Contacts of the strand formed by residues 5021 - 5025 (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 HIS5021 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5014E LEU 3.7 0.3 - - - +
5015E TYR* 4.5 1.3 - - - -
5016E CYS* 2.7 38.1 + - + +
5019E GLY* 3.5 12.7 + - - -
5020E GLY* 1.3 78.7 - - - +
5022E PHE* 1.3 61.2 + - - +
5023E LEU 3.7 0.5 + - - -
5033E GLY* 3.6 29.2 - - - -
5034E THR* 3.6 14.1 - - - +
5035E ARG* 3.5 35.2 + - + +
5111E LEU* 3.9 9.4 - - + +
5112E LYS 4.2 3.8 + - - -
5113E LYS 3.0 28.7 - - - -
5114E ASN 3.9 4.6 + - - -
5115E GLY* 3.5 22.4 + - - -
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Residues in contact with PHE5022 (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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5013E LEU* 3.9 31.9 - - + -
5014E LEU 3.3 3.8 - - - +
5015E TYR* 3.9 37.2 - + + -
5020E GLY 5.2 1.3 - - - -
5021E HIS* 1.3 73.4 - - - +
5023E LEU* 1.3 65.5 + - - +
5024E ARG 3.3 1.2 + - - -
5033E GLY* 3.4 1.8 - - - -
5034E THR 2.7 43.0 + - - +
5035E ARG* 3.8 13.5 - - - -
5036E ASP 4.0 12.1 - - - -
5037E ARG* 3.6 44.6 - - + -
5042E ILE* 3.8 25.3 - - + +
5135E LEU* 5.2 5.6 - - + -
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Residues in contact with LEU5023 (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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5014E LEU* 2.8 36.9 + - + +
5021E HIS 3.7 1.4 + - - -
5022E PHE* 1.3 71.6 - - - +
5024E ARG* 1.3 66.0 + - - +
5025E ILE* 5.2 2.9 - - + -
5031E VAL* 3.9 20.9 - - + -
5032E ASP 3.8 10.1 - - - +
5042E ILE* 3.3 24.9 - - - +
5044E LEU* 4.1 23.0 - - + +
5056E ILE* 4.7 1.8 - - + -
5065E LEU* 4.0 28.5 - - + -
5073E LEU* 4.9 0.7 - - + -
5109E VAL* 4.6 14.1 - - + -
5111E LEU* 4.0 22.2 - - + +
5132E PHE* 4.4 10.1 - - + -
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Residues in contact with ARG5024 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5022E PHE 4.1 2.7 - - - +
5023E LEU* 1.3 76.8 - - - +
5025E ILE* 1.3 66.2 + - - +
5026E LEU* 3.6 28.6 - - + +
5031E VAL* 3.3 7.4 - - - +
5032E ASP* 2.6 79.4 + - - +
5033E GLY 4.3 5.1 + - - -
5034E THR* 3.9 21.2 + - + -
5039E ASP* 2.9 36.2 + - - -
5041E HIS* 3.5 21.5 - - + +
5042E ILE* 3.6 6.7 - - + -
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Residues in contact with ILE5025 (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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5023E LEU* 5.2 3.8 - - + -
5024E ARG* 1.3 77.8 - - - +
5026E LEU* 1.3 63.0 + - - +
5027E PRO 3.8 0.5 - - - -
5030E THR 3.7 2.7 - - - +
5031E VAL* 4.4 13.5 - - + -
5041E HIS* 3.1 25.4 + - - +
5044E LEU* 3.9 24.9 - - + -
5056E ILE* 4.2 6.3 - - + +
5058E SER* 4.3 21.1 + - - +
5061E THR* 4.8 2.3 + - - +
5063E GLN* 4.0 21.1 - - + +
5065E LEU* 4.0 37.5 - - + +
5075E GLY* 3.8 26.7 - - - -
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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