Contacts of the strand formed by residues 248 - 261 (chain A) in PDB entry 3RBH
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 TYR 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A GLU* 5.3 14.2 - - + +
204A ARG* 4.7 9.7 + - - -
230A ASP* 4.1 25.6 + - - +
234A LEU* 3.9 5.1 - - - +
246A LYS* 3.4 12.0 + - - +
247A THR* 1.3 93.2 - - - +
249A THR* 1.3 76.8 + - - +
250A GLY* 5.1 0.9 - - - -
252A LEU* 5.4 4.8 - - + +
285A ARG* 3.5 54.5 + - + +
286A ASP 3.2 12.1 - - - +
287A ASN* 3.1 18.6 - - - +
345A GLN* 3.6 19.9 + - - -
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Residues in contact with THR 249 (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 ASP* 3.5 23.5 + - + +
232A GLY 3.9 20.1 + - - +
234A LEU* 3.4 25.5 - - + +
246A LYS* 4.1 15.3 - - + -
248A TYR* 1.3 88.1 - - - +
250A GLY* 1.3 57.4 + - - +
285A ARG* 3.3 3.8 - - - -
286A ASP* 2.6 51.4 + - - +
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Residues in contact with GLY 250 (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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228A ALA 3.9 0.5 - - - +
229A ASP* 3.6 4.1 - - - +
230A ASP* 2.7 42.3 + - - +
248A TYR* 5.4 0.9 - - - -
249A THR* 1.3 80.4 + - - +
251A GLN* 1.3 59.3 + - - -
252A LEU* 5.4 1.8 - - - -
284A ASP* 3.4 19.1 - - - -
285A ARG* 4.2 2.2 - - - -
286A ASP* 4.7 0.4 - - - -
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Residues in contact with GLN 251 (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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227A HIS* 3.1 24.3 - - + -
228A ALA 3.2 8.3 - - - +
229A ASP* 3.8 20.9 - - - +
250A GLY* 1.3 75.5 - - - +
252A LEU* 1.3 64.2 + - - +
253A THR* 4.2 2.9 + - - -
283A GLY* 3.2 17.4 - - - -
284A ASP* 2.9 52.5 + - - +
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Residues in contact with LEU 252 (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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226A HIS 3.9 0.2 - - - +
227A HIS* 2.9 8.4 + - - -
228A ALA* 2.9 35.4 + - + +
248A TYR* 5.4 4.7 - - + +
250A GLY 5.4 0.9 - - - -
251A GLN* 1.3 84.2 + - - +
253A THR* 1.3 64.2 + - - +
254A TRP* 3.8 26.1 - - + -
281A LEU* 3.9 13.0 - - + -
282A THR 3.7 2.0 - - - +
283A GLY* 4.2 3.4 - - - -
284A ASP 4.2 17.0 - - - +
285A ARG* 4.9 8.7 - - + -
307A VAL* 4.2 23.6 - - + -
345A GLN* 3.7 37.9 - - + +
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Residues in contact with THR 253 (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 ILE* 4.2 15.5 - - + -
226A HIS 3.3 9.9 - - - +
227A HIS* 2.6 29.3 + - + +
251A GLN* 4.2 2.3 + - - -
252A LEU* 1.3 72.0 - - - +
254A TRP* 1.3 65.7 + - - +
255A LEU* 3.7 26.0 - - + +
280A TRP 3.5 1.7 - - - +
281A LEU* 3.3 7.3 - - - +
282A THR* 2.8 43.9 + - - -
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Residues in contact with TRP 254 (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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160A TRP* 3.6 25.1 - + + -
204A ARG* 5.9 1.6 - - - -
225A ILE* 3.3 10.2 - - - +
226A HIS* 2.9 59.1 + + - +
228A ALA* 4.1 11.4 - - + -
252A LEU* 3.8 32.5 - - + -
253A THR* 1.3 76.4 - - - +
255A LEU* 1.3 61.8 + - - +
279A THR* 3.9 8.1 - - + -
280A TRP 3.3 4.5 - - - -
