Contacts of the helix formed by residues 241 - 258 (chain B) in PDB entry 2R5Z
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 THR 241 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235B ALA* 4.8 0.2 - - - -
240B ILE* 1.3 76.7 - - - +
242B VAL* 1.3 75.6 + - - +
243B SER* 3.3 15.4 + - - +
244B GLN* 2.7 66.8 + - + +
245B VAL* 3.1 20.8 + - - +
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Residues in contact with VAL 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B GLU* 5.3 4.9 - - + +
231B LYS* 3.9 26.6 - - + +
232B GLU* 5.0 9.4 - - + +
235B ALA* 4.0 17.7 - - + +
241B THR* 1.3 75.5 + - - +
243B SER* 1.3 64.6 + - - +
245B VAL* 3.6 4.3 - - - +
246B SER* 2.8 29.0 + - - -
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Residues in contact with SER 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LYS* 5.9 4.9 - - - +
241B THR* 3.3 15.5 + - - -
242B VAL* 1.3 82.3 - - - +
244B GLN* 1.3 53.2 + - - +
246B SER* 2.9 9.4 + - - -
247B ASN* 2.6 47.3 + - - -
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Residues in contact with GLN 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B PHE* 3.7 26.7 - - + -
240B ILE* 3.5 16.3 - - + +
241B THR* 2.7 54.2 + - + +
243B SER* 1.3 76.1 - - - +
245B VAL* 1.3 56.1 + - - +
247B ASN* 3.5 5.0 + - - +
248B TRP* 2.9 28.8 + - - +
9C A 2.9 38.3 + - - +
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Residues in contact with VAL 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LEU* 4.4 6.1 - - + -
231B LYS* 3.5 25.1 - - + +
234B LEU* 4.3 15.3 - - + -
235B ALA* 3.6 26.9 - - + +
240B ILE* 3.3 24.9 - - + -
241B THR 3.1 10.9 + - - +
242B VAL 3.6 7.2 - - - +
243B SER 3.1 0.4 - - - -
244B GLN* 1.3 71.9 - - - +
246B SER* 1.3 68.7 + - - +
248B TRP* 3.0 8.5 + - - +
249B PHE* 2.9 43.0 + - + -
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Residues in contact with SER 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B LYS* 3.7 29.7 + - - +
242B VAL* 2.8 19.6 + - - -
243B SER* 3.2 9.0 - - - -
245B VAL* 1.3 78.2 - - - +
247B ASN* 1.3 63.5 + - - +
249B PHE* 3.4 5.0 + - - +
250B GLY* 3.1 18.2 + - - -
253B ARG* 5.2 0.9 + - - -
29D T 4.7 5.0 + - - +
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Residues in contact with ASN 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B SER* 2.6 31.8 + - - +
244B GLN* 3.8 5.2 - - - +
246B SER* 1.3 70.9 - - - +
248B TRP* 1.3 69.3 + - - +
250B GLY* 3.0 3.3 + - - -
251B ASN* 2.9 29.0 + - - +
8C G 5.3 1.1 - - + -
9C A 3.6 42.2 + - + +
10C T 3.6 33.6 + - + +
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Residues in contact with TRP 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B PHE* 4.0 12.9 - + + -
213B SER* 4.7 6.9 + - - -
216B LEU* 3.6 56.7 - - + +
217B ASN* 3.7 27.4 - - - -
220B PHE* 4.2 5.8 - - + -
244B GLN 2.9 15.2 + - - +
245B VAL* 3.0 12.3 + - - +
247B ASN* 1.3 76.9 - - - +
249B PHE* 1.3 83.6 + + - +
251B ASN* 3.5 7.0 + - + +
252B LYS* 2.8 66.1 + - + +
8C G 3.5 30.4 + - + +
9C A 5.2 0.6 + - - -
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Residues in contact with PHE 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LEU* 4.2 6.1 - - + -
219B TYR* 3.5 33.0 - + + -
220B PHE* 4.0 26.7 - + - -
224B PRO* 3.1 28.7 - - + -
226B PRO* 3.6 20.2 - - + -
231B LYS* 5.9 1.6 - - + +
234B LEU* 4.0 18.6 - - + -
245B VAL* 2.9 31.4 + - + +
246B SER* 3.9 5.6 - - - +
248B TRP* 1.3 95.2 - + - +
250B GLY* 1.3 65.9 + - - +
252B LYS* 3.7 1.5 - - - +
253B ARG* 2.9 42.7 + - - +
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Residues in contact with GLY 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B SER 3.1 10.7 + - - -
247B ASN* 3.0 6.7 + - - -
249B PHE* 1.3 79.4 - - - +
251B ASN* 1.3 63.2 + - - +
253B ARG* 3.3 18.0 + - - +
254B ILE* 3.2 26.4 + - - +
30D T 4.6 17.3 - - - -
