Contacts of the strand formed by residues 65 - 72 (chain E) 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 ALA 65 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62E GLY 2.7 36.1 + - - +
64E PHE* 1.3 80.5 - - - +
66E LYS* 1.3 58.8 + - - +
82E LYS* 4.2 6.3 - - + -
83E ILE 3.2 6.3 - - - -
84E ILE* 3.6 20.2 - - + -
200E PHE* 3.8 26.2 - - - +
201E THR 4.7 0.7 - - - +
202E VAL* 3.2 11.6 - - + +
271F PHE* 3.8 6.2 - - - -
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Residues in contact with LYS 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E THR* 4.5 15.7 - - - +
60E GLY 3.4 9.2 - - - +
61E LYS* 4.2 13.5 - - + +
65E ALA* 1.3 75.1 - - - +
67E VAL* 1.3 63.4 + - - +
68E LYS* 3.5 37.7 - - + +
81E VAL 3.6 0.2 - - - +
82E LYS* 3.3 4.0 - - - +
83E ILE* 2.7 49.5 + - + +
271F PHE* 3.8 31.6 - - + -
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Residues in contact with VAL 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E THR* 3.5 2.5 - - - -
59E ILE* 2.6 62.8 + - + +
60E GLY* 2.6 19.7 + - - +
66E LYS* 1.3 77.2 - - - +
68E LYS* 1.3 57.4 + - - +
80E ALA* 4.3 15.0 - - + -
81E VAL 3.5 4.9 - - - +
82E LYS* 3.9 26.5 - - + +
129E MET* 6.3 1.3 - - + -
202E VAL* 4.2 20.6 - - + -
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Residues in contact with LYS 68 (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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48E PRO* 5.6 7.6 - - - -
55E LEU* 4.1 30.7 - - + -
56E GLN 3.8 9.0 + - - +
57E LYS 3.5 4.7 - - - +
58E THR* 3.0 41.2 - - - +
59E ILE* 4.3 1.8 - - - -
66E LYS* 3.5 26.6 - - + +
67E VAL* 1.3 74.1 - - - +
69E LEU* 1.3 66.7 + - - +
81E VAL* 2.8 36.3 + - - +
83E ILE* 3.8 24.7 - - + -
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Residues in contact with LEU 69 (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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56E GLN* 2.7 38.6 + - + +
57E LYS* 2.8 38.0 + - + +
59E ILE* 3.8 23.3 - - + +
68E LYS* 1.3 74.4 - - - +
70E ALA* 1.3 64.0 + - - +
78E GLU* 3.4 22.0 - - + +
79E VAL 3.2 20.4 - - - +
131E TYR* 3.8 43.5 - - + +
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Residues in contact with ALA 70 (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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53E TYR* 4.4 4.7 - - + -
54E ARG 3.2 14.1 - - - +
55E LEU* 3.8 10.5 - - + -
56E GLN* 2.8 15.8 + - - +
69E LEU* 1.3 77.4 - - - +
71E ARG* 1.3 57.7 + - - +
78E GLU* 3.4 1.9 - - - -
79E VAL* 2.6 44.7 + - + +
81E VAL* 3.4 29.6 - - + -
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Residues in contact with ARG 71 (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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53E TYR* 3.5 3.0 - - - -
54E ARG* 3.0 56.8 + - + +
56E GLN* 3.1 11.1 - - - +
70E ALA* 1.3 74.2 - - - +
72E HIS* 1.3 75.2 + - - +
73E VAL* 3.3 9.2 + - - +
76E GLY* 3.3 29.6 + - - -
77E ARG 3.3 4.5 + - - +
78E GLU* 2.3 36.1 + - - +
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Residues in contact with HIS 72 (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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52E ASN* 3.4 23.7 + - + +
53E TYR* 3.4 37.2 + + + -
70E ALA 4.1 0.4 + - - -
71E ARG* 1.3 71.5 - - - +
73E VAL* 1.3 57.8 + - - +
74E LEU* 3.8 14.0 - - + +
75E THR* 2.9 41.6 + - + +
76E GLY* 2.8 30.7 + - - -
77E ARG 2.8 16.0 + - - +
79E VAL* 4.7 1.7 - - + +
117E GLU* 4.8 1.6 + - - -
353E GLU 5.2 0.6 + - - -
357E THR* 3.6 25.5 + - - -
360E LEU* 3.1 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