Contacts of the helix formed by residues 244 - 262 (chain A) in PDB entry 1B72
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 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A ARG* 4.5 2.4 - - - +
233A ARG* 3.0 51.7 + - + +
234A VAL* 3.2 39.4 - - + +
237A ALA* 4.1 7.1 - - + +
243A ASN* 1.3 73.9 - - - +
245A THR* 1.3 53.4 + - - +
247A VAL* 3.2 3.6 + - - +
248A LYS* 2.7 37.0 + - - +
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Residues in contact with THR 245 (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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243A ASN* 3.2 9.0 - - - +
244A GLU* 1.3 79.4 - - - +
246A GLN* 1.3 59.2 + - + +
248A LYS* 3.4 18.3 + - + +
249A ILE* 2.8 55.2 + - + +
14D T 5.7 0.9 - - - +
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Residues in contact with GLN 246 (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 THR* 2.5 41.4 + - - +
210A PHE* 4.5 12.3 - - + -
242A LEU* 3.6 22.4 - - + +
243A ASN* 2.8 49.3 + - - +
244A GLU 3.3 0.6 - - - -
245A THR* 1.3 78.3 - - + +
247A VAL* 1.3 56.9 + - - +
249A ILE* 3.5 2.7 + - - +
250A TRP* 2.9 29.6 + - - +
13D A 3.2 22.4 + - - +
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Residues in contact with VAL 247 (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* 4.5 11.4 - - + -
228A LEU* 3.8 27.4 - - + -
233A ARG* 4.4 13.0 - - + +
236A ILE* 4.6 7.4 - - + -
237A ALA* 3.9 27.1 - - + +
240A LEU* 5.6 0.2 - - + -
242A LEU* 4.3 16.6 - - + -
243A ASN 3.2 14.1 - - - +
244A GLU* 3.2 9.1 + - - +
246A GLN* 1.3 75.8 - - - +
248A LYS* 1.3 58.6 + - - +
250A TRP* 3.3 5.3 + - - +
251A PHE* 3.0 44.3 + - + -
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Residues in contact with LYS 248 (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 LEU* 6.1 0.9 - - - -
233A ARG* 4.3 22.0 - - - +
244A GLU 2.7 21.3 + - - +
245A THR* 3.4 20.4 - - + +
247A VAL* 1.3 74.8 - - - +
249A ILE* 1.3 62.9 + - + +
251A PHE* 3.4 6.6 + - - +
252A GLN* 3.0 26.9 + - + +
255A ARG* 4.9 0.2 + - - -
23E A 5.1 1.2 - - - +
24E G 3.4 51.5 + - - +
25E C 3.8 23.7 + - - +
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Residues in contact with ILE 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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245A THR* 2.8 42.1 + - + +
246A GLN* 3.9 5.4 - - + +
248A LYS* 1.3 77.3 - - + +
250A TRP* 1.3 67.7 + - - +
252A GLN* 3.2 7.8 + - + +
253A ASN* 2.9 41.6 + - - +
12D G 4.8 1.8 - - + -
13D A 3.7 39.5 - - + +
14D T 3.9 31.9 - - + +
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Residues in contact with TRP 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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210A PHE* 3.6 22.7 - + + -
215A LEU* 3.6 22.0 - - + +
218A LEU* 3.6 57.2 - - + -
219A GLU* 3.0 34.3 - - + -
222A PHE* 4.2 6.5 - + + -
246A GLN 2.9 18.9 + - - +
247A VAL* 3.6 5.4 - - - +
249A ILE* 1.3 78.8 - - - +
251A PHE* 1.3 76.4 + + - +
253A ASN* 3.8 6.3 - - - +
254A ARG* 2.8 54.9 + - + +
12D G 3.5 24.4 + - - -
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Residues in contact with PHE 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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218A LEU* 4.0 12.3 - - + -
221A GLU* 3.7 21.8 - - + -
222A PHE* 3.7 31.0 - + + -
225A ASN 3.8 5.4 - - - -
226A LYS 3.6 17.7 - - - -
228A LEU* 3.2 51.4 - - + -
236A ILE* 4.5 0.9 - - + -
247A VAL* 3.0 35.1 + - + +
248A LYS* 3.8 6.3 - - - +
250A TRP* 1.3 91.4 - + - +
252A GLN* 1.3 64.1 + - - +
254A ARG* 3.5 2.5 - - - +
255A ARG* 2.9 40.8 + - - +
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Residues in contact with GLN 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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248A LYS* 3.0 15.4 + - + +
249A ILE* 3.2 12.3 + - + +
251A PHE* 1.3 79.2 - - - +
253A ASN* 1.3 66.5 + - - +
255A ARG* 2.8 25.6 + - - +
256A MET* 3.2 30.2 + - + +
14D T 6.0 1.1 - - - +
25E C 2.7 39.3 + - + +
26E C 2.6 49.2 + - + -
27E G 5.7 1.8 - - - +
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Residues in contact with ASN 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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249A ILE* 2.9 29.4 + - - +
