Contacts of the helix formed by residues 77 - 92 (chain A) in PDB entry 2KHW
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 PRO 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A GLU 4.3 2.2 - - - +
76A LEU* 1.3 96.4 - - + +
78A GLU* 1.3 60.4 + - - +
79A ALA* 3.4 6.7 - - + +
80A VAL* 3.4 25.8 + - + +
81A GLN* 2.8 23.9 + - - +
244B ILE* 4.0 30.7 - - + -
247B GLY* 4.1 22.4 - - - +
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Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LEU 3.7 0.4 + - - -
77A PRO* 1.3 69.2 - - - +
79A ALA* 1.3 70.3 + - - +
81A GLN* 2.6 30.3 + - - +
82A LYS* 2.7 48.5 + - + +
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PRO* 3.4 3.9 - - + +
78A GLU* 1.3 79.4 - - - +
80A VAL* 1.3 66.2 + - + +
82A LYS* 3.6 7.7 + - - +
83A GLU* 3.3 26.9 + - - +
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU* 4.9 2.7 - - + -
77A PRO* 3.4 29.9 + - + +
78A GLU 3.1 0.4 - - - -
79A ALA* 1.3 79.2 - - + +
81A GLN* 1.3 67.7 + - - +
83A GLU* 3.3 15.4 + - - +
84A LEU* 3.0 33.4 + - + +
242B ARG* 6.0 2.5 - - - +
244B ILE* 3.8 11.9 - - + -
249B GLN* 6.0 1.8 - - - +
270B VAL* 3.8 35.9 - - + -
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Residues in contact with GLN 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PHE* 3.3 38.5 + - + +
74A TYR* 3.6 44.5 + - - +
76A LEU* 4.5 7.7 + - - +
77A PRO 2.8 13.7 + - - +
78A GLU* 2.6 32.3 + - + +
80A VAL* 1.3 72.7 - - - +
82A LYS* 1.3 61.0 + - + +
84A LEU* 3.1 4.1 + - - +
85A LEU* 2.8 43.7 + - + +
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Residues in contact with LYS 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A GLU* 2.7 51.0 + - + +
79A ALA* 3.8 8.1 - - - +
81A GLN* 1.3 75.1 + - + +
83A GLU* 1.3 54.7 + - + +
85A LEU* 3.1 16.2 + - + +
86A ALA* 2.7 38.5 + - - +
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Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ALA* 3.3 15.7 + - - +
80A VAL* 3.3 17.6 + - + +
81A GLN 3.3 0.6 - - - -
82A LYS* 1.3 77.5 - - + +
84A LEU* 1.3 66.4 + - + +
86A ALA* 3.8 6.2 - - - +
87A GLU* 3.1 22.3 + - - +
242B ARG* 4.1 17.8 + - - -
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PHE* 3.6 32.3 - - + -
76A LEU* 4.2 14.1 - - + -
80A VAL* 3.0 33.4 + - + +
81A GLN 3.7 0.2 - - - +
83A GLU* 1.3 80.4 - - + +
85A LEU* 1.3 63.9 + - - +
87A GLU* 3.3 7.5 + - + +
88A TRP* 3.1 41.3 + - + +
208B LEU* 5.1 10.1 - - + -
270B VAL* 4.3 10.5 - - + -
271B LEU 4.1 20.0 - - - +
272B ARG 5.9 0.2 - - - +
273B LEU* 6.1 4.3 - - + -
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ILE* 4.0 26.7 - - + -
63A THR 5.4 0.7 - - - +
73A PHE* 4.0 9.9 - - + -
81A GLN* 2.8 39.3 + - + +
82A LYS* 3.7 16.6 - - + +
84A LEU* 1.3 76.9 - - - +
86A ALA* 1.3 59.4 + - - +
88A TRP* 3.1 27.9 + - + +
89A LYS* 2.8 57.3 + - + +
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A LYS 2.7 22.9 + - - +
83A GLU* 3.8 7.6 - - - +
85A LEU* 1.3 73.5 - - - +
87A GLU* 1.3 58.3 + - - +
89A LYS* 3.8 9.9 - - - +
90A ARG* 2.9 34.1 + - - +
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Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLU 3.1 13.8 + - - +
84A LEU* 3.5 12.8 - - + +
85A LEU 3.1 0.8 - - - -
86A ALA* 1.3 77.2 - - - +
88A TRP* 1.3 72.5 + - + +
90A ARG* 3.0 38.1 + - - +
91A THR* 3.1 20.2 - - + +
273B LEU* 3.7 39.6 - - + +
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Residues in contact with TRP 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A THR 4.0 17.0 - - - +
64A PHE* 3.4 22.4 - + - -
65A PRO* 3.6 26.6 - - + +
68A ILE* 3.6 35.5 - - + +
73A PHE* 3.1 46.4 - + - -
84A LEU* 3.1 24.7 + - + +
85A LEU* 3.1 23.6 + - + +
87A GLU* 1.3 87.7 - - + +
89A LYS* 1.3 55.7 + - + +
91A THR* 3.6 7.5 - - + +
92A GLY* 2.6 31.2 + - - -
208B LEU* 6.2 0.9 - - + -
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Residues in contact with LYS 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LEU* 2.8 44.3 + - + +
86A ALA* 3.8 8.5 - - - +
88A TRP* 1.3 79.3 - - + +
90A ARG* 1.3 68.6 + - - +
91A THR 3.1 2.2 + - - -
92A GLY* 3.2 14.4 + - - -
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ALA* 2.9 14.4 + - - +
87A GLU* 3.0 43.3 + - - +
89A LYS* 1.3 76.7 - - - +
91A THR* 1.3 67.0 + - - +
92A GLY 4.9 0.3 - - - -
273B LEU* 5.4 5.3 - - - +
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Residues in contact with THR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A GLU* 3.1 27.1 - - + +
88A TRP* 3.6 9.6 - - + +
90A ARG* 1.3 83.1 - - - +
92A GLY* 1.3 74.2 + - - +
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Residues in contact with GLY 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A TRP 2.6 28.5 + - - -
89A LYS* 3.2 11.3 + - - -
90A ARG 4.9 0.4 - - - -
91A THR* 1.3 85.3 - - - +
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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