Contacts of the helix formed by residues 257 - 271 (chain A) in PDB entry 1HMU
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 SER 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A ALA 3.4 4.1 + - - -
256A LEU* 1.3 78.5 - - - +
258A THR* 1.3 65.0 + - - +
259A GLU* 3.7 20.7 + - - +
260A LYS* 3.2 33.3 + - - +
261A LEU* 2.9 21.7 + - - +
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Residues in contact with THR 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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256A LEU 3.8 0.2 + - - -
257A SER* 1.3 72.8 - - - +
259A GLU* 1.3 94.3 + - - +
261A LEU* 3.2 6.6 + - - +
262A ALA* 3.0 23.4 + - - +
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Residues in contact with GLU 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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257A SER* 3.8 18.3 + - - +
258A THR* 1.3 108.0 + - - +
260A LYS* 1.3 64.5 + - + +
262A ALA* 3.3 4.8 + - - +
263A ILE* 3.1 32.8 + - + +
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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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201A LYS 5.5 0.4 + - - -
204A PHE* 2.8 35.5 + - + +
205A TYR* 4.2 9.3 + - - +
207A VAL* 3.4 37.8 - - + +
208A GLN* 5.2 4.9 - - - +
256A LEU* 3.6 22.7 - - + -
257A SER* 3.2 19.1 + - - +
259A GLU* 1.3 80.5 - - + +
261A LEU* 1.3 60.1 + - - +
263A ILE* 4.4 4.5 - - + -
264A PHE* 2.8 32.2 + - - +
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Residues in contact with LEU 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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246A ALA* 5.1 1.8 - - + -
256A LEU* 3.7 26.4 - - + +
257A SER 2.9 17.6 + - - +
258A THR* 3.8 6.5 - - - +
260A LYS* 1.3 75.8 - - - +
262A ALA* 1.3 57.9 + - + +
264A PHE* 3.6 14.6 - - + +
265A SER* 2.8 30.6 + - - -
311A ILE* 3.7 31.6 - - + +
312A ASP* 3.4 37.0 - - + +
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Residues in contact with ALA 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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220A TYR* 5.4 0.2 - - - -
258A THR 3.0 16.9 + - - +
259A GLU* 3.6 4.9 - - - +
261A LEU* 1.3 79.3 - - + +
263A ILE* 1.3 58.8 + - + +
265A SER* 3.4 6.9 + - - -
266A LYS* 2.9 30.9 + - - +
269A ARG* 4.7 1.4 + - - -
315A HIS* 6.0 4.9 - - + -
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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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207A VAL* 4.4 21.1 - - + +
208A GLN* 5.1 3.8 - - - +
209A PHE* 4.0 33.9 - - + -
216A LEU* 3.4 31.6 - - + -
220A TYR* 3.8 13.0 - - + +
259A GLU* 3.1 24.8 + - + +
260A LYS* 3.8 6.1 - - + +
261A LEU 3.3 0.4 - - - -
262A ALA* 1.3 74.9 - - + +
264A PHE* 1.3 61.4 + - - +
266A LYS 3.4 0.3 + - - -
267A TYR* 2.9 28.2 + - - +
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Residues in contact with PHE 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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207A VAL* 4.4 6.7 - - + +
216A LEU* 6.2 0.2 - - - -
238A PHE* 5.1 10.1 - + + -
239A ILE* 3.8 36.8 - - + -
242A VAL* 3.5 31.2 - - + -
243A LEU* 3.8 36.8 - - + -
256A LEU* 4.9 1.1 - - + -
260A LYS 2.8 19.3 + - - +
261A LEU* 3.6 20.2 - - + +
263A ILE* 1.3 79.3 - - - +
265A SER* 1.3 68.9 + - - +
