Contacts of the helix formed by residues 254 - 269 (chain E) in PDB entry 1HVU
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 VAL 254 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253E THR* 1.3 75.9 - - - +
255E ASN* 1.3 59.3 + - - +
257E ILE* 2.8 12.9 + - - +
258E GLN* 2.8 22.3 + - - +
283E LEU* 5.8 8.5 - - + +
287E LYS* 4.7 14.8 - - + +
288E ALA 3.8 15.9 - - - +
289E LEU* 3.2 14.3 + - - +
291E GLU* 2.9 9.8 + - + +
293E ILE* 5.4 5.4 - - - -
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Residues in contact with ASN 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534D ALA* 5.2 14.8 - - + -
253E THR* 4.1 0.6 - - - -
254E VAL* 1.3 77.2 - - - +
256E ASP* 1.3 58.0 + - - +
258E GLN* 3.5 14.6 - - + -
259E LYS* 2.6 36.3 + - - +
289E LEU* 3.4 22.3 + - + +
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Residues in contact with ASP 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E SER 4.6 2.9 - - - +
252E TRP* 4.1 9.6 - - + -
253E THR* 3.4 31.1 + - - +
254E VAL 3.1 1.2 - - - -
255E ASN* 1.3 77.3 - - - +
257E ILE* 1.3 60.6 + - - +
259E LYS* 3.2 17.1 - - - +
260E LEU* 3.3 9.5 + - - +
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Residues in contact with ILE 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252E TRP* 5.6 5.6 - - + +
253E THR 3.3 7.5 + - - +
254E VAL* 2.8 11.2 + - - +
256E ASP* 1.3 78.3 - - - +
258E GLN* 1.3 67.1 + - - +
259E LYS 3.1 0.2 - - - -
260E LEU* 3.3 7.2 + - - +
261E VAL* 2.8 26.0 + - - +
279E LEU* 5.4 13.3 - - + +
282E LEU* 5.4 8.3 - - + -
283E LEU* 5.6 7.4 - - + +
293E ILE* 6.2 3.1 - - + -
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Residues in contact with GLN 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534D ALA* 6.5 0.4 - - + -
535D TRP 4.9 10.0 - - - +
536D VAL* 5.1 16.8 - - + +
254E VAL 2.8 8.4 + - - +
255E ASN* 2.8 22.9 + - + +
257E ILE* 1.3 77.4 - - - +
259E LYS* 1.3 64.8 + - - +
261E VAL* 3.3 7.2 + - - +
262E GLY* 2.9 17.7 + - - -
283E LEU* 6.0 4.0 - - - +
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Residues in contact with LYS 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535D TRP 5.7 2.0 - - - -
255E ASN 2.6 20.1 + - - +
256E ASP* 3.2 10.1 - - - +
258E GLN* 1.3 70.4 - - - +
260E LEU* 1.3 66.6 + - - +
262E GLY* 2.7 16.7 + - - -
263E LYS* 3.1 12.1 + - - +
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Residues in contact with LEU 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E ASP 3.3 9.4 + - - +
257E ILE* 3.3 11.0 + - - +
259E LYS* 1.3 79.3 - - - +
261E VAL* 1.3 63.8 + - - +
263E LYS* 3.3 6.0 + - - +
264E LEU* 2.9 27.3 + - - +
279E LEU* 6.3 2.5 - - + -
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Residues in contact with VAL 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537D PRO* 5.6 3.6 - - + -
257E ILE 2.8 16.2 + - - +
258E GLN* 3.4 11.9 - - - +
260E LEU* 1.3 73.9 - - - +
262E GLY* 1.3 63.2 + - - +
264E LEU* 3.4 1.9 + - - +
265E ASN* 2.9 22.9 + - - +
276E VAL* 4.4 21.6 - - + +
279E LEU* 5.1 12.3 - - + +
280E CYS* 5.4 8.3 - - + +
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Residues in contact with GLY 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535D TRP 5.6 4.0 - - - -
536D VAL* 5.8 0.2 - - - -
537D PRO* 4.7 16.3 - - - +
258E GLN 2.9 9.6 + - - -
259E LYS* 2.7 14.1 + - - -
261E VAL* 1.3 70.7 - - - +
263E LYS* 1.3 56.2 + - - -
265E ASN* 3.0 25.1 - - - +
266E TRP* 3.1 8.5 + - - +
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Residues in contact with LYS 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259E LYS 3.1 9.7 + - - +
260E LEU* 3.7 9.0 - - - +
262E GLY* 1.3 70.4 - - - +
264E LEU* 1.3 51.1 + - - +
265E ASN 2.9 3.8 - - - -
266E TRP* 2.7 13.6 + - - +
267E ALA* 2.7 35.8 + - + +
425E LEU* 5.4 15.7 - - - +
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Residues in contact with LEU 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260E LEU 2.9 18.5 + - - +
261E VAL 4.0 2.7 - - - +
263E LYS* 1.3 76.1 - - - +
265E ASN* 1.3 63.6 + - - +
267E ALA* 3.7 10.7 - - - +
268E SER* 3.3 17.0 + - - -
274E ILE* 4.6 13.2 - - + +
275E LYS 5.6 1.3 - - - -
276E VAL* 4.6 18.8 + - + +
306E ASN* 6.1 4.7 - - + -
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Residues in contact with ASN 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537D PRO* 4.6 14.8 - - + -
261E VAL 2.9 14.3 + - - +
262E GLY* 3.0 15.0 - - - +
263E LYS 2.8 0.8 + - - -
264E LEU* 1.3 75.7 - - - +
266E TRP* 1.3 64.8 + - - +
268E SER* 2.9 22.3 + - - -
269E GLN 4.1 1.0 + - - -
276E VAL* 5.1 5.4 - - + +
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Residues in contact with TRP 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E GLY 3.1 6.7 + - - +
263E LYS* 2.7 13.8 + - - +
265E ASN* 1.3 77.8 - - - +
267E ALA* 1.3 61.4 + - - +
269E GLN* 3.0 23.7 + - - +
270E ILE* 4.1 1.6 + - - +
425E LEU* 6.0 6.3 - - + -
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Residues in contact with ALA 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263E LYS 2.7 19.3 + - - +
264E LEU* 3.8 12.3 - - - +
266E TRP* 1.3 73.6 - - - +
268E SER* 1.3 59.1 + - - +
270E ILE* 3.0 11.8 + - - +
271E TYR* 2.9 25.7 + - + +
274E ILE* 5.1 6.5 - - + -
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Residues in contact with SER 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264E LEU 3.3 6.7 + - - -
265E ASN* 2.9 16.7 + - - -
267E ALA* 1.3 72.0 - - - +
269E GLN* 1.3 61.4 + - - +
270E ILE 2.9 7.2 + - - -
271E TYR 3.0 28.0 - - - -
272E PRO* 3.0 12.8 - - - +
274E ILE* 3.6 23.8 - - - -
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Residues in contact with GLN 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E ASN 4.1 1.0 + - - +
266E TRP* 3.0 17.5 + - - +
268E SER* 1.3 77.7 - - - +
270E ILE* 1.3 56.7 + - - +
346E PHE* 3.5 23.0 - - + +
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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