Contacts of the helix formed by residues 5119 - 5123 (chain E) in PDB entry 1HKN
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 ARG5119 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1040A GLN* 4.9 3.2 + - - -
5070E ASP* 4.5 11.9 + - - +
5071E GLY 3.3 9.6 - - - +
5072E LEU* 3.3 34.6 - - + +
5112E LYS* 5.6 1.6 - - - +
5117E CYS* 3.8 6.1 + - - +
5118E LYS* 1.3 74.6 - - - +
5120E GLY* 1.3 68.6 + - - +
5121E PRO* 3.9 20.4 - - + +
5122E ARG* 2.8 54.9 + - + +
5123E THR 3.3 6.2 + - - -
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Residues in contact with GLY5120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5067E MET* 3.9 10.0 - - - +
5071E GLY 2.7 17.4 + - - -
5107E TRP* 3.5 32.1 - - - -
5108E PHE 4.0 2.0 - - - -
5118E LYS 3.3 1.6 + - - -
5119E ARG* 1.3 70.3 - - - +
5121E PRO* 1.3 61.0 - - - +
5123E THR* 2.6 34.6 + - - +
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Residues in contact with PRO5121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040A GLN* 3.8 22.7 - - + +
5070E ASP 3.7 22.7 - - - +
5071E GLY* 3.8 1.6 - - - -
5107E TRP* 3.3 37.4 - - + +
5119E ARG* 3.4 24.9 - - + +
5120E GLY* 1.3 88.1 - - - +
5122E ARG* 1.3 76.9 + - - +
5123E THR 3.4 3.8 - - - +
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Residues in contact with ARG5122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040A GLN* 3.8 15.8 + - - +
1060A GLU* 3.1 39.2 + - - -
5118E LYS* 2.8 36.1 + - + +
5119E ARG* 2.8 49.3 + - + +
5121E PRO* 1.3 96.1 + - - +
5123E THR* 1.3 60.7 + - - +
5124E HIS* 4.3 3.0 - - - -
5127E GLN* 3.2 9.4 + - - -
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Residues in contact with THR5123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5106E ASN 3.8 5.7 + - - +
5107E TRP* 5.8 0.2 - - - -
5108E PHE* 2.9 46.2 + - + +
5110E GLY 4.9 1.8 - - - +
5118E LYS* 3.4 25.6 - - + +
5119E ARG 3.3 15.7 - - - +
5120E GLY 2.6 20.6 + - - +
5121E PRO 4.4 3.6 - - - +
5122E ARG* 1.3 81.5 - - - +
5124E HIS* 1.3 67.5 + - - +
5127E GLN* 3.1 10.3 - - - +
5130E ILE* 3.9 7.2 - - + -
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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