Contacts of the helix formed by residues 250 - 265 (chain A) in PDB entry 4HRE
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 GLY 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A LYS* 1.3 76.8 - - - +
251A ASP* 1.3 66.8 + - - -
252A LEU 3.2 2.2 - - - -
253A GLU* 3.3 7.4 + - - +
254A ASN* 3.2 21.5 + - - +
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Residues in contact with ASP 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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125A GLU* 3.1 41.8 - - + +
126A ASP* 5.6 1.0 - - - +
129A ILE* 3.8 1.9 - - - +
167A PHE* 3.7 30.6 - - + -
249A LYS 3.9 0.2 + - - -
250A GLY* 1.3 72.4 - - - -
252A LEU* 1.3 53.8 + - - +
254A ASN* 3.3 8.5 + - - +
255A ALA* 2.8 36.0 + - - +
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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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166A ASP* 3.7 30.7 - - + +
167A PHE* 3.8 33.8 - - + +
170A LEU* 4.1 9.4 - - + -
210A VAL* 4.1 14.6 - - + -
214A ILE* 5.4 0.2 - - + -
248A VAL* 4.5 15.9 - - + -
249A LYS* 3.8 15.2 + - - +
250A GLY 3.2 0.2 - - - -
251A ASP* 1.3 77.8 - - - +
253A GLU* 1.3 57.7 + - - +
255A ALA* 3.3 2.1 + - - +
256A PHE* 2.9 63.4 + - + -
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Residues in contact with GLU 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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244A ILE* 3.9 15.3 - - + +
245A LYS* 3.5 30.4 - - - +
248A VAL* 3.3 39.1 - - - +
249A LYS* 3.3 21.7 + - - +
250A GLY 3.3 6.0 + - - +
251A ASP 3.3 0.6 - - - -
252A LEU* 1.3 74.8 - - - +
254A ASN* 1.3 61.9 + - - +
256A PHE* 3.2 2.4 + - - +
257A LEU* 2.8 46.1 + - + +
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Residues in contact with ASN 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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126A ASP* 3.1 23.8 - - - +
129A ILE* 3.1 21.0 - - + +
250A GLY 3.2 11.7 + - - +
251A ASP* 3.7 8.7 - - - +
253A GLU* 1.3 80.0 - - - +
255A ALA* 1.3 62.1 + - - +
257A LEU* 3.3 11.1 + - - +
258A ASN* 2.6 59.6 + - - +
273A ARG* 6.1 1.0 - - - +
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Residues in contact with ALA 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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129A ILE* 3.5 16.4 - - + +
133A CYS* 3.6 7.6 - - - -
167A PHE* 3.6 23.8 - - + -
170A LEU* 3.7 20.2 - - + -
171A MET* 4.1 4.9 - - - -
251A ASP 2.8 20.6 + - - +
252A LEU 3.4 5.2 - - - +
254A ASN* 1.3 74.4 - - - +
256A PHE* 1.3 62.2 + - - +
258A ASN* 3.6 0.3 + - - +
259A LEU* 3.1 23.6 + - - +
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Residues in contact with PHE 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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170A LEU* 4.1 20.0 - - + -
210A VAL* 4.1 9.4 - - + -
213A TRP* 4.0 29.8 - + + -
214A ILE* 3.9 24.0 - - + -
217A MET* 4.0 33.9 - - + -
244A ILE* 3.7 20.4 - - + -
248A VAL* 4.3 11.7 - - + -
252A LEU* 2.9 53.8 + - + +
253A GLU 3.2 3.8 + - - +
255A ALA* 1.3 68.0 - - - +
257A LEU* 1.3 67.4 + - - +
259A LEU* 3.2 10.5 + - + +
260A VAL* 3.1 25.8 + - - +
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Residues in contact with LEU 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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241A LEU* 3.8 33.1 - - + +
244A ILE* 3.7 23.1 - - + -
245A LYS* 4.3 20.6 - - + +
253A GLU* 2.8 46.1 + - + +
254A ASN* 3.7 11.0 - - + +
256A PHE* 1.3 71.7 - - - +
258A ASN* 1.3 65.2 + - - +
260A VAL* 3.2 4.7 + - - +
261A GLN* 3.2 36.2 + - - +
