Contacts of the helix formed by residues 73 - 88 (chain B) in PDB entry 2FHP
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 ASN 73 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71B GLU* 2.8 24.3 + - - +
72B LYS* 1.3 112.4 + - - +
74B PHE* 1.3 66.9 + - - +
75B ALA* 4.4 7.6 - - + +
76B ALA* 3.0 18.0 + - + +
77B LEU* 3.8 1.6 + - - +
97B LYS* 3.6 3.6 - - - -
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Residues in contact with PHE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ASN* 1.3 70.4 - - - +
75B ALA* 1.3 67.3 + - - +
77B LEU* 3.0 44.7 + - + +
78B LYS* 4.3 2.9 + - + +
97B LYS* 3.3 20.3 - - + +
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 5.3 0.2 - - - -
17B ASP* 4.1 12.8 + - + +
73B ASN* 3.1 6.3 + - + +
74B PHE* 1.3 83.5 - - - +
76B ALA* 1.3 60.4 + - - +
78B LYS* 2.9 41.2 + - - +
79B VAL* 4.0 5.7 - - - +
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 3.5 31.4 - - + -
51B GLY 4.0 2.9 - - - +
71B GLU* 3.3 37.2 - - - +
73B ASN* 3.0 7.5 + - + +
75B ALA* 1.3 78.8 - - - +
77B LEU* 1.3 65.6 + - - +
78B LYS 3.3 0.2 - - - -
79B VAL* 3.0 4.4 + - - +
80B ILE* 3.0 24.5 + - - +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLU* 4.1 18.8 - - + -
73B ASN 4.1 4.5 - - - +
74B PHE* 3.0 45.0 + - + +
76B ALA* 1.3 77.3 - - - +
78B LYS* 1.3 57.4 + - - +
80B ILE* 3.3 6.5 - - + +
81B LYS* 2.9 30.9 + - - +
95B VAL* 3.7 27.8 - - + -
97B LYS* 4.1 27.1 - - + +
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Residues in contact with LYS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LYS* 6.6 0.4 - - - +
17B ASP* 2.8 37.8 + - - -
74B PHE* 4.3 2.3 + - + +
75B ALA* 2.9 33.0 + - - +
77B LEU* 1.3 79.1 - - - +
79B VAL* 1.3 63.8 + - + +
81B LYS* 3.8 7.6 - - - +
82B GLU* 3.1 28.1 + - - +
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Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LYS* 3.5 40.8 - - + +
15B ALA 3.6 24.0 - - - +
16B LEU* 4.0 19.1 - - + -
17B ASP* 4.2 14.1 - - - +
52B SER* 4.1 3.8 - - - -
75B ALA 4.0 15.5 - - - +
76B ALA 3.0 6.8 + - - +
78B LYS* 1.3 82.0 - - + +
80B ILE* 1.3 66.3 + - - +
82B GLU* 3.1 6.7 + - - +
83B ASN* 3.0 25.8 + - - +
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B SER* 3.3 30.1 - - - +
51B GLY 3.8 12.5 + - - +
52B SER 3.7 12.6 - - - +
53B GLY* 3.4 15.7 - - - +
57B ILE* 5.5 0.4 - - + -
69B CYS* 3.7 24.0 - - + -
71B GLU* 5.8 3.1 - - + -
76B ALA 3.0 14.6 + - - +
77B LEU* 3.3 18.4 - - + +
79B VAL* 1.3 77.0 - - - +
81B LYS* 1.3 60.3 - - + +
83B ASN* 3.3 1.3 + - + +
84B ILE* 2.8 43.9 + - + +
95B VAL* 4.0 22.0 - - + -
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Residues in contact with LYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B LEU 2.9 20.5 + - - +
78B LYS* 3.8 7.9 - - - +
80B ILE* 1.3 79.9 - - + +
82B GLU* 1.3 57.3 + - - +
84B ILE* 3.4 10.5 + - + +
85B ALA* 2.9 29.0 + - + +
95B VAL* 6.0 0.7 - - + -
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Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LYS* 3.4 37.6 + - + +
78B LYS 3.1 18.7 + - - +
79B VAL* 3.1 5.6 + - - +
81B LYS* 1.3 76.3 - - - +
83B ASN* 1.3 62.9 + - - +
85B ALA* 3.2 10.2 + - + +
86B ILE* 3.1 34.1 + - + +
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Residues in contact with ASN 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ARG 4.7 1.2 - - - +
13B LEU* 3.5 16.9 - - + +
14B LYS* 2.8 52.0 + - - +
52B SER* 2.9 25.8 + - - +
57B ILE* 3.5 25.4 - - + +
79B VAL 3.0 16.5 + - - +
80B ILE 3.7 3.4 - - - +
82B GLU* 1.3 77.3 - - - +
84B ILE* 1.3 64.2 + - - +
86B ILE* 3.2 26.7 - - - +
87B THR* 3.6 3.3 + - - +
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Residues in contact with ILE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ILE* 4.4 6.1 - - + -
69B CYS* 5.1 0.7 - - - -
80B ILE* 2.8 35.1 + - + +
81B LYS* 3.7 7.9 - - + +
83B ASN* 1.3 71.4 - - - +
85B ALA* 1.3 63.7 + - - +
87B THR* 2.6 32.1 + - - -
88B LYS* 3.6 1.4 + - - -
89B GLU 4.5 0.9 + - - -
90B PRO* 3.7 34.2 - - + +
93B PHE* 3.7 38.6 - - + -
95B VAL* 3.5 32.3 - - + -
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LYS* 2.9 15.6 + - + +
82B GLU* 3.2 14.5 + - + +
84B ILE* 1.3 78.5 - - - +
86B ILE* 1.3 57.7 + - + +
88B LYS* 3.0 26.9 + - - +
90B PRO* 5.8 4.7 - - - -
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Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B VAL* 4.9 2.2 - - + -
8B TYR* 5.9 0.9 - - + -
11B ARG* 3.0 58.1 + - + -
12B ARG 2.9 35.9 - - - +
13B LEU* 4.1 10.3 - - + -
82B GLU* 3.1 24.5 + - + +
83B ASN* 3.2 21.2 + - - +
84B ILE 3.1 1.2 - - - -
85B ALA* 1.3 77.0 - - + +
87B THR* 1.3 61.3 + - + +
88B LYS* 4.0 8.1 - - - +
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Residues in contact with THR 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B TYR* 3.5 51.1 - - + -
11B ARG* 3.4 14.4 + - - +
57B ILE* 3.8 16.4 - - + -
83B ASN 3.7 10.3 - - - +
84B ILE* 2.6 22.2 + - - +
86B ILE* 1.3 78.9 - - + +
88B LYS* 1.3 68.2 + - - +
89B GLU* 3.0 14.3 + - - +
93B PHE* 3.6 20.9 - - + -
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Residues in contact with LYS 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ARG* 4.7 11.2 - - - +
84B ILE 3.6 1.0 + - - -
85B ALA* 3.0 20.5 + - - +
86B ILE* 4.0 8.5 - - - +
87B THR* 1.3 81.8 + - - +
89B GLU* 1.3 62.3 + - + +
90B PRO* 3.4 12.3 - - - +
91B GLU* 4.8 0.5 - - - +
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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