Contacts of the strand formed by residues 78 - 85 (chain H) 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 GLU 78 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56H GLN* 2.4 31.9 + - - -
69H LEU* 3.7 18.4 - - + +
70H ALA 3.0 10.4 - - - +
71H ARG* 2.8 45.2 + - - +
76H GLY 3.6 1.4 + - - +
77H ARG* 1.3 74.2 - - - +
79H VAL* 1.3 63.0 + - - +
116H PHE* 5.0 2.6 - - - -
131H TYR* 4.1 15.8 + - + +
360H LEU* 5.4 0.3 - - - +
364H LYS* 3.0 42.1 + - - +
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Residues in contact with VAL 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H TYR* 3.7 26.5 - - + -
69H LEU* 3.4 7.1 - - - +
70H ALA* 2.8 48.2 + - + +
77H ARG 4.3 4.0 - - - +
78H GLU* 1.3 79.1 - - - +
80H ALA* 1.3 60.2 + - - +
81H VAL* 4.0 4.5 - - + -
116H PHE* 3.6 28.0 - - + -
128H VAL* 3.8 16.4 - - + -
129H MET 3.7 7.2 - - - +
131H TYR* 3.9 10.5 - - - +
360H LEU* 4.0 20.2 - - + -
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Residues in contact with ALA 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59H ILE* 4.5 11.4 - - + -
67H VAL* 3.8 21.8 - - + -
68H LYS 3.3 4.7 - - - +
69H LEU* 4.6 0.4 - - - +
79H VAL* 1.3 74.2 - - - +
81H VAL* 1.3 61.6 + - - +
82H LYS 4.0 0.2 - - - -
127H LEU 3.5 1.9 - - - +
128H VAL* 3.6 1.7 - - - -
129H MET* 3.0 48.4 + - + +
130H GLU 4.4 8.1 - - - +
131H TYR* 4.0 9.1 - - + +
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Residues in contact with VAL 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H ILE* 4.8 5.6 - - + -
53H TYR* 5.0 4.0 - - + -
55H LEU* 4.4 7.6 - - + -
66H LYS 3.6 0.2 - - - +
67H VAL* 3.2 3.2 - - - -
68H LYS* 2.6 46.2 + - + +
70H ALA* 3.6 28.5 - - + -
79H VAL* 4.0 4.3 - - + -
80H ALA* 1.3 76.8 - - - +
82H LYS* 1.3 70.7 + - - +
83H ILE* 3.5 5.9 + - + +
126H TYR* 4.0 29.8 - - + -
127H LEU 3.5 7.6 - - - +
128H VAL* 4.0 20.0 - - + -
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Residues in contact with LYS 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65H ALA* 4.1 10.5 - - + -
66H LYS 3.2 7.4 - - - +
67H VAL* 3.8 23.9 - - + +
80H ALA 4.0 1.2 + - - -
81H VAL* 1.3 70.0 - - - +
83H ILE* 1.3 59.0 + - - +
84H ILE* 4.0 18.6 - - + +
100H GLU* 5.0 4.2 + - - -
104H MET* 3.3 29.1 - - - +
125H LEU 3.4 2.1 - - - +
126H TYR* 3.4 5.5 - - - -
127H LEU* 2.9 36.2 + - + +
129H MET* 3.6 25.4 - - + +
193H ASP* 3.6 17.5 + - - -
196H PHE* 5.4 0.2 - - - -
200H PHE* 3.1 31.6 + - + +
201H THR 5.1 3.4 - - - -
202H VAL* 5.3 4.3 - - - +
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Residues in contact with ILE 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55H LEU* 4.7 11.4 - - + -
65H ALA* 3.1 8.0 - - - -
66H LYS* 2.5 49.9 + - + +
68H LYS* 3.7 33.4 - - + -
81H VAL* 4.2 7.4 - - + +
82H LYS* 1.3 69.1 - - - +
84H ILE* 1.3 68.2 + - - +
85H ASP* 4.1 2.6 + - + +
124H THR* 4.3 9.2 - - - +
125H LEU 3.5 3.1 - - - -
126H TYR* 3.5 37.2 - - + +
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Residues in contact with ILE 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64H PHE 3.9 11.0 - - - +
65H ALA* 3.7 15.5 - - + -
82H LYS* 4.0 15.7 - - + -
83H ILE* 1.3 83.4 - - - +
85H ASP* 1.3 69.6 + - - +
86H LYS* 3.1 4.9 + - - +
89H LEU* 4.4 8.5 - - + -
97H LEU* 3.8 39.5 - - + -
124H THR* 4.4 1.8 - - - -
125H LEU* 2.8 46.6 + - + +
127H LEU* 3.7 30.7 - - + -
200H PHE* 4.5 9.4 - - + -
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Residues in contact with ASP 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64H PHE* 4.1 9.0 + - - +
83H ILE* 4.1 4.4 + - + +
84H ILE* 1.3 70.1 - - - +
86H LYS* 1.3 62.1 + - - +
87H THR* 2.7 38.2 + - - +
88H GLN* 4.2 7.8 - - - +
89H LEU* 3.7 15.4 - - - +
123H LYS* 3.6 12.5 - - - +
124H THR* 4.5 5.5 - - - +
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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