Contacts of the helix formed by residues 276 - 281 (chain P) in PDB entry 2QJK
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 276 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147P TYR* 3.6 22.1 + - - +
154P MET* 3.6 21.7 - - + -
275P GLY* 1.3 71.6 - - - -
277P PRO* 1.3 60.1 - - + +
278P ASP* 2.8 58.8 + - + +
279P ASN* 2.8 32.4 + - - +
280P TYR* 4.5 4.2 + - - -
291P HIS* 2.9 29.5 + - + +
293P VAL* 3.8 25.2 - - + +
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Residues in contact with PRO 277 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272P ASN 5.8 1.3 - - - +
275P GLY 3.0 11.6 - - - +
276P HIS* 1.3 91.2 - - + +
278P ASP* 1.3 65.7 + - - +
279P ASN 3.1 2.0 + - - -
280P TYR* 3.3 14.5 + - + +
105Q LYS 4.0 16.8 - - - +
106Q ALA* 3.3 23.7 - - - +
107Q ARG* 4.1 14.8 - - - +
108Q ALA* 4.6 7.9 - - + +
120Q GLN* 5.5 1.6 - - - +
125Q ILE* 4.3 23.3 - - + -
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Residues in contact with ASP 278 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153P GLN* 3.2 13.7 - - + +
154P MET* 3.6 15.3 - - + -
276P HIS* 2.8 32.3 + - + +
277P PRO* 1.3 79.2 - - - +
279P ASN* 1.3 55.9 + - - +
280P TYR 3.1 5.4 - - - -
281P ILE* 3.1 32.7 - - + +
289P PRO* 2.9 29.4 - - - +
291P HIS* 4.6 9.0 + - - +
106Q ALA 5.0 4.2 - - - +
107Q ARG* 5.7 0.9 + - - -
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Residues in contact with ASN 279 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77P PHE* 3.6 16.1 - - - -
94P ARG* 5.7 2.6 + - - +
147P TYR* 3.4 35.9 + - + +
150P PRO* 4.6 11.0 - - - +
152P GLY* 3.1 12.5 - - - -
153P GLN 4.2 0.4 - - - +
154P MET* 3.0 28.3 + - + +
155P SER* 3.0 25.9 + - - -
276P HIS 2.8 14.1 + - - +
278P ASP* 1.3 77.1 - - - +
280P TYR* 1.3 60.9 + - + +
281P ILE 3.0 8.7 + - - +
502P HEM 5.0 2.8 + - - -
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Residues in contact with TYR 280 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77P PHE* 3.8 17.5 - + - -
81P GLU* 4.6 5.4 - - - -
84P MET* 4.5 0.7 - - - +
94P ARG* 4.5 21.6 + - - -
95P TYR* 3.6 9.0 + - - -
272P ASN* 2.5 32.7 + - + -
276P HIS 5.0 2.5 - - - -
277P PRO* 3.7 17.3 - - + +
278P ASP 3.1 1.8 - - - -
279P ASN* 1.3 83.3 - - - +
281P ILE* 1.3 61.2 + - - +
282P GLU 4.1 0.2 + - - -
102Q LEU* 3.8 34.7 - - + +
105Q LYS* 2.9 60.5 + - + -
106Q ALA* 3.8 15.0 - - + +
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Residues in contact with ILE 281 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77P PHE* 4.3 1.3 - - - -
152P GLY* 3.2 6.4 - - - -
153P GLN* 2.9 44.1 + - + +
278P ASP* 3.1 28.9 - - + +
279P ASN 3.0 0.2 - - - -
280P TYR* 1.3 83.4 - - - +
282P GLU* 1.3 73.2 + - - +
284P ASN* 6.1 0.2 - - + -
103Q MET* 6.0 1.6 - - + -
106Q ALA* 4.0 11.2 - - + -
107Q ARG* 3.6 31.6 - - - +
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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