281A LEU* 3.5 19.5 - - + +
344A PHE* 3.9 20.2 - + - -
345A GLN* 2.7 34.7 + - + -
346A GLN* 3.4 29.4 - - - +
347A THR* 3.8 19.7 - - + +
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Residues in contact with LEU 255 (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 ARG 3.7 2.9 - - - -
225A ILE* 4.8 11.2 - - + +
253A THR* 3.7 25.8 - - + +
254A TRP* 1.3 80.6 - - - +
256A GLY* 1.3 58.5 + - - +
279A THR* 3.4 1.9 - - - -
280A TRP* 2.7 62.9 + - + +
282A THR* 4.2 16.4 - - + -
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Residues in contact with GLY 256 (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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160A TRP* 4.1 8.5 - - - -
223A VAL* 3.3 10.0 - - - +
224A ARG* 2.8 37.1 + - - -
255A LEU* 1.3 75.3 - - - +
257A ILE* 1.3 61.2 + - - +
258A GLU* 5.3 0.4 - - - -
278A ALA 3.3 9.2 - - - -
279A THR* 4.0 10.1 - - - -
280A TRP* 5.1 1.8 - - - -
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Residues in contact with ILE 257 (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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221A ILE* 4.3 20.4 - - + -
222A GLY 3.5 10.3 - - - +
223A VAL* 4.5 10.8 - - + +
256A GLY* 1.3 76.0 - - - +
258A GLU* 1.3 71.5 + - - +
259A ALA* 6.2 0.4 - - + -
277A SER* 3.3 4.3 - - - -
278A ALA* 2.9 55.4 + - + +
279A THR* 5.1 0.2 + - - -
280A TRP* 4.2 12.7 - - + -
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Residues in contact with GLU 258 (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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155A GLU* 5.3 1.6 - - - +
157A SER* 5.2 5.7 + - - -
160A TRP* 4.2 11.7 + - - -
210A ASP* 5.4 0.2 - - - +
221A ILE* 3.3 7.5 - - - +
222A GLY* 2.9 42.7 + - - +
223A VAL 4.9 2.3 - - - +
224A ARG* 3.2 50.5 + - + +
256A GLY 5.3 0.4 - - - -
257A ILE* 1.3 81.3 - - - +
259A ALA* 1.3 62.7 + - - +
260A THR* 5.4 6.7 - - + -
276A ALA 3.3 4.9 - - - +
277A SER* 4.0 13.9 - - - -
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Residues in contact with ALA 259 (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 TRP* 6.1 0.4 - - - +
220A ARG 3.4 9.6 - - - +
221A ILE* 4.1 12.8 - - + -
257A ILE* 6.2 0.4 - - + -
258A GLU* 1.3 74.8 - - - +
260A THR* 1.3 66.8 + - - +
274A TYR* 4.2 12.3 - - + +
275A TRP* 3.5 1.0 - - - -
276A ALA* 2.7 46.1 + - + +
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Residues in contact with THR 260 (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 HIS 3.9 0.2 - - - +
219A HIS* 3.4 2.9 - - - -
220A ARG* 2.9 54.1 + - - +
258A GLU* 5.4 7.0 - - + -
259A ALA* 1.3 81.9 - - - +
261A GLY* 1.3 58.4 + - - +
262A ASP 3.9 2.4 + - - -
263A ALA* 3.7 26.2 - - + -
264A TYR* 4.5 12.6 - - + -
274A TYR* 3.5 13.9 + - - -
275A TRP* 4.1 7.2 - - + -
276A ALA 5.0 0.2 - - - +
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Residues in contact with GLY 261 (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 HIS 3.4 8.3 - - - -
219A HIS* 4.0 2.0 - - - -
260A THR* 1.3 71.9 - - - +
262A ASP* 1.3 69.1 + - - +
263A ALA 3.1 1.2 + - - -
270A MSE 3.5 9.2 - - - -
273A ASN* 3.1 27.7 + - - +
274A TYR* 2.9 33.6 + - - -
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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