Contacts of the strand formed by residues 227 - 235 (chain A) in PDB entry 4X2N
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 GLU 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A LYS* 3.3 6.9 - - - -
224A TRP* 2.9 43.8 + - + +
225A ARG* 4.0 14.3 - - - +
226A GLY* 1.4 81.1 - - - +
228A GLU* 1.3 69.6 + - - +
229A VAL* 4.2 5.0 - - + +
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Residues in contact with GLU 228 (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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208A GLN* 2.8 30.4 + - - +
221A ARG* 2.9 26.4 + - + +
222A GLY 3.4 0.9 - - - +
223A LYS* 4.1 14.6 - - - -
226A GLY 4.4 1.6 + - - +
227A GLU* 1.3 77.9 - - - +
229A VAL* 1.3 64.4 + - - +
281A ASP* 5.4 0.3 - - - -
282A TYR* 3.6 38.5 + - + +
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Residues in contact with VAL 229 (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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205A ILE* 4.3 3.8 - - + -
221A ARG* 3.5 5.7 - - - +
222A GLY 2.8 46.5 + - - +
224A TRP* 3.8 36.6 - - + -
227A GLU* 4.2 5.6 - - + +
228A GLU* 1.3 77.1 - - - +
230A ALA* 1.3 57.0 + - - +
231A VAL* 4.0 10.3 - - + -
263A ILE* 3.8 24.9 - - + -
279A VAL* 3.9 17.0 - - + -
280A SER 3.5 8.7 - - - +
281A ASP* 5.5 0.7 - - - -
282A TYR* 3.7 9.4 - - - +
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Residues in contact with ALA 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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211A ILE* 5.5 0.9 - - + -
219A VAL* 4.7 12.6 - - + -
220A TRP 3.6 6.7 - - - +
229A VAL* 1.3 72.3 - - - +
231A VAL* 1.3 59.3 + - - +
232A LYS 4.1 0.9 - - - -
260A LEU* 6.0 0.2 - - + -
278A LEU 3.7 0.5 - - - +
279A VAL* 3.4 5.0 - - - +
280A SER* 2.9 51.5 + - - +
281A ASP 3.7 11.0 - - - +
282A TYR* 3.8 14.1 - - + +
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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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205A ILE* 4.0 26.2 - - + -
207A LEU* 4.1 13.2 - - + -
218A GLU 3.6 2.1 - - - +
219A VAL* 3.4 4.3 - - - -
220A TRP* 2.8 39.3 + - + +
222A GLY* 4.3 5.8 - - - -
229A VAL* 4.0 12.8 - - + -
230A ALA* 1.3 77.2 - - - +
232A LYS* 1.3 59.8 + - - +
233A ILE* 3.6 17.7 + - + -
277A TRP* 3.4 38.6 - - + -
278A LEU 3.5 6.1 - - - +
279A VAL* 4.5 5.2 - - + -
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Residues in contact with LYS 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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214A GLY* 6.3 1.3 - - - -
215A ARG* 6.2 0.8 - - - +
216A PHE* 3.2 27.7 + - - +
217A GLY 5.2 0.4 - - - -
218A GLU 3.4 10.3 - - - +
219A VAL* 4.0 24.5 - - + +
230A ALA 4.1 0.6 - - - -
231A VAL* 1.3 71.7 - - - +
233A ILE* 1.3 61.2 + - - +
234A PHE* 3.7 28.2 - - + -
245A GLU* 3.1 31.5 + - - +
276A LEU 3.6 1.4 - - - +
277A TRP* 3.4 4.3 - - - -
278A LEU* 2.8 46.9 + - + +
351A ASP* 4.0 19.2 + - - +
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Residues in contact with ILE 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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207A LEU* 3.7 30.3 - - + -
217A GLY* 3.0 3.1 - - - -
218A GLU* 2.8 42.2 + - + +
220A TRP* 3.7 19.3 - - + +
231A VAL* 3.6 17.3 - - + -
232A LYS* 1.3 71.9 - - - +
234A PHE* 1.3 67.7 + - - +
275A GLN* 3.7 35.9 - - + +
276A LEU 3.4 2.2 - - - -
277A TRP* 3.6 26.2 - - + +
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Residues in contact with PHE 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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216A PHE* 3.8 33.0 - - + -
217A GLY 4.1 4.0 - - - -
232A LYS* 3.7 26.5 - - + -
233A ILE* 1.3 79.8 - - - +
235A SER* 1.3 63.5 + - - +
238A GLU* 3.3 21.8 - - + +
241A SER* 4.1 3.8 - - - -
242A TRP* 3.6 42.2 - + + -
245A GLU* 3.6 23.8 - - - -
275A GLN* 3.8 4.5 - - - -
276A LEU* 2.8 44.2 + - + +
278A LEU* 3.6 26.0 - - + -
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Residues in contact with SER 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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234A PHE* 1.3 77.6 - - - +
236A SER* 1.3 65.7 + - - +
237A ARG* 3.3 29.4 + - - +
238A GLU* 2.8 35.7 + - - +
273A TRP* 6.1 4.3 - - - -
274A THR 4.6 4.7 - - - -
275A GLN* 5.4 0.2 - - - +
276A LEU* 3.6 9.8 - - - +
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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