Contacts of the helix formed by residues 257 - 269 (chain A) in PDB entry 3DGR
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 HIS 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A TRP* 3.5 35.6 + - + +
254A GLY* 2.9 9.0 + - - -
256A ASP* 1.3 100.4 + - + +
258A GLU* 1.3 63.7 + - - +
259A LYS* 3.2 3.4 - - - +
260A ASP* 3.1 32.0 + - + +
261A ALA 3.0 17.8 + - - -
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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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250A ILE* 3.8 16.3 - - + +
254A GLY 3.8 3.3 + - - -
255A LYS 4.1 3.5 + - - +
256A ASP 3.6 2.0 - - - -
257A HIS* 1.3 76.3 - - - +
259A LYS* 1.3 58.1 + - - +
261A ALA* 3.2 9.9 + - - +
262A PHE* 2.8 62.5 + - + -
278A SER 3.9 12.1 - - - +
280A SER* 4.1 12.6 + - - -
281A TYR* 3.6 37.8 + - + +
282A ASP 5.0 3.3 - - - +
285A ASN* 4.9 4.0 + - - -
286A ALA* 4.7 3.7 - - - +
290A ILE* 3.6 19.0 - - + +
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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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256A ASP 6.0 0.7 - - - +
257A HIS* 3.2 1.3 - - - -
258A GLU* 1.3 76.4 - - - +
260A ASP* 1.3 74.4 + - - +
262A PHE* 3.5 1.3 - - - +
263A GLU* 2.7 44.8 + - - +
290A ILE* 3.6 35.7 - - + +
294A ASP* 3.8 26.9 - - + +
295A LEU* 3.7 24.2 - - + +
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Residues in contact with ASP 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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253A TRP* 4.0 20.1 - - + -
257A HIS* 3.1 36.2 + - + +
259A LYS* 1.3 95.9 + - - +
261A ALA* 1.3 57.4 + - - +
263A GLU* 3.7 8.2 - - - +
264A HIS* 2.8 32.9 + - - +
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Residues in contact with ALA 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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250A ILE* 3.9 27.6 - - + +
253A TRP* 3.5 41.7 - - + +
257A HIS 3.0 8.6 + - - +
258A GLU* 3.2 9.6 + - - +
260A ASP* 1.3 76.0 - - - +
262A PHE* 1.3 63.5 + - - +
264A HIS* 3.7 1.4 - - - +
265A ILE* 3.1 29.7 + - + +
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Residues in contact with PHE 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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250A ILE* 3.9 12.3 - - + -
258A GLU* 2.8 50.0 + - + +
259A LYS 3.5 1.6 - - - +
261A ALA* 1.3 72.7 - - - +
263A GLU* 1.3 66.1 + - - +
265A ILE* 3.2 4.3 + - - +
266A VAL* 3.1 27.2 + - - +
276A VAL* 3.7 15.3 - - + -
277A VAL 3.6 16.4 - - - -
278A SER* 3.9 19.1 - - - -
286A ALA* 3.9 14.6 - - + -
290A ILE* 3.6 26.9 - - + -
291A TRP* 3.4 37.7 - + + -
295A LEU* 3.5 16.2 - - + -
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Residues in contact with GLU 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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259A LYS* 2.7 34.0 + - - +
260A ASP* 3.7 11.0 - - - +
262A PHE* 1.3 75.8 - - - +
264A HIS* 1.3 64.8 + - - +
266A VAL* 3.4 5.8 + - - +
267A THR* 2.9 31.0 + - - +
295A LEU* 3.6 22.6 - - + +
297A HIS* 5.3 3.6 + - - -
298A LEU* 3.9 23.8 - - + +
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Residues in contact with HIS 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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253A TRP* 3.5 34.0 - + + -
260A ASP 2.8 20.5 + - - +
261A ALA 3.7 1.1 - - - +
263A GLU* 1.3 75.2 - - - +
265A ILE* 1.3 59.3 + - + +
267A THR* 3.4 4.3 + - - -
268A GLN* 2.8 52.0 + - + +
24B LYS 2.8 29.9 + - - -
25B GLN* 3.9 10.1 - - - -
26B TYR 4.0 9.9 + - - -
28B PRO* 4.6 14.1 - - + +
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Residues in contact with ILE 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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245A ALA* 4.0 5.2 - - + -
249A THR* 4.3 3.6 - - - +
250A ILE* 3.4 33.4 - - + -
261A ALA* 3.1 16.0 + - + +
262A PHE* 3.2 3.8 + - - +
264A HIS* 1.3 74.1 - - + +
266A VAL* 1.3 65.4 + - - +
267A THR 3.1 1.8 - - - -
268A GLN* 3.3 5.1 + - - -
269A PHE* 3.0 33.2 + - + +
274A VAL* 3.8 22.9 - - + -
276A VAL* 4.1 13.9 - - + -
25B GLN* 3.7 52.5 - - + +
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Residues in contact with VAL 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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262A PHE 3.1 12.7 + - - +
263A GLU* 3.4 19.5 - - - +
265A ILE* 1.3 76.0 - - - +
267A THR* 1.3 58.4 + - - +
270A SER* 3.2 13.9 + - - -
274A VAL* 4.3 7.2 - - + -
276A VAL* 4.3 6.3 - - + -
291A TRP* 3.8 31.0 - - + -
295A LEU* 5.3 0.4 - - + -
298A LEU* 4.2 27.6 - - + +
299A ILE* 6.0 2.5 - - + -
302A ARG* 2.6 38.2 + - - +
308A LEU* 3.9 17.5 - - + -
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Residues in contact with THR 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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263A GLU* 2.9 26.7 + - - +
264A HIS* 3.7 5.2 - - - -
265A ILE 3.1 0.6 - - - -
266A VAL* 1.3 79.5 - - - +
268A GLN* 1.3 65.1 + - - +
269A PHE 3.2 1.3 + - - -
270A SER* 3.6 18.2 + - - -
298A LEU* 4.3 8.5 - - - +
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Residues in contact with GLN 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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264A HIS* 2.8 41.2 + - + +
265A ILE* 3.5 7.4 - - - +
267A THR* 1.3 78.3 - - - +
269A PHE* 1.3 76.9 + - + +
270A SER* 3.6 1.8 + - - -
24B LYS* 3.4 48.0 + - + +
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Residues in contact with PHE 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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243A PRO* 3.6 26.5 - - + -
265A ILE* 3.0 26.5 + - + +
266A VAL 3.4 4.3 - - - -
268A GLN* 1.3 90.5 - - + +
270A SER* 1.3 53.7 + - - +
271A SER 3.3 3.1 - - - +
272A VAL* 3.1 31.4 - - + +
274A VAL* 3.9 26.3 - - + +
302A ARG* 2.8 17.3 + - - -
21B THR* 3.6 34.3 - - + -
24B LYS* 4.2 29.2 - - + -
25B GLN* 3.9 26.9 - - + -
95B VAL* 4.3 4.9 - - + -
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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