Contacts of the helix formed by residues 253 - 267 (chain A) in PDB entry 2V5E
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 ASN 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A SER 4.4 5.6 - - - +
250A CYS* 3.0 10.2 + - - +
251A LYS 3.2 0.2 - - - -
252A THR* 1.3 79.8 + - - +
254A TYR* 1.3 60.4 + - - +
255A ILE* 3.2 12.0 + - - +
256A CYS* 2.9 30.6 + - + +
257A ARG* 2.8 34.2 + - - +
295A THR* 5.6 0.7 - - - +
296A VAL* 6.4 0.4 - - + -
1C GU4 2.7 41.0 + - - -
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Residues in contact with TYR 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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252A THR 4.2 1.0 + - - -
253A ASN* 1.3 74.8 - - - +
255A ILE* 1.3 66.8 + - + +
257A ARG* 3.9 29.1 - - - +
258A SER* 3.1 28.8 + - - -
1353A EDO 3.6 33.5 - - - -
1C GU4 3.3 32.9 + - - +
2C YYJ 3.6 18.9 - - - -
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Residues in contact with ILE 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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197A ARG* 4.0 22.9 - - - +
253A ASN* 3.2 8.3 + - - +
254A TYR* 1.3 81.5 - - + +
256A CYS* 1.3 59.8 + - - +
258A SER* 3.3 1.4 + - - -
259A ARG* 2.9 59.6 + - + +
295A THR* 4.1 14.4 - - + -
1351A EDO 3.8 21.5 - - - -
1353A EDO 3.9 18.6 - - - -
1C GU4 3.4 40.9 + - - +
2C YYJ 4.3 5.4 - - - +
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Residues in contact with CYS 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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250A CYS* 2.1 58.8 - - - +
253A ASN* 2.9 17.1 + - + +
255A ILE* 1.3 78.4 - - - +
257A ARG* 1.3 54.9 + - - +
259A ARG* 4.7 0.4 - - - -
260A LEU* 2.8 36.6 + - - +
292A LEU* 5.1 1.3 - - - -
295A THR* 3.5 37.7 - - - -
296A VAL* 4.0 10.1 - - + +
297A MET* 4.0 4.3 - - - -
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Residues in contact with ARG 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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250A CYS* 3.3 6.3 + - - -
251A LYS* 3.0 50.8 + - + +
252A THR 4.3 3.0 + - - -
253A ASN 2.8 35.1 + - - +
254A TYR* 3.9 29.0 - - - +
256A CYS* 1.3 71.4 - - - +
258A SER* 1.3 58.2 + - - +
260A LEU* 3.8 2.9 - - - +
261A ALA* 3.1 29.4 + - + +
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Residues in contact with SER 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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254A TYR* 3.1 28.7 + - - -
255A ILE 3.7 3.1 - - - -
257A ARG* 1.3 75.4 - - - +
259A ARG* 1.3 58.9 + - - +
261A ALA* 3.5 5.2 + - - +
262A ASP* 3.1 35.7 + - - +
1353A EDO 2.8 30.8 + - - -
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Residues in contact with ARG 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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197A ARG* 5.0 9.9 + - - +
200A PHE* 6.2 1.4 - - - +
201A ASP* 4.7 7.5 + - - +
255A ILE* 2.9 41.5 + - + +
256A CYS* 3.9 2.5 - - - +
258A SER* 1.3 69.8 - - - +
260A LEU* 1.3 66.2 + - - +
262A ASP* 3.3 11.9 + - - +
263A PHE* 3.0 23.6 + - - +
287A LEU 5.6 0.7 - - - -
288A ALA* 4.2 6.2 - - - +
291A GLY* 2.8 52.7 + - - +
292A LEU* 3.7 19.3 - - + +
293A ILE 5.3 0.4 + - - -
295A THR* 4.7 1.1 - - + -
1351A EDO 2.7 33.5 + - - -
1353A EDO 2.8 35.7 + - - +