31D A 5.9 3.1 - - - -
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Residues in contact with ASN 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B ASN* 2.9 19.2 + - - +
248B TRP* 3.8 5.2 - - - +
250B GLY* 1.3 75.8 - - - +
252B LYS* 1.3 63.7 + - - +
254B ILE* 4.9 4.3 - - - +
255B ARG* 3.0 63.2 + - - +
8C G 3.4 9.1 - - + +
9C A 3.1 44.9 + - - +
10C T 4.5 3.2 + - - -
31D A 5.6 3.6 + - - +
32D A 4.4 7.5 - - - +
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Residues in contact with LYS 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B ASN* 2.8 28.0 + - - -
220B PHE* 3.7 39.3 - - + -
221B TYR* 2.8 26.1 + - - -
248B TRP* 2.8 49.4 + - + +
249B PHE* 3.7 4.7 - - - +
250B GLY 3.2 0.2 - - - -
251B ASN* 1.3 75.4 - - - +
253B ARG* 1.3 58.2 + - - +
255B ARG* 3.7 2.7 - - + +
256B TYR* 2.9 33.4 + - + +
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Residues in contact with ARG 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TRP* 3.5 27.3 - - + -
220B PHE* 4.1 12.1 - - + -
224B PRO* 3.3 19.5 + - + -
225B TYR* 3.3 51.1 - - - +
226B PRO* 5.0 1.2 - - - +
231B LYS* 6.0 1.8 - - - +
246B SER 5.2 1.0 + - - -
249B PHE* 2.9 45.5 + - - +
250B GLY* 3.3 9.1 + - - +
252B LYS* 1.3 76.4 - - - +
254B ILE* 1.3 63.7 + - + +
256B TYR* 3.1 6.4 + - - +
257B LYS* 2.9 32.3 + - - +
29D T 4.0 8.9 + - - +
30D T 2.4 34.6 + - - +
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Residues in contact with ILE 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B GLY 3.2 15.6 + - - +
251B ASN* 4.3 4.0 - - - +
253B ARG* 1.3 83.5 - - + +
255B ARG* 1.3 70.9 + - + +
257B LYS* 3.1 12.8 + - - +
258B LYS* 2.9 52.8 + - + +
30D T 3.9 29.2 - - + +
31D A 3.7 54.7 - - + +
32D A 5.8 2.7 - - - +
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Residues in contact with ARG 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LYS* 4.6 0.5 - - - +
251B ASN* 3.0 44.8 + - - +
252B LYS* 4.1 2.9 - - + +
254B ILE* 1.3 85.5 - - + +
256B TYR* 1.3 63.9 + - - +
258B LYS* 4.1 15.9 - - - +
259B ASN* 3.6 18.2 + - - +
6C A 6.3 0.7 - - - -
7C A 4.2 27.5 + - - +
8C G 2.7 51.1 + - - -
9C A 3.2 11.7 - - - +
33D T 3.3 13.1 + - - +
34D C 4.8 0.4 - - - +
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Residues in contact with TYR 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LYS* 3.2 47.9 + - + +
77A ASN 4.4 2.4 + - - -
78A PRO* 3.1 29.6 - - + +
79A PRO* 4.7 1.6 - - - +
84A TRP* 3.8 17.0 - + - -
85A MET* 3.2 28.7 - - + -
220B PHE* 4.0 19.1 - + + -
221B TYR* 4.2 21.5 - + - -
252B LYS* 2.9 17.2 + - + +
253B ARG* 3.3 9.4 - - - +
254B ILE 3.0 0.2 - - - -
255B ARG* 1.3 78.3 - - - +
257B LYS* 1.3 67.0 + - - +
259B ASN 3.0 10.6 + - - -
260B ILE* 3.5 8.6 + - + -
1223B LEU* 3.6 25.1 - - + +
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Residues in contact with LYS 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A TRP* 3.5 32.2 + - + +
85A MET* 3.2 27.1 - - - +
86A LYS 2.9 18.8 + - - +
87A ARG* 4.0 28.4 + - - +
88A VAL* 4.6 5.7 - - - +
253B ARG 2.9 15.0 + - - +
254B ILE* 3.1 20.4 + - - +
256B TYR* 1.3 72.6 - - - +
258B LYS* 1.3 58.8 + - + +
259B ASN 2.7 12.7 + - - -
260B ILE* 3.1 29.2 + - + +
30D T 4.7 3.9 + - - -
31D A 2.6 33.9 + - - -
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Residues in contact with LYS 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ARG* 4.4 20.0 - - - +
254B ILE* 2.9 41.4 + - + +
255B ARG* 4.4 15.7 - - - +
256B TYR 3.4 0.2 - - - -
257B LYS* 1.3 71.7 - - + +
259B ASN* 1.3 58.9 + - - +
260B ILE 3.7 0.7 - - - -
31D A 5.8 1.1 - - + -
32D A 4.4 19.1 - - - +
33D T 6.0 5.8 - - - +
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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
------------------------------------------------------------
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