Contacts of the strand formed by residues 78 - 85 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56F GLN* 2.9 28.7 + - - +
69F LEU* 3.7 16.5 - - + +
70F ALA 3.3 1.1 - - - -
71F ARG* 2.9 53.0 + - - +
76F GLY 3.6 2.0 + - - +
77F ARG* 1.3 75.9 - - - +
79F VAL* 1.4 65.4 + - - +
116F PHE* 5.1 1.6 - - - -
131F TYR* 4.1 30.2 + - + +
360F LEU* 5.2 0.3 - - - +
364F LYS 5.9 0.2 + - - -
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Residues in contact with VAL 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F TYR* 3.6 20.2 - - + -
69F LEU* 3.4 8.7 - - - +
70F ALA* 2.6 37.3 + - + +
77F ARG 4.1 6.7 - - - +
78F GLU* 1.4 80.7 - - - +
80F ALA* 1.3 62.4 + - - +
81F VAL* 4.1 8.3 - - + -
116F PHE* 3.8 11.2 - - + -
128F VAL* 3.6 23.8 - - + -
129F MET 3.5 9.0 - - - +
131F TYR* 3.7 8.1 - - - +
360F LEU* 3.6 35.9 - - + -
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Residues in contact with ALA 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F ILE* 4.5 8.7 - - + -
67F VAL* 4.2 16.2 - - + -
68F LYS 3.5 4.3 - - - +
69F LEU* 5.0 0.7 - - - +
79F VAL* 1.3 74.6 - - - +
81F VAL* 1.3 60.8 + - - +
127F LEU 3.3 3.1 - - - +
128F VAL* 3.5 0.7 - - - -
129F MET* 2.7 60.5 + - + +
130F GLU 4.0 9.4 - - - +
131F TYR* 4.0 8.5 - - + +
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Residues in contact with VAL 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F ILE* 4.4 8.5 - - + -
53F TYR* 4.6 6.5 - - + -
55F LEU* 4.2 11.7 - - + -
66F LYS 3.6 1.4 - - - +
67F VAL* 3.4 3.0 - - - +
68F LYS* 2.7 44.9 + - + +
70F ALA* 3.7 25.1 - - + -
79F VAL* 4.1 10.3 - - + -
80F ALA* 1.3 73.6 - - - +
82F LYS* 1.3 62.2 + - - +
83F ILE* 3.9 6.2 + - + +
126F TYR* 3.9 35.4 - - + -
127F LEU 3.5 4.3 - - - +
128F VAL* 4.2 15.0 - - + -
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Residues in contact with LYS 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F ALA* 4.1 6.5 - - + -
66F LYS 3.2 5.8 - - - +
67F VAL* 3.3 26.1 - - + +
80F ALA 4.0 0.6 + - - -
81F VAL* 1.3 72.2 - - - +
83F ILE* 1.3 60.0 + - - +
84F ILE* 3.3 29.0 - - + +
97F LEU* 6.1 0.4 - - - -
100F GLU* 6.0 0.2 - - - -
104F MET* 5.2 6.5 - - + +
125F LEU 3.5 1.7 - - - +
126F TYR* 3.3 4.5 - - - -
127F LEU* 2.6 50.7 + - + +
129F MET* 4.2 18.2 - - + -
193F ASP* 3.7 21.4 + - - -
200F PHE* 2.8 37.1 + - - -
201F THR* 4.8 0.2 - - - +
202F VAL* 4.6 9.9 - - - +
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Residues in contact with ILE 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F LEU* 4.9 7.9 - - + -
65F ALA* 3.4 3.1 - - - -
66F LYS* 2.8 49.2 + - + +
68F LYS* 3.8 39.3 - - + -
81F VAL* 4.2 9.6 - - + +
82F LYS* 1.3 73.7 - - - +
84F ILE* 1.3 65.5 + - - +
85F ASP* 4.0 3.2 + - + +
124F THR* 3.8 11.7 - - - +
125F LEU 3.4 2.9 - - - -
126F TYR* 3.7 38.4 - - + +
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Residues in contact with ILE 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F PHE 3.6 12.6 - - - +
65F ALA* 3.6 17.5 - - + -
82F LYS* 3.3 39.9 - - + +
83F ILE* 1.3 80.0 - - - +
85F ASP* 1.3 70.6 + - - +
86F LYS* 3.3 2.6 + - - +
89F LEU* 4.4 2.5 - - + -
97F LEU* 3.8 38.6 - - + -
124F THR* 3.5 3.7 - - - -
125F LEU* 2.7 49.8 + - + +
127F LEU* 4.3 9.6 - - + -
200F PHE* 4.1 14.6 - - + -
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Residues in contact with ASP 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F PHE* 4.1 10.2 + - - +
65F ALA* 5.3 0.2 - - - +
83F ILE* 4.0 4.9 + - + +
84F ILE* 1.3 71.1 - - - +
86F LYS* 1.3 61.7 + - - +
87F THR* 2.7 31.5 + - - +
88F GLN* 3.6 25.3 + - - +
89F LEU* 3.7 17.5 - - - +
123F LYS 3.7 6.6 - - - +
124F THR* 4.8 3.8 - - - -
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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