Contacts of the helix formed by residues 72 - 97 (chain B) in PDB entry 2KPF
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 72 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A GLU* 4.0 4.9 - - - +
75A LEU* 3.6 32.7 - - + +
70B GLU 4.9 2.0 - - - +
71B PRO* 1.3 80.3 - - - +
73B ILE* 1.3 77.0 + - + +
74B THR* 3.2 2.1 + - - +
75B LEU* 3.0 23.4 + - - +
76B ILE* 3.1 19.4 + - + +
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Residues in contact with ILE 73 (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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72B GLU* 1.3 83.6 - - + +
74B THR* 1.3 66.6 + - - +
76B ILE* 3.0 12.2 + - + +
77B ILE* 2.9 34.7 + - + +
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Residues in contact with THR 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PRO* 5.0 14.2 - - - +
72B GLU 3.2 1.0 + - - +
73B ILE* 1.3 79.0 - - - +
75B LEU* 1.3 61.7 + - + +
77B ILE* 3.2 9.3 + - + +
78B PHE* 2.8 33.3 + - + +
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLU* 3.2 42.8 - - + -
75A LEU* 4.9 4.5 - - + -
76A ILE* 3.6 29.9 - - + +
71B PRO* 4.4 16.6 - - + +
72B GLU* 3.0 22.0 + - - +
74B THR* 1.3 82.8 - - + +
76B ILE* 1.3 63.6 + - + +
78B PHE* 3.3 7.4 + - + +
79B GLY* 2.9 22.5 + - - -
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Residues in contact with ILE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 3.3 56.5 - - + +
78A PHE* 5.0 13.7 - - + -
79A GLY* 4.1 5.4 - - - -
72B GLU* 3.3 18.6 - - + +
73B ILE* 3.0 10.7 + - + +
75B LEU* 1.3 75.6 - - - +
77B ILE* 1.3 66.0 + - + +
79B GLY* 3.9 0.5 - - - -
80B VAL* 3.1 38.7 + - + +
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Residues in contact with ILE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 2.9 30.4 + - + +
74B THR* 3.5 9.0 - - + +
76B ILE* 1.3 77.7 - - + +
78B PHE* 1.3 61.5 + - - +
80B VAL* 3.3 5.9 + - + +
81B MET* 2.8 52.4 + - + +
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Residues in contact with PHE 78 (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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76A ILE* 4.9 17.3 - - + -
80A VAL* 6.2 0.4 - - + -
74B THR* 2.8 24.0 + - + +
75B LEU* 3.6 10.1 - - + +
77B ILE* 1.3 74.0 - - - +
79B GLY* 1.3 64.2 + - - +
81B MET* 3.1 8.8 + - + +
82B ALA* 2.8 42.8 + - + +
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Residues in contact with GLY 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 4.1 8.7 - - - -
79A GLY* 4.5 0.7 - - - -
80A VAL* 2.9 41.7 - - - +
75B LEU 2.9 15.2 + - - -
76B ILE 3.9 1.1 - - - -
78B PHE* 1.3 85.7 - - - +
80B VAL* 1.3 57.2 + - - +
82B ALA* 3.3 1.0 + - - +
83B GLY 2.9 18.9 + - - -
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Residues in contact with VAL 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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78A PHE* 6.3 0.2 - - + -
79A GLY* 2.9 30.3 - - - +
80A VAL* 4.1 1.1 - - - +
82A ALA* 5.0 4.5 - - + -
83A GLY* 3.3 23.8 - - - +
76B ILE* 3.1 25.4 + - + +
77B ILE* 3.8 6.1 - - + +
79B GLY* 1.3 74.0 - - - +
81B MET* 1.3 57.7 + - + +
84B VAL* 2.9 43.1 + - + +
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Residues in contact with MET 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 ILE* 2.8 41.3 + - + +
78B PHE* 3.4 9.0 - - + +
80B VAL* 1.3 78.2 - - + +
82B ALA* 1.3 61.9 + - - +
84B VAL* 4.0 2.4 - - - +
85B ILE* 3.1 39.2 + - + +
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Residues in contact with ALA 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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80A VAL* 4.9 4.7 - - + -
78B PHE* 2.8 33.8 + - + +
79B GLY* 3.8 4.0 - - - +
81B MET* 1.3 74.2 - - - +
83B GLY* 1.3 62.0 + - - +
85B ILE* 3.9 3.6 - - - +
86B GLY* 2.9 26.2 + - - -
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Residues in contact with GLY 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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80A VAL* 3.3 30.2 - - - +
84A VAL* 3.3 13.2 - - - +
79B GLY 2.9 12.2 + - - -
80B VAL 4.0 0.4 - - - -
82B ALA* 1.3 74.6 - - - +
84B VAL* 1.3 64.6 + - - +
86B GLY* 3.1 2.1 + - - -
87B THR* 2.9 26.9 + - - -
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Residues in contact with VAL 84 (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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83A GLY* 3.3 31.0 - - - +
84A VAL 4.0 1.0 - - - +
87A THR* 3.1 20.3 + - + +
80B VAL* 2.9 34.6 + - + +
81B MET* 4.0 3.8 - - - +
83B GLY* 1.3 76.6 - - - +
85B ILE* 1.3 68.5 + - + +
87B THR* 3.2 3.2 + - - -
88B ILE* 3.1 39.3 + - + +
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Residues in contact with ILE 85 (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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81B MET* 3.1 27.4 + - + +
