Contacts of the helix formed by residues 278 - 287 (chain B) in PDB entry 1HQR
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 TYR 278 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ILE* 5.5 1.9 + - + +
9A GLN* 2.9 38.6 + - - +
24A PHE* 4.4 3.7 - + - -
213B TYR* 3.5 9.8 + - + +
215B CYS* 3.3 35.0 - - - -
226B PHE* 3.3 28.7 - + - -
274B ALA* 2.9 21.3 + - + +
276B ASP 3.0 1.0 + - - -
277B THR* 1.3 80.9 + - - +
279B CYS* 1.3 61.5 + - - +
281B HIS* 3.6 1.9 - - - +
282B ASN* 2.9 46.9 + - - +
410C LYS* 3.2 35.4 - - - +
412C ILE* 3.4 31.0 - - + -
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Residues in contact with CYS 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B CYS* 2.0 52.9 - - - -
217B PHE* 3.1 18.5 - - + -
224B VAL* 3.7 17.0 - - + -
226B PHE* 3.9 17.0 - - - -
274B ALA 2.7 17.6 + - - +
275B VAL* 3.8 5.4 - - - +
278B TYR* 1.3 76.1 - - - +
280B ARG* 1.3 70.0 + - - +
281B HIS 3.0 1.6 + - - -
282B ASN* 3.1 3.1 + - - +
283B TYR 2.8 21.1 + - - -
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Residues in contact with ARG 280 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B PHE* 3.8 8.3 - - - -
221B THR* 2.7 24.9 + - + -
222B GLU 2.7 28.5 + - - -
223B ARG* 4.0 16.0 - - - +
224B VAL* 3.8 15.8 - - + +
275B VAL* 3.4 22.4 + - - +
276B ASP* 3.2 29.0 + - - +
279B CYS* 1.3 78.5 - - - +
281B HIS* 1.3 65.5 + - - +
283B TYR* 3.5 2.2 + - - +
284B GLY* 3.0 17.2 + - - -
662D THR 4.5 3.8 - - - +
663D LYS* 3.2 56.0 + - - +
665D GLY* 4.5 9.6 - - - +
667D HIS* 5.1 1.2 - - - -
700D SER* 4.1 9.0 - - - +
701D HIS* 4.9 2.0 - - + -
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Residues in contact with HIS 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B ASP 3.6 4.1 + - - +
277B THR 3.7 11.2 - - - +
278B TYR 3.6 7.4 - - - +
279B CYS 3.0 0.4 + - - -
280B ARG* 1.3 77.3 - - - +
282B ASN* 1.3 80.6 + - - +
284B GLY* 2.8 6.9 + - - -
285B VAL* 2.8 31.8 + - + +
407C HIS* 5.8 0.2 - - - -
408C PHE 3.3 19.6 + - - -
410C LYS* 4.0 14.8 - - + -
605D ASN* 4.0 4.5 - - - -
607D PHE* 4.0 8.5 - + - -
659D GLU* 5.7 0.2 - - - -
667D HIS* 3.4 7.8 + + - -
701D HIS* 3.8 13.0 - - + -
703D ASP* 2.8 21.8 + - - -
705D TYR* 4.1 9.6 - - - -
709D ZN 1.9 37.7 - - - -
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Residues in contact with ASN 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 4.2 16.5 - - + +
24A PHE* 4.0 11.6 - - + -
215B CYS* 5.5 1.7 - - - -
278B TYR* 2.9 38.4 + - - +
279B CYS* 3.9 2.0 - - - +
281B HIS* 1.3 82.4 - - - +
283B TYR* 1.3 67.0 + - - +
285B VAL* 2.9 15.9 + - - +
286B GLY* 3.0 9.9 + - - -
409C PHE* 3.5 23.4 - - + -
410C LYS 2.8 46.0 + - - -
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Residues in contact with TYR 283 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A HIS* 4.7 12.5 - + + -
7A ILE* 3.9 13.8 - - + +
26A PHE* 5.8 1.8 - + - -
217B PHE* 3.2 56.1 - + + -
220B GLY* 3.8 22.5 - - - -
221B THR* 3.4 21.5 - - + -
279B CYS 2.8 12.1 + - - +
280B ARG 3.5 3.8 - - - +
282B ASN* 1.3 71.9 - - - +
284B GLY* 1.3 58.0 + - - +
286B GLY* 3.2 0.7 + - - -
287B GLU* 2.7 43.0 + - + -
290B THR* 5.0 1.4 + - - -
291B VAL* 3.6 41.6 - - + +
664D ASP 5.4 3.1 - - - -
665D GLY* 5.1 3.8 - - - -
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Residues in contact with GLY 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B ARG 3.0 5.2 + - - -
281B HIS 2.8 8.6 + - - -
283B TYR* 1.3 83.8 - - - +
285B VAL* 1.3 60.5 + - - +
286B GLY 3.2 0.4 + - - -
287B GLU* 3.9 19.7 - - - +
288B SER 5.2 0.3 + - - -
407C HIS* 4.7 7.3 + - - -
665D GLY 3.5 23.9 - - - +
667D HIS* 4.3 12.6 + - - -
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A PHE 4.6 0.9 - - - +
52A ALA* 4.2 7.7 - - + +
281B HIS* 2.8 43.8 + - + +
282B ASN* 2.9 10.7 + - - +
284B GLY* 1.3 79.1 - - - +
286B GLY* 1.3 59.7 + - - +
288B SER* 5.7 0.9 - - - -
289B PHE* 3.6 13.2 - - - -
407C HIS* 3.7 40.9 - - + +
408C PHE 3.6 16.2 - - - +
409C PHE* 3.9 24.2 - - + -
667D HIS* 4.5 2.7 - - + -
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Residues in contact with GLY 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B ASN 3.0 9.9 + - - -
283B TYR 3.8 1.1 - - - -
285B VAL* 1.3 80.9 - - - +
287B GLU* 1.3 66.4 + - - +
288B SER 3.1 2.9 - - - -
289B PHE* 2.6 39.5 + - - -
290B THR* 3.3 16.8 + - - -
409C PHE* 4.2 7.4 - - - -
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Residues in contact with GLU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B TYR* 2.7 26.5 + - + +
284B GLY* 3.9 15.9 - - - +
285B VAL 3.6 0.2 - - - -
286B GLY* 1.3 74.4 - - - +
288B SER* 1.3 68.8 + - - +
289B PHE 3.0 1.0 + - - -
290B THR* 3.3 11.6 + - - -
291B VAL* 3.3 30.2 - - + +
292B GLN* 2.5 43.9 + - - +
665D GLY 4.3 11.9 - - - +
666D LYS* 5.6 1.6 - - - +
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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