Contacts of the helix formed by residues 301 - 306 (chain A) in PDB entry 2HAK
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 ASP 301 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A ASP 4.3 1.7 - - - +
279A ASN* 4.6 1.6 - - - +
280A LEU* 3.4 38.0 + - + +
283A LYS* 2.8 34.0 + - + +
297A GLN 3.7 2.6 + - - +
298A ILE* 2.7 26.3 + - - +
299A MET 3.3 0.4 - - - -
300A LYS* 1.3 75.5 - - - +
302A ARG* 1.3 67.1 + - - +
303A TRP* 2.7 29.7 + - - +
304A MET* 2.9 16.6 + - + +
305A ASN* 3.1 15.8 + - - -
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Residues in contact with ARG 302 (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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276A ASP* 3.4 34.6 + - + +
283A LYS* 4.6 1.2 - - - +
300A LYS 3.7 1.3 + - - -
301A ASP* 1.3 75.5 + - - +
303A TRP* 1.3 69.0 + - - +
305A ASN* 2.9 14.6 + - - +
306A VAL* 3.2 20.7 + - + +
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Residues in contact with TRP 303 (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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149A GLU* 2.8 51.0 + - + -
152A ALA* 3.8 5.2 - - + -
153A ARG* 2.7 88.1 + - + +
156A PHE* 4.2 12.6 - + + -
240A LEU* 3.6 26.9 - - + -
244A VAL* 4.5 1.3 - - + -
274A SER* 3.8 0.4 - - - -
276A ASP* 3.6 30.2 + - + +
277A CYS* 3.3 29.9 - - + +
280A LEU* 3.7 20.2 - - + -
301A ASP* 2.7 17.2 + - - +
302A ARG* 1.3 76.2 - - - +
304A MET* 1.3 58.8 + - + -
305A ASN 3.2 0.7 + - - -
306A VAL* 3.5 3.8 + - + -
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Residues in contact with MET 304 (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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153A ARG* 3.7 13.1 - - - +
156A PHE* 3.6 34.1 - - - -
157A ARG* 2.7 45.0 + - + -
160A VAL* 4.3 9.6 - - + -
280A LEU* 4.5 3.1 - - + -
298A ILE* 3.6 22.7 - - + +
299A MET* 4.0 6.1 - - - +
301A ASP* 2.9 23.5 + - + +
302A ARG 3.1 0.4 - - - -
303A TRP* 1.3 86.6 - - + +
305A ASN* 1.3 62.8 + - - +
313A LEU* 3.0 37.7 - - + -
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Residues in contact with ASN 305 (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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157A ARG* 3.0 16.9 + - - +
299A MET 3.0 25.0 + - - -
300A LYS* 3.7 9.1 + - - +
301A ASP 3.1 18.3 + - - +
302A ARG* 2.9 7.3 + - - +
304A MET* 1.3 77.8 - - - +
306A VAL* 1.3 57.2 + - - +
307A GLY 2.9 1.0 + - - -
308A HIS* 2.6 39.2 + - + +
309A GLU* 3.6 8.8 + - + +
312A GLU* 3.7 16.1 + - + +
313A LEU* 2.9 28.2 + - - +
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Residues in contact with VAL 306 (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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153A ARG* 3.3 44.9 + - - +
276A ASP* 3.8 22.7 - - - +
302A ARG* 3.2 21.6 + - + +
303A TRP* 3.5 3.8 + - - +
305A ASN* 1.3 73.2 - - - +
307A GLY* 1.3 60.0 + - - +
308A HIS* 3.1 15.1 + - - -
309A GLU* 4.0 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