82B ALA* 4.1 3.4 - - - +
84B VAL* 1.3 78.4 - - + +
86B GLY* 1.3 63.3 + - - +
88B ILE* 3.3 20.1 + - + +
89B LEU* 3.1 38.2 + - + +
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Residues in contact with GLY 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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82B ALA 2.9 17.3 + - - -
83B GLY* 3.1 4.2 + - - -
85B ILE* 1.3 76.7 - - - +
87B THR* 1.3 62.2 + - - +
89B LEU* 3.2 13.5 + - - +
90B LEU* 3.1 32.9 + - - +
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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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84A VAL* 3.0 30.0 - - + +
87A THR* 4.5 5.2 - - + -
88A ILE* 3.3 39.9 - - + +
91A ILE* 6.5 0.2 - - + -
83B GLY 2.9 15.4 + - - -
84B VAL 3.2 5.4 + - - -
86B GLY* 1.3 73.8 - - - +
88B ILE* 1.3 55.1 + - - +
90B LEU* 3.2 10.1 + - + +
91B ILE* 2.7 54.7 + - + +
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Residues in contact with ILE 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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87A THR* 3.3 21.1 - - + -
91A ILE* 5.2 11.4 - - + -
84B VAL* 3.1 37.6 + - + +
85B ILE* 3.5 20.4 - - + +
86B GLY 3.3 0.2 - - - -
87B THR* 1.3 75.8 - - - +
89B LEU* 1.3 59.1 + - + +
91B ILE* 3.7 7.0 - - + +
92B SER* 2.8 38.1 + - - -
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Residues in contact with LEU 89 (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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85B ILE* 3.1 33.3 + - + +
86B GLY* 3.2 9.6 + - - +
88B ILE* 1.3 81.7 - - + +
90B LEU* 1.3 63.2 + - + +
92B SER* 2.7 25.2 + - - +
93B TYR* 3.1 8.8 + - - +
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Residues in contact with LEU 90 (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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86B GLY* 3.1 22.5 + - - +
87B THR* 3.6 9.6 - - + +
89B LEU* 1.3 79.4 - - + +
91B ILE* 1.3 69.1 - - + +
93B TYR* 2.9 23.0 + - - +
94B GLY* 3.2 5.0 + - - -
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Residues in contact with ILE 91 (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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88A ILE* 5.0 10.8 - - + -
91A ILE* 3.9 36.8 - - + -
87B THR* 2.7 45.3 + - + +
88B ILE* 3.7 7.0 - - + +
90B LEU* 1.3 78.8 - - + +
92B SER* 1.3 61.4 + - - +
94B GLY* 2.9 19.9 + - - +
95B ILE* 3.3 21.0 + - + +
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Residues in contact with SER 92 (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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88B ILE* 2.8 24.4 + - - -
89B LEU* 2.7 20.2 + - - +
91B ILE* 1.3 77.2 - - - +
93B TYR* 1.3 59.6 + - - +
95B ILE* 3.6 9.8 + - - +
96B ARG* 3.5 22.9 + - - +
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Residues in contact with TYR 93 (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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89B LEU 3.1 7.4 + - - +
90B LEU* 2.9 16.9 + - + +
92B SER* 1.3 81.8 + - - +
94B GLY* 1.3 63.2 + - - +
96B ARG* 3.2 8.5 + - + +
97B ARG* 3.1 17.7 + - - -
98B LEU 3.1 38.4 + - - -
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Residues in contact with GLY 94 (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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90B LEU 3.2 5.1 + - - -
91B ILE* 2.9 8.3 + - - -
93B TYR* 1.3 80.2 - - - +
95B ILE* 1.3 63.9 + - - +
97B ARG* 3.2 17.6 + - - +
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Residues in contact with ILE 95 (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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95A ILE* 4.3 27.4 - - + -
91B ILE* 3.3 22.8 + - + +
92B SER* 3.9 9.4 - - - +
93B TYR 3.3 0.4 - - - -
94B GLY* 1.3 78.2 - - - +
96B ARG* 1.3 61.9 + - + +
97B ARG* 3.6 2.8 + - - +
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Residues in contact with ARG 96 (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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92B SER 3.5 11.3 + - - +
93B TYR* 3.2 13.1 + - + +
94B GLY 3.2 0.2 - - - -
95B ILE* 1.3 80.2 - - + +
97B ARG* 1.3 70.4 + - - +
98B LEU* 3.2 39.9 + - - +
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Residues in contact with ARG 97 (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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93B TYR 3.1 8.7 + - - -
94B GLY* 3.2 13.6 + - - +
95B ILE 4.5 2.5 - - - +
96B ARG* 1.3 79.6 - - - +
98B LEU* 1.3 63.5 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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