Contacts of the helix formed by residues 72 - 84 (chain A) in PDB entry 2KQF
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 VAL 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ARG* 5.2 12.6 - - - +
36A VAL* 4.8 4.9 - - + -
38A HIS* 3.8 4.3 - - - -
70A GLY 3.7 1.5 + - - +
71A LEU* 1.3 77.8 - - - +
73A HIS* 1.3 73.5 + - + +
74A THR* 3.5 22.4 - - + +
75A GLU* 2.8 40.7 + - + +
76A VAL 3.4 6.9 + - - -
107B SER 6.1 0.7 - - - +
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Residues in contact with HIS 73 (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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21A LEU 3.9 10.7 + - - +
22A ARG* 5.0 3.6 - - - -
23A ALA* 3.2 39.8 - - + +
38A HIS* 4.0 3.8 - - - -
72A VAL* 1.3 79.2 - - + +
74A THR* 1.3 62.2 + - + +
76A VAL* 3.2 21.0 - - - +
77A VAL* 3.5 6.2 - - - +
104B SER 4.1 3.8 + - - -
105B HIS 5.1 0.9 - - - -
107B SER 3.7 6.2 + - - +
108B GLY* 3.6 24.9 - - - -
109B GLY 3.1 28.7 - - - -
110B GLU* 3.8 2.6 - - - -
111B THR* 3.0 47.3 + - - -
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Residues in contact with THR 74 (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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72A VAL* 3.2 12.3 - - + +
73A HIS* 1.3 84.0 - - + +
75A GLU* 1.3 61.4 + - - +
76A VAL 3.4 0.7 - - - -
77A VAL* 3.6 9.9 - - - +
78A GLU* 2.9 42.2 + - - +
108B GLY* 5.1 4.7 - - - +
111B THR* 4.7 14.8 - - + +
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Residues in contact with GLU 75 (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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70A GLY 4.1 3.8 - - - +
71A LEU* 3.4 31.3 - - + +
72A VAL* 2.8 46.0 + - + +
74A THR* 1.3 79.6 + - - +
76A VAL* 1.3 59.6 - - - +
78A GLU* 3.3 9.3 + - - +
79A LEU* 2.8 34.2 + - + +
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Residues in contact with VAL 76 (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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21A LEU* 3.4 34.8 - - + +
38A HIS* 3.2 39.7 - - + +
63A VAL* 4.9 1.4 - - + +
68A VAL* 3.8 24.7 - - + -
71A LEU* 3.8 9.0 - - + -
72A VAL 3.4 3.5 + - - +
73A HIS 3.2 18.6 - - - +
75A GLU* 1.3 73.3 - - - +
77A VAL* 1.3 74.3 + - - +
79A LEU* 3.2 10.1 + - - +
80A ILE* 3.0 28.4 + - + +
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Residues in contact with VAL 77 (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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21A LEU* 4.5 4.7 - - + -
73A HIS 3.5 17.7 - - - +
74A THR* 3.6 9.4 - - - +
76A VAL* 1.3 80.0 - - + +
78A GLU* 1.3 57.4 - - + +
80A ILE* 3.1 5.2 + - - +
81A LEU* 2.9 47.2 + - + +
111B THR* 3.9 33.4 - - + +
112B ARG 4.5 2.9 - - - +
113B LEU* 3.4 38.5 - - + +
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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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74A THR* 2.9 30.1 + - - +
75A GLU* 3.6 8.8 - - - +
77A VAL* 1.3 73.6 - - + +
79A LEU* 1.3 57.6 + - + +
81A LEU* 3.6 14.6 - - + +
82A LYS* 2.7 42.4 + - - +
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Residues in contact with LEU 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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63A VAL* 3.6 37.9 - - + +
64A ASN* 4.8 8.4 + - + +
66A GLU* 4.3 19.5 - - + -
71A LEU* 4.1 18.4 - - + -
75A GLU* 2.8 17.4 + - + +
76A VAL* 3.2 11.4 + - - +
78A GLU* 1.3 74.9 - - - +
80A ILE* 1.3 61.1 + - - +
82A LYS* 3.5 30.0 - - + +
83A SER* 3.3 19.4 + - - -
87A VAL* 4.6 1.4 - - - +
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Residues in contact with ILE 80 (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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17A TYR* 3.4 43.5 + - + -
19A PHE* 3.6 17.5 - - + -
21A LEU* 3.4 28.0 - - + -
63A VAL* 3.6 22.4 - - + -
76A VAL 3.0 18.5 + - - +
77A VAL 3.3 5.6 - - - +
79A LEU* 1.3 75.1 - - - +
81A LEU* 1.3 65.1 + - - +
83A SER* 3.1 19.4 + - - -
84A GLY 3.7 0.2 + - - -
86A LYS 4.0 0.7 - - - +
87A VAL* 3.6 25.1 - - + -
89A ILE* 5.3 2.9 - - + -
113B LEU* 3.7 11.0 - - + -
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Residues in contact with LEU 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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12A ARG* 6.1 3.8 - - - +
17A TYR* 3.9 26.5 - - + +
77A VAL* 2.9 38.9 + - + +
78A GLU* 3.7 12.8 - - + +
80A ILE* 1.3 75.0 - - - +
82A LYS* 1.3 63.1 + - - +
84A GLY* 3.2 16.3 + - - +
113B LEU* 4.0 10.1 - - + -
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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 25.6 + - - +
79A LEU* 3.5 36.1 - - + +
81A LEU* 1.3 71.2 - - - +
83A SER* 1.3 66.0 + - - +
84A GLY* 3.1 2.1 + - - -
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Residues in contact with SER 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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64A ASN* 2.9 37.2 + - - +
79A LEU 3.3 4.2 + - - -
80A ILE 3.1 10.2 + - - -
82A LYS* 1.3 79.9 - - - +
84A GLY* 1.3 55.1 + - - +
86A LYS* 2.7 37.8 + - - +
87A VAL* 3.6 9.8 - - - -
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Residues in contact with GLY 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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12A ARG* 4.9 3.5 + - - -
17A TYR* 2.7 27.4 + - - -
80A ILE 3.7 0.2 + - - -
81A LEU 3.2 10.5 + - - +
82A LYS 3.1 6.0 - - - -
83A SER* 1.3 81.3 - - - +
85A ASN* 1.3 53.4 + - - -
86A LYS 3.1 4.5 - - - -
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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