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Residues in contact with LEU 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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247A GLN* 3.9 32.8 - - + +
250A CYS* 3.7 19.1 - - + -
251A LYS* 4.4 13.7 - - + -
256A CYS 2.8 22.1 + - - +
257A ARG 3.8 3.8 - - - +
259A ARG* 1.3 73.1 - - - +
261A ALA* 1.3 61.4 + - - +
263A PHE* 3.1 5.6 + - + +
264A PHE* 3.1 36.6 + - + -
292A LEU* 3.6 10.4 - - + +
297A MET* 3.6 30.5 - - + -
328A PHE* 4.2 13.9 - - + -
332A PHE* 4.3 4.7 - - + -
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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
----------------------------------------------------------
257A ARG* 3.1 19.0 + - + +
258A SER* 3.8 6.3 - - - +
260A LEU* 1.3 72.7 - - - +
262A ASP* 1.3 67.6 + - - +
264A PHE* 3.3 4.7 + - - +
265A THR* 2.9 32.2 + - - +
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Residues in contact with ASP 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 SER* 3.1 26.3 + - - +
259A ARG* 3.3 15.0 + - - +
261A ALA* 1.3 76.0 - - - +
263A PHE* 1.3 52.5 + - - +
265A THR* 4.3 4.3 - - - -
266A ASN* 2.7 50.8 + - - +
287A LEU* 6.2 0.2 - - - +
288A ALA* 3.5 16.3 - - + -
1353A EDO 4.9 2.9 + - - -
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Residues in contact with PHE 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 ARG 3.0 13.7 + - - +
260A LEU* 3.3 9.2 - - + +
261A ALA 3.1 0.4 - - - -
262A ASP* 1.3 76.1 - - - +
264A PHE* 1.3 72.8 + + - +
267A CYS* 2.9 63.7 + - + +
288A ALA* 3.5 9.4 - - + +
289A TYR* 3.7 34.5 - + + -
292A LEU* 4.0 10.8 - - + -
331A PHE* 3.6 30.6 - + - -
332A PHE* 3.5 41.3 - + - -
335A ASN* 4.4 1.6 - - - -
338A LEU* 4.0 17.0 - - + -
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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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247A GLN* 5.5 1.1 - - - -
260A LEU* 3.1 27.9 + - + +
261A ALA* 4.1 4.7 - - - +
263A PHE* 1.3 91.4 - + - +
265A THR* 1.3 59.8 + - - +
268A GLN* 3.0 34.5 + - - +
327A LYS* 5.0 2.2 - - + -
328A PHE* 3.5 46.4 - + - -
331A PHE* 3.4 53.8 - + + -
332A PHE* 4.1 5.4 - + - -
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Residues in contact with THR 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 ALA* 2.9 24.8 + - - +
262A ASP* 3.7 5.6 - - - -
264A PHE* 1.3 79.2 - - - +
266A ASN* 1.3 73.2 + - - +
267A CYS 3.7 0.2 + - - -
268A GLN* 3.8 11.0 - - - +
278A LEU* 5.7 0.7 - - - +
279A LYS* 3.4 32.2 - - + +
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Residues in contact with ASN 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 ASP* 2.7 35.7 + - - +
265A THR* 1.3 87.8 - - - +
267A CYS* 1.3 57.1 + - - +
268A GLN 3.4 2.3 + - - +
277A CYS* 4.9 1.9 - - - +
279A LYS* 4.4 24.3 + - - +
281A ASN 4.4 4.3 - - - +
284A ASP* 3.2 50.2 + - + +
285A CYS* 3.5 13.9 + - - +
287A LEU* 5.9 2.6 - - - +
288A ALA* 3.9 6.1 - - + +
337A CYS* 4.0 6.4 - - - -
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Residues in contact with CYS 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 PHE* 2.9 45.6 + - + +
266A ASN* 1.3 76.2 - - - +
268A GLN* 1.3 63.9 + - - +
269A PRO* 3.2 3.1 - - - +
285A CYS* 2.1 62.1 - - - -
331A PHE* 3.5 4.9 - - + -
335A ASN* 3.2 31.9 + - - +
337A CYS* 3.5 6.1 - - - +
338A LEU* 4.7 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