250A TRP* 3.9 4.9 - - - +
252A GLN* 1.3 79.3 - - - +
254A ARG* 1.3 61.4 - - - +
256A MET* 3.3 10.4 + - - +
257A LYS* 3.1 23.7 + - - +
11D T 5.8 2.5 - - + -
12D G 3.6 27.2 + - - +
13D A 3.0 48.8 + - - +
14D T 4.8 2.1 - - - +
28E A 4.8 2.1 + - - -
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Residues in contact with ARG 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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219A GLU* 2.5 39.1 + - - -
222A PHE* 3.4 33.5 - - + -
223A HIS* 4.2 7.5 - - - -
250A TRP* 2.8 38.3 + - + +
251A PHE* 3.5 5.2 - - - +
253A ASN* 1.3 75.0 - - - +
255A ARG* 1.3 66.2 + - - +
257A LYS* 3.1 39.8 - - - +
258A GLN* 2.9 50.2 + - - +
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Residues in contact with ARG 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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222A PHE* 3.8 22.7 - - + -
226A LYS* 3.0 23.9 + - + +
227A TYR* 3.5 47.4 - - - +
228A LEU 5.0 0.6 - - - +
248A LYS 4.9 0.2 + - - -
251A PHE* 2.9 32.0 + - - +
252A GLN* 2.8 40.4 + - - +
254A ARG* 1.3 76.6 - - - +
256A MET* 1.3 64.1 + - - +
258A GLN* 3.1 6.6 + - - +
259A LYS* 3.0 21.3 + - - +
25E C 3.4 24.5 + - - -
26E C 2.7 24.3 + - - +
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Residues in contact with MET 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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252A GLN* 3.2 28.1 + - + +
253A ASN* 3.6 11.4 - - - +
254A ARG 3.2 0.2 - - - -
255A ARG* 1.3 78.8 - - - +
257A LYS* 1.3 56.9 + - - +
259A LYS* 2.7 43.9 + - - +
260A LYS* 3.0 26.2 + - - +
26E C 3.8 16.6 - - - +
27E G 3.5 47.1 - - + +
28E A 5.3 3.4 - - + +
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Residues in contact with LYS 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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253A ASN 3.1 11.9 + - - +
254A ARG* 3.1 53.7 - - - +
256A MET* 1.3 73.7 - - - +
258A GLN* 1.3 65.5 + - - +
260A LYS* 3.4 10.3 + - - +
261A ARG* 3.1 21.5 + - - +
11D T 3.2 26.9 + - - +
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Residues in contact with GLN 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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222A PHE* 3.5 19.3 - - + -
223A HIS* 5.7 2.1 - - - -
226A LYS* 4.7 9.6 + - - +
254A ARG* 2.9 43.7 + - - +
255A ARG* 3.1 12.9 + - - +
257A LYS* 1.3 75.7 + - - +
259A LYS* 1.3 60.5 + - - +
261A ARG* 2.8 28.1 + - - +
262A GLU* 2.9 20.0 + - - +
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Residues in contact with LYS 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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255A ARG 3.0 11.8 + - - +
256A MET* 2.7 46.6 - - + +
258A GLN* 1.3 77.2 - - - +
260A LYS* 1.3 57.6 + - - +
261A ARG 3.0 4.6 + - - -
262A GLU* 3.5 6.6 + - - +
263A ARG* 3.1 31.1 + - + +
27E G 2.9 40.4 + - - +
28E A 4.5 4.4 + - - -
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Residues in contact with LYS 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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256A MET 3.0 16.8 + - - +
257A LYS* 3.6 10.5 - - - +
258A GLN 3.1 0.4 - - - -
259A LYS* 1.3 78.7 - - - +
261A ARG* 1.3 57.3 + - - +
263A ARG* 4.2 6.3 - - - -
264A GLU* 3.5 21.3 - - - +
278B SER* 5.3 8.6 + - - +
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Residues in contact with ARG 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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257A LYS 3.1 11.4 + - - +
258A GLN* 2.8 23.0 + - - +
260A LYS* 1.3 78.6 - - - +
262A GLU* 1.3 61.5 + - - +
263A ARG 3.0 4.9 - - - -
264A GLU 3.2 22.3 + - - +
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Residues in contact with GLU 262 (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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258A GLN* 2.9 17.3 + - - +
259A LYS* 4.2 6.1 - - - +
261A ARG* 1.3 75.6 - - - +
263A ARG* 1.3 57.7 + - - +
264A GLU 3.4 0.4 - - - -
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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