Contacts of the helix formed by residues 267 - 276 (chain A) in PDB entry 1QHP
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 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A ASP* 2.8 24.7 + - - -
261A ASP 3.3 20.1 - - - +
262A PRO* 3.6 16.8 - - + +
263A GLY 4.4 2.7 - - - +
264A THR* 3.3 17.6 + - - +
266A ASN* 1.3 78.4 - - - +
268A LEU* 1.3 66.0 + - + +
270A LYS* 3.1 7.7 + - - +
271A VAL* 3.0 29.5 + - + +
285A ASP* 3.2 33.9 - - - -
314A GLU* 2.7 32.5 + - - -
315A TYR* 3.8 8.5 - - - -
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Residues in contact with LEU 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 THR 4.8 0.4 + - - -
265A ALA 4.9 3.9 + - - +
266A ASN 3.4 1.0 - - - -
267A HIS* 1.3 81.9 - - + +
269A GLU* 1.3 58.3 + - - +
271A VAL* 3.2 12.2 + - + -
272A ARG* 2.8 39.4 + - + +
601A TYR* 5.7 3.6 - - - +
616A THR* 3.8 18.6 - - - +
617A SER* 4.3 2.7 - - - -
618A GLY* 4.0 24.9 - - - +
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Residues in contact with GLU 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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180A ARG* 2.9 54.8 + - - +
184A GLN* 4.8 1.2 + - - -
235A SER* 4.7 3.0 + - - +
257A TRP* 3.5 13.7 - - + -
265A ALA 5.6 0.2 + - - -
266A ASN* 3.3 15.7 + - - +
267A HIS 3.2 1.0 - - - -
268A LEU* 1.3 76.5 - - - +
270A LYS* 1.3 57.6 + - - +
272A ARG* 3.3 10.7 + - + +
273A TYR* 2.9 28.3 + - + +
625A GLY 5.8 2.2 - - - +
626A PRO* 5.6 14.0 - - + +
637A TYR* 4.3 13.3 + - - -
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Residues in contact with LYS 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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257A TRP* 3.5 60.9 + - + +
259A GLY 2.8 20.9 + - - +
260A ASP* 3.2 13.5 + - + -
266A ASN 3.3 5.7 + - - +
267A HIS* 3.1 11.3 + - - +
269A GLU* 1.3 78.5 - - - +
271A VAL* 1.3 60.1 + - - +
273A TYR* 3.2 4.1 + - - +
274A ALA* 2.9 22.7 + - - +
281A VAL* 4.8 13.2 - - + -
282A LEU 5.4 2.5 + - - +
284A PHE* 4.2 11.3 - - - +
285A ASP* 2.7 27.0 + - - +
315A TYR* 3.3 21.3 + - - +
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Residues in contact with VAL 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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267A HIS* 3.0 39.2 + - + +
268A LEU* 3.6 13.2 - - + +
270A LYS* 1.3 76.3 - - - +
272A ARG* 1.3 62.3 + - - +
274A ALA* 3.2 2.6 + - - +
275A ASN* 2.9 30.6 + - - +
314A GLU* 3.5 42.4 - - + +
315A TYR* 3.9 22.2 - - + +
618A GLY* 4.5 10.5 - - - -
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Residues in contact with ARG 272 (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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268A LEU* 2.8 31.1 + - + +
269A GLU* 3.7 7.9 - - + +
271A VAL* 1.3 76.2 - - - +
273A TYR* 1.3 58.1 + - - +
275A ASN* 3.3 2.6 + - - -
276A ASN* 2.9 46.4 + - - +
601A TYR* 4.2 5.6 + - - -
616A THR* 3.5 21.0 + - - -
617A SER 2.9 32.2 + - - +
618A GLY* 3.8 10.1 - - - -
619A ALA 4.9 0.4 + - - -
622A ASN* 2.9 27.2 + - - +
623A ALA 2.8 23.0 + - - -
624A GLN* 4.0 3.8 - - - +
625A GLY 3.0 35.1 + - - +
626A PRO* 5.2 2.6 - - - +
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Residues in contact with TYR 273 (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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227A ILE* 5.2 0.2 - - - +
230A VAL* 3.4 33.5 - - + +
235A SER* 3.5 28.5 - - - +
238A SER* 2.9 38.4 + - - -
255A GLY* 5.1 0.2 - - - -
257A TRP* 3.8 20.4 - + + -
269A GLU* 2.9 14.4 + - + +
270A LYS 3.2 7.6 + - - +
272A ARG* 1.3 76.1 - - - +
274A ALA* 1.3 64.6 + - - +
276A ASN* 5.1 0.9 - - - -
277A SER* 2.8 54.0 + - - +
279A VAL* 3.5 27.4 - - + +
281A VAL* 3.9 20.2 - - + -
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Residues in contact with ALA 274 (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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270A LYS 2.9 12.4 + - - +
271A VAL 3.6 6.7 - - - +
273A TYR* 1.3 79.8 - - - +
275A ASN* 1.3 63.1 + - - +
277A SER 4.7 0.9 + - - -
278A GLY* 5.1 2.6 + - - -
279A VAL 3.8 18.7 - - - +
280A ASN* 4.9 5.9 - - - +
281A VAL* 4.0 18.8 - - + +
315A TYR* 3.7 29.8 - - + -
317A TYR* 4.8 9.5 - - - +
321A LEU* 5.8 0.2 - - + -
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Residues in contact with ASN 275 (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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271A VAL* 2.9 23.5 + - - +
272A ARG 3.9 3.1 - - - +
274A ALA* 1.3 82.8 - - - +
276A ASN* 1.3 58.6 + - - +
278A GLY 5.5 0.4 - - - -
314A GLU 3.0 22.8 + - - -
315A TYR* 3.6 5.7 - - - +
316A LYS* 2.9 37.6 + - + +
317A TYR* 4.4 11.7 + - - -
618A GLY 2.8 31.1 + - - +
620A VAL* 3.4 23.7 - - + +
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Residues in contact with ASN 276 (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 LYS* 3.8 22.1 + - + +
272A ARG* 2.9 35.4 + - - +
273A TYR* 3.3 0.9 + - - -
275A ASN* 1.3 84.8 - - - +
277A SER* 1.3 64.5 + - - +
278A GLY 3.3 3.8 + - - -
508A MET* 4.3 3.6 - - - +
575A ASN* 4.7 6.6 + - - +
619A ALA 3.0 22.7 + - - -
620A VAL* 3.3 7.4 - - - +
621A ASN* 2.9 32.1 + - - +
622A ASN* 4.8 4.1 + - - -
624A GLN* 5.0 8.7 + - - +
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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