7 0.5 - - - +
247A GLN 4.4 0.2 - - - +
248A ARG* 3.7 3.6 - - - +
249A HIS* 3.0 43.9 + - + +
251A PHE* 3.6 20.6 - - + -
308A TRP* 4.0 24.5 - - + +
325A GLY* 5.0 1.8 - - - -
326A PHE 3.4 9.6 - - - +
327A TYR* 3.7 37.7 - - + +
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Residues in contact with GLU 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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236A PHE* 4.0 8.5 - - + -
237A VAL* 1.3 82.3 - - - +
239A PRO* 1.3 72.9 - - + +
247A GLN 4.0 5.8 - - - +
248A ARG* 2.7 49.0 + - + +
325A GLY* 3.8 2.4 - - - -
326A PHE* 2.9 38.3 + - + +
376A ARG* 2.3 34.8 + - - -
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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