Contacts of the helix formed by residues 276 - 281 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147M TYR* 3.6 22.1 + - - +
154M MET* 3.6 21.3 - - + -
275M GLY* 1.3 71.1 - - - -
277M PRO* 1.3 59.3 - - + +
278M ASP* 2.8 58.7 + - + +
279M ASN* 2.8 33.3 + - - +
280M TYR* 4.5 3.6 + - - -
291M HIS* 2.9 30.4 + - + +
293M VAL* 3.8 23.6 - - + +
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Residues in contact with PRO 277 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272M ASN 5.8 1.8 - - - +
275M GLY 3.0 11.9 - - - +
276M HIS* 1.3 91.6 - - + +
278M ASP* 1.3 61.9 + - - +
279M ASN 3.1 2.0 + - - -
280M TYR* 3.3 15.6 + - + +
105N LYS 3.6 16.2 - - - +
106N ALA* 3.2 41.4 - - - +
107N ARG* 4.3 4.0 - - - +
108N ALA* 4.6 10.1 - - + +
120N GLN* 5.5 2.7 - - - +
125N ILE* 4.4 20.4 - - + -
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Residues in contact with ASP 278 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153M GLN* 3.2 13.6 - - + +
154M MET* 3.6 15.0 - - + -
276M HIS* 2.8 32.4 + - + +
277M PRO* 1.3 77.8 - - - +
279M ASN* 1.3 57.3 + - - +
280M TYR 3.1 5.6 - - - -
281M ILE* 3.1 33.1 + - + +
289M PRO* 3.0 29.1 - - - +
291M HIS* 4.6 9.1 + - - +
106N ALA 4.0 8.0 - - - +
107N ARG* 5.8 0.9 - - - -
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Residues in contact with ASN 279 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77M PHE* 3.7 15.9 - - - -
94M ARG* 5.6 3.7 + - - +
147M TYR* 3.4 35.3 + - + +
150M PRO* 4.6 11.4 - - - +
152M GLY* 3.0 13.6 - - - -
153M GLN 4.2 0.2 - - - +
154M MET* 3.0 28.3 + - + +
155M SER* 2.9 25.5 + - - -
276M HIS 2.8 14.5 + - - +
278M ASP* 1.3 76.9 - - - +
280M TYR* 1.3 62.5 + - + +
281M ILE 3.0 8.1 + - - +
502M HEM 5.2 1.6 + - - -
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Residues in contact with TYR 280 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77M PHE* 3.8 15.3 - + - -
81M GLU* 4.6 7.9 - - - -
84M MET* 5.3 0.2 - - + -
94M ARG* 4.3 22.7 + - - -
95M TYR* 3.6 10.4 + - - -
272M ASN* 2.5 32.4 + - + -
276M HIS 5.0 2.9 - - - -
277M PRO* 3.3 16.1 + - + +
278M ASP 3.1 1.6 - - - -
279M ASN* 1.3 84.1 - - + +
281M ILE* 1.3 64.3 + - - +
282M GLU 4.2 0.2 + - - -
102N LEU* 3.6 37.3 - - + +
105N LYS* 3.3 59.8 + - + -
106N ALA* 4.1 12.3 - - - +
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Residues in contact with ILE 281 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77M PHE* 4.3 1.6 - - - -
152M GLY* 3.1 6.9 - - - -
153M GLN* 2.9 43.8 + - + +
278M ASP* 3.1 28.7 - - + +
279M ASN 3.0 0.4 - - - -
280M TYR* 1.3 85.7 - - - +
282M GLU* 1.3 71.8 + - - +
284M ASN* 6.0 0.2 - - + -
103N MET* 5.7 1.8 - - - -
106N ALA* 3.8 12.8 - - + +
107N ARG* 3.5 31.2 - - - +
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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