Contacts of the helix formed by residues 280 - 287 (chain A) in PDB entry 2O07
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 ASN 280 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A GLN* 6.1 0.2 - - - +
271A VAL* 3.9 18.8 - - + -
278A TYR 3.7 1.0 + - - -
279A TYR* 1.3 86.7 - - - +
281A SER* 1.3 59.2 + - - +
282A ASP* 3.0 12.6 + - - +
283A VAL* 2.8 45.5 + - - +
284A HIS* 3.0 26.5 + - - +
290B LEU 4.4 1.8 + - - -
292B GLU* 2.9 34.4 + - - +
295B ARG* 4.1 13.3 - - - +
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Residues in contact with SER 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A PRO* 4.1 12.7 - - - +
264A GLN 4.6 0.3 + - - -
265A PRO* 3.5 8.1 - - - +
266A LEU* 2.7 45.2 + - - +
271A VAL* 5.1 0.2 - - - +
279A TYR* 4.7 2.9 + - - -
280A ASN* 1.3 77.2 - - - +
282A ASP* 1.3 61.1 + - - +
284A HIS* 3.3 9.5 - - - +
285A ARG* 3.2 43.3 + - - +
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Residues in contact with ASP 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ASN* 3.0 8.8 + - - +
281A SER* 1.3 74.4 - - - +
283A VAL* 1.3 61.1 + - - +
285A ARG* 2.6 39.3 + - - +
286A ALA* 2.9 29.5 + - - +
289B VAL* 3.6 18.7 - - + +
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A MET* 4.1 12.1 - - + -
278A TYR* 3.7 49.1 - - + +
279A TYR* 4.4 1.8 - - - -
280A ASN* 2.8 32.4 + - - +
282A ASP* 1.3 68.8 - - - +
284A HIS* 1.3 66.2 + - - +
286A ALA* 3.3 2.3 + - - +
287A ALA* 2.9 27.2 + - + +
289B VAL* 3.8 12.6 - - + +
290B LEU 3.2 32.3 - - - +
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Residues in contact with HIS 284 (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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82A MET* 5.2 0.4 - - - -
85A ASN 4.1 5.1 + - - -
86A LEU* 3.6 22.1 + - + -
89A CYS* 4.3 1.8 - - + +
90A SER* 3.4 17.3 + - - -
259A PHE 2.7 31.7 + - - -
260A GLN 3.8 4.9 + - - -
262A PRO* 3.9 23.7 - - + +
279A TYR* 2.7 44.4 - + + +
280A ASN 3.0 10.1 + - - +
281A SER* 3.3 12.8 - - - +
283A VAL* 1.3 77.4 - - - +
285A ARG* 1.3 63.7 + - - +
287A ALA* 3.3 5.1 + - - +
288A PHE* 3.1 32.4 - + - -
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Residues in contact with ARG 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A GLN* 3.4 26.7 - - - +
261A GLU* 3.0 38.0 + - - +
262A PRO* 3.6 19.4 - - + +
265A PRO* 5.1 5.7 - - - +
281A SER* 3.2 26.8 + - - +
282A ASP* 2.6 37.6 + - - +
284A HIS* 1.3 74.7 - - - +
286A ALA* 1.3 64.0 + - - +
287A ALA 3.2 0.7 + - - -
288A PHE* 3.4 16.8 + - - +
289A VAL* 4.0 8.3 - - - +
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Residues in contact with ALA 286 (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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235A TYR* 4.8 2.8 + - - -
282A ASP 2.9 16.3 + - - +
283A VAL* 3.8 3.4 - - - +
285A ARG* 1.3 77.3 - - - +
287A ALA* 1.3 56.4 + - - +
288A PHE 3.1 0.7 - - - -
289A VAL* 3.0 36.9 + - - +
286B ALA* 4.1 17.2 - - + +
289B VAL* 3.7 31.2 - - + +
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Residues in contact with ALA 287 (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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82A MET* 3.6 18.6 - - + -
86A LEU* 4.5 0.9 - - + -
234A ALA* 3.4 12.1 - - + -
235A TYR* 3.1 58.8 + - - +
283A VAL* 2.9 18.7 + - + +
284A HIS 3.4 9.6 - - - +
285A ARG 3.2 0.8 - - - -
286A ALA* 1.3 74.8 - - - +
288A PHE* 1.3 57.6 + - + +
289A VAL 3.5 0.4 - - - -
290A LEU* 4.2 0.2 - - - +
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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