267A TYR* 3.3 6.1 + + - +
268A TYR* 2.9 46.3 + + - +
308A ALA* 5.2 4.3 - - + -
311A ILE* 6.4 0.4 - - + -
312A ASP* 6.3 1.8 - - + -
319A TRP* 5.3 1.8 - + - -
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Residues in contact with SER 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 LEU* 2.8 23.7 + - - -
262A ALA* 3.6 8.3 - - - -
264A PHE* 1.3 83.1 - - - +
266A LYS* 1.3 57.4 + - - +
268A TYR* 3.4 3.1 + - - +
269A ARG* 2.9 52.9 + - - +
312A ASP* 2.6 34.1 + - - -
315A HIS* 3.6 1.5 + - - -
319A TRP* 3.5 5.4 - - - -
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Residues in contact with LYS 266 (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 TYR* 3.3 51.0 - - + +
262A ALA 2.9 17.9 + - - +
263A ILE 3.8 0.2 - - - +
265A SER* 1.3 73.6 - - - +
267A TYR* 1.3 59.8 + - - +
269A ARG* 3.6 14.6 - - - +
270A ASP* 2.6 67.9 + - + +
339A TYR* 5.7 1.0 + - - -
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Residues in contact with TYR 267 (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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216A LEU* 3.4 19.5 - - + -
220A TYR* 3.2 39.7 - + + -
221A SER 4.2 0.9 - - - -
222A TYR* 3.3 25.4 - - + +
231A ILE* 2.6 39.7 + - + +
235A GLY* 3.9 5.9 - - - -
238A PHE* 4.2 15.0 - + + -
239A ILE* 3.5 35.0 - - + -
263A ILE 2.9 17.8 + - - +
264A PHE* 3.7 7.2 - + - +
266A LYS* 1.3 76.3 - - - +
268A TYR* 1.3 65.3 + - - +
271A SER* 3.1 30.6 + - - -
272A TYR* 3.2 10.2 + - + -
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Residues in contact with TYR 268 (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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239A ILE* 3.8 29.6 - - + -
243A LEU* 4.4 8.3 - - + -
264A PHE* 2.9 36.8 + + + +
265A SER* 3.6 4.9 - - - +
267A TYR* 1.3 83.7 - - - +
269A ARG* 1.3 57.3 + - - +
272A TYR* 3.4 27.0 - + - +
273A LEU* 2.8 39.4 + - + +
301A GLU* 2.7 23.0 + - - -
304A ARG* 3.4 17.2 - - - +
305A LEU* 3.5 14.7 - - + +
308A ALA* 4.1 13.7 - - + -
319A TRP* 3.6 26.7 - + + -
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Residues in contact with ARG 269 (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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262A ALA 4.7 1.0 + - - -
265A SER* 2.9 36.2 + - - +
266A LYS* 3.6 20.1 - - - +
268A TYR* 1.3 76.9 - - - +
270A ASP* 1.3 74.7 + - - +
273A LEU* 3.3 26.7 - - + +
274A LYS* 3.5 13.4 + - - +
315A HIS* 3.1 40.4 + - - -
318A GLU* 2.9 44.4 + - + +
319A TRP* 3.4 33.7 - - + -
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Residues in contact with ASP 270 (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 TYR* 5.9 2.0 - - + -
266A LYS* 2.6 58.4 + - + +
269A ARG* 1.3 88.6 + - - +
271A SER* 1.3 59.6 + - - +
274A LYS* 3.3 47.7 + - - +
318A GLU* 4.9 1.7 - - - +
339A TYR* 4.3 13.7 + - - +
343A PHE* 5.0 1.1 - - - -
350A GLN* 3.7 5.9 - - - +
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Residues in contact with SER 271 (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 TYR* 2.7 41.9 + - - +
231A ILE* 3.8 10.6 - - - +
267A TYR* 3.1 24.7 + - - -
270A ASP* 1.3 80.7 - - - +
272A TYR* 1.3 68.0 + - - +
273A LEU 3.6 0.2 - - - -
275A ALA* 3.4 6.6 + - - +
343A PHE* 3.6 18.0 - - - -
350A GLN* 3.4 21.5 + - - -
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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