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Residues in contact with ASN 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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126A ASP 5.7 0.3 - - - +
129A ILE* 3.8 23.0 - - + +
130A GLU* 5.1 0.2 - - - -
133A CYS* 4.5 4.3 - - + -
254A ASN* 2.6 47.2 + - - +
257A LEU* 1.3 77.0 - - - +
259A LEU* 1.3 58.7 + - - +
261A GLN* 3.2 9.0 + - - +
262A CYS* 2.8 32.6 + - - +
269A TYR* 2.3 45.7 + - + +
273A ARG* 4.1 12.1 + - - -
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Residues in contact with LEU 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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133A CYS* 4.0 30.2 - - + +
170A LEU* 4.4 16.2 - - + -
174A LEU* 4.0 22.2 - - + -
179A ARG* 4.1 13.0 - - - +
217A MET* 4.0 31.9 - - + +
255A ALA 3.1 12.8 + - - +
256A PHE* 3.4 17.3 - - + +
257A LEU 3.2 0.2 - - - -
258A ASN* 1.3 79.0 - - - +
260A VAL* 1.3 59.1 + - + +
262A CYS* 3.3 4.2 + - - +
263A ILE* 2.9 44.3 + - + +
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Residues in contact with VAL 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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217A MET* 4.2 9.9 - - - -
229A PHE* 3.9 24.7 - - + -
240A MET* 3.9 18.4 - - + -
241A LEU* 3.7 21.1 - - + -
244A ILE* 3.6 19.7 - - + -
256A PHE 3.1 13.8 + - - +
257A LEU 3.2 1.1 + - - +
259A LEU* 1.3 73.1 - - + +
261A GLN* 1.3 55.3 + - - +
263A ILE* 3.0 5.1 + - - +
264A GLN* 2.7 66.8 + - - +
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Residues in contact with GLN 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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241A LEU* 4.6 19.3 - - + +
257A LEU* 3.2 30.9 + - - +
258A ASN* 3.4 13.3 - - - +
260A VAL* 1.3 74.1 - - - +
262A CYS* 1.3 59.2 + - - +
264A GLN* 4.3 8.7 - - - +
265A ASN 2.9 37.1 + - - +
269A TYR* 3.6 31.2 - - + -
272A ASP* 4.1 18.7 - - - +
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Residues in contact with CYS 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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133A CYS* 3.4 31.9 - - - +
134A SER* 3.8 13.5 - - - -
222A VAL* 5.4 1.6 - - - +
258A ASN 2.8 17.7 + - - +
259A LEU* 3.3 10.8 - - + +
261A GLN* 1.3 75.4 - - - +
263A ILE* 1.3 62.7 + - + +
266A LYS* 3.5 40.4 + - - +
269A TYR* 3.5 36.3 - - - -
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Residues in contact with ILE 263 (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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179A ARG* 4.5 5.2 - - - +
217A MET* 4.3 5.8 - - + +
222A VAL* 3.5 45.7 - - + +
225A LEU* 3.6 38.6 - - + -
226A GLN* 2.8 28.7 + - + -
229A PHE* 4.0 21.3 - - + -
259A LEU* 2.9 40.0 + - + +
260A VAL* 3.6 4.7 - - + +
262A CYS* 1.3 76.1 - - + +
264A GLN* 1.3 59.3 + - - +
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Residues in contact with GLN 264 (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 GLN* 3.3 24.4 + - + +
229A PHE* 4.0 27.9 - - + +
239A ASP* 6.3 0.4 - - - +
240A MET* 4.9 5.9 - - - +
241A LEU* 4.6 13.7 - - - +
260A VAL* 2.7 47.3 + - + +
261A GLN* 3.9 6.6 - - - +
263A ILE* 1.3 73.0 - - + +
265A ASN* 1.3 62.4 + - + +
266A LYS 4.2 0.4 - - - -
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Residues in contact with ASN 265 (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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261A GLN* 2.9 15.0 + - - +
264A GLN* 1.3 78.4 - - + +
266A LYS* 1.3 58.4 + - - +
267A PRO* 3.2 13.4 - - - +
268A LEU* 3.0 43.0 + - + +
269A TYR* 2.9 22.9 + - - +
306A GLU* 3.3 28.7 + - - +
309A ARG* 5.1 2.8 - - - +
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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