Contacts of the strand formed by residues 233 - 242 (chain A) in PDB entry 5EJK
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 TRP 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A LYS* 3.5 44.1 + - - +
226A ILE 3.5 6.3 - - - -
227A ARG* 3.5 40.8 - - + +
231A GLY 4.2 5.7 + - - -
232A GLU* 1.3 80.3 - - - +
234A GLU* 1.3 59.4 + - - +
235A LYS 4.1 0.5 + - - -
263A ARG 3.6 13.2 - - - -
264A LYS* 3.2 40.2 - - - -
265A VAL 3.8 4.0 - - - -
266A LYS* 3.6 38.5 - - + +
244B ARG* 5.3 3.1 - - - -
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Residues in contact with GLU 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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225A LYS* 3.3 21.6 - - - +
226A ILE* 3.1 18.2 + - + +
228A ILE* 4.3 26.6 - - + +
232A GLU* 4.0 0.4 + - + -
233A TRP* 1.3 71.9 - - - +
235A LYS* 1.3 76.5 + - - +
237A TRP* 3.7 29.2 + - - +
251A ASN* 5.3 2.9 + - - -
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Residues in contact with LYS 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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224A VAL 4.5 0.7 - - - -
225A LYS* 3.7 34.1 - - + +
233A TRP 4.1 0.6 + - - -
234A GLU* 1.3 91.9 - - - +
236A GLY* 1.3 63.1 + - - +
237A TRP* 3.6 3.0 + - - -
252A ARG* 5.7 0.2 - - - +
268A ASP* 3.3 34.5 + - - +
269A ILE* 3.8 22.1 - - + +
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Residues in contact with GLY 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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235A LYS* 1.3 77.1 - - - +
237A TRP* 1.3 64.9 + - - +
251A ASN* 4.1 5.8 + - - -
252A ARG* 3.0 56.8 + - - +
253A ASP* 4.6 1.0 + - - -
268A ASP* 4.1 1.0 + - - -
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Residues in contact with TRP 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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224A VAL* 2.7 45.2 + - + +
226A ILE* 3.4 34.0 - - + +
234A GLU* 3.7 43.6 - - - -
235A LYS 3.8 3.5 + - - -
236A GLY* 1.3 83.0 - - - +
238A ASN* 1.3 60.5 + - - +
249A VAL* 4.2 12.3 - - + -
250A LYS 3.4 8.7 - - - -
251A ASN* 3.3 53.5 - - + +
252A ARG* 2.7 10.7 + - - -
256A LYS* 4.6 15.0 - - - -
258A ILE* 3.6 37.7 - - + -
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Residues in contact with ASN 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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220A GLU* 3.6 20.2 + - - +
221A GLY* 2.6 32.5 + - - +
222A PRO* 3.2 17.5 - - - +
223A PRO* 3.3 7.9 - - - +
224A VAL* 3.7 4.3 - - - -
237A TRP* 1.3 75.4 - - - +
239A VAL* 1.3 58.3 + - - +
240A LEU* 5.1 0.4 - - + -
249A VAL* 3.4 1.0 - - - +
250A LYS* 2.6 47.6 + - - +
252A ARG* 2.4 42.0 + - - +
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Residues in contact with VAL 239 (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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218A LEU* 4.0 2.1 - - - +
221A GLY* 3.5 19.9 - - - -
222A PRO* 3.1 16.7 + - + +
224A VAL* 3.5 33.5 - - + +
238A ASN* 1.3 71.5 - - - +
240A LEU* 1.3 64.9 + - - +
241A VAL 3.4 26.2 - - - +
242A TRP* 4.1 18.2 - - + -
247A ALA* 4.5 1.1 - - + -
248A ALA 3.6 6.3 - - - +
249A VAL* 4.0 9.0 - - + -
265A VAL* 4.9 0.7 - - + -
241B VAL* 3.7 26.4 - - + +
259B TRP* 4.1 0.4 - - + -
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Residues in contact with LEU 240 (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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55A LEU* 4.9 10.3 - - + -
218A LEU* 3.6 38.7 + - + +
219A THR 5.5 0.4 - - - +
220A GLU* 4.8 1.3 - - - -
221A GLY* 3.9 24.2 - - - +
238A ASN 4.9 0.9 - - - +
239A VAL* 1.3 76.3 - - - +
241A VAL* 1.3 67.8 + - + +
248A ALA* 2.7 17.0 + - + +
250A LYS* 3.7 43.7 - - + -
257A VAL* 3.8 25.1 - - + -
240B LEU 5.5 0.2 - - - +
241B VAL* 5.3 2.1 - - - +
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Residues in contact with VAL 241 (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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53A ARG* 5.4 2.5 - - - +
54A GLY 5.7 0.2 - - - +
55A LEU* 5.0 11.4 - - + +
239A VAL* 3.4 4.0 - - - +
240A LEU* 1.3 87.2 - - + +
242A TRP* 1.3 65.6 + - - +
243A GLY* 4.3 8.7 - - - +
246A TYR 5.1 1.3 - - - +
247A ALA* 3.1 6.8 - - - +
248A ALA* 2.8 45.4 + - + +
259A TRP* 4.2 23.1 - - + -
241B VAL* 5.9 0.4 - - - -
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Residues in contact with TRP 242 (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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224A VAL* 4.2 4.0 - - + -
239A VAL* 4.1 11.4 - - + -
241A VAL* 1.3 76.3 - - - +
243A GLY* 1.3 71.5 + - - +
247A ALA* 3.9 9.0 - - + -
262A SER* 3.6 25.2 + - - +
265A VAL* 3.5 50.9 - - + -
266A LYS* 4.1 6.7 - - - -
267A PRO* 4.4 7.0 - - + -
241B VAL* 3.5 34.5 - - + +
242B TRP 3.7 16.4 + - - +
243B GLY* 3.3 22.2 - - - -
244B ARG* 3.7 24.2 - - + +
259B TRP* 3.7 23.6 - + - -
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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