Contacts of the helix formed by residues 78 - 96 (chain A) in PDB entry 3KHE
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 SER 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A VAL* 1.3 77.1 - - - +
79A ASP* 1.3 62.1 + - - +
80A LEU* 2.7 25.8 + - - +
81A ASP* 2.9 28.1 + - - -
82A SER* 3.0 26.7 + - - -
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Residues in contact with ASP 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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78A SER* 1.3 77.6 + - - +
80A LEU* 1.3 76.9 + - - +
82A SER* 3.3 8.7 - - - -
83A SER* 3.2 23.2 + - - -
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Residues in contact with LEU 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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78A SER* 2.7 13.2 + - - +
79A ASP* 1.3 88.5 + - - +
81A ASP* 1.3 60.5 + - - +
82A SER 3.3 0.9 - - - -
83A SER* 3.0 13.5 + - - +
84A GLN* 2.9 26.3 + - - +
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Residues in contact with ASP 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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70A MET* 4.2 29.0 - - + +
77A VAL* 4.1 9.1 - - + -
78A SER* 2.9 37.2 + - - +
80A LEU* 1.3 74.6 - - - +
82A SER* 1.3 53.1 + - - +
84A GLN* 2.9 11.3 + - - +
85A ILE* 2.7 40.1 + - - +
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Residues in contact with SER 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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67A ARG* 2.8 28.6 + - - +
77A VAL* 3.8 2.4 + - - +
78A SER 3.0 15.5 + - - -
79A ASP* 3.3 14.9 - - - -
81A ASP* 1.3 74.9 - - - +
83A SER* 1.3 58.0 + - - +
85A ILE* 3.1 13.0 + - - +
86A GLU* 2.8 34.3 + - - +
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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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79A ASP 3.2 8.2 + - - -
80A LEU* 3.0 29.1 + - - +
82A SER* 1.3 76.1 - - - +
84A GLN* 1.3 63.2 + - - +
86A GLU* 3.5 12.5 - - - +
87A ALA* 3.1 21.1 + - - +
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Residues in contact with GLN 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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13A LYS* 6.3 0.2 - - - +
80A LEU 2.9 15.9 + - - +
81A ASP* 2.9 14.3 + - - +
83A SER* 1.3 76.1 + - - +
85A ILE* 1.3 59.7 + - + +
87A ALA* 3.0 16.5 + - - +
88A GLU* 2.2 63.9 + - + +
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Residues in contact with ILE 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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63A ILE* 4.0 30.1 - - + +
66A TYR* 3.5 38.4 - - + -
67A ARG* 3.9 24.2 - - + +
70A MET* 4.5 17.0 - - + -
77A VAL* 4.1 10.5 - - + -
81A ASP 2.7 28.1 + - - +
82A SER* 3.1 10.5 + - - +
84A GLN* 1.3 71.4 - - + +
86A GLU* 1.3 66.0 + - + +
88A GLU* 3.1 17.6 + - + +
89A VAL* 3.1 14.6 + - + +
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Residues in contact with GLU 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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59A ARG* 2.2 41.9 + - - +
63A ILE* 3.8 22.5 - - - +
82A SER* 2.8 24.6 + - - +
83A SER* 3.5 16.2 - - - +
84A GLN 3.3 0.2 - - - -
85A ILE* 1.3 72.7 - - - +
87A ALA* 1.3 60.5 + - - +
89A VAL* 3.5 4.1 + - - +
90A ASP* 3.1 33.1 + - - +
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Residues in contact with ALA 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 SER 3.1 14.4 + - - +
84A GLN* 3.0 25.2 + - - +
86A GLU* 1.3 74.5 - - - +
88A GLU* 1.3 64.4 + - - +
90A ASP* 3.5 11.1 + - - +
91A HIS* 3.2 22.3 + - - +
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Residues in contact with GLU 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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13A LYS* 3.2 46.6 + - + +
66A TYR* 4.2 24.5 - - + +
84A GLN* 2.2 51.7 + - + +
85A ILE* 3.1 12.3 + - + +
87A ALA* 1.3 75.4 - - - +
89A VAL* 1.3 57.8 + - - +
91A HIS* 3.4 13.3 - - - +
92A ILE* 3.0 30.6 + - - +
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Residues in contact with VAL 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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59A ARG* 3.9 34.1 - - + +
62A LEU* 3.9 33.0 - - + +
63A ILE* 3.8 31.0 - - + +
66A TYR* 4.5 7.6 - - + -
85A ILE* 3.1 19.2 + - + +
86A GLU 3.9 3.6 - - - +
87A ALA 3.3 0.2 - - - -
88A GLU* 1.3 74.7 - - - +
90A ASP* 1.4 57.4 + - - +
92A ILE* 3.1 7.2 + - + +
93A LEU* 2.7 38.7 + - + +
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Residues in contact with ASP 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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59A ARG* 2.6 32.6 + - - +
86A GLU* 3.1 21.7 + - - +
87A ALA* 3.6 11.5 - - - +
89A VAL* 1.4 74.8 - - - +
91A HIS* 1.3 63.4 + - - +
93A LEU* 3.4 6.0 + - - +
94A GLN* 3.2 22.5 + - - +
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Residues in contact with HIS 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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12A MET 3.1 14.0 + - - -
13A LYS* 2.4 35.5 + - - -
15A PHE 3.0 24.9 - - - -
16A GLN* 3.7 16.7 + - - -
87A ALA 3.2 10.3 + - - +
88A GLU* 3.4 21.1 - - - +
90A ASP* 1.3 78.2 - - - +
92A ILE* 1.3 67.3 + - + +
94A GLN* 3.2 6.6 + - - +
95A SER* 3.0 31.6 + - - -
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Residues in contact with ILE 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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12A MET* 3.9 50.0 - - + +
13A LYS* 4.9 0.4 - - - +
62A LEU* 4.0 14.8 - - + -
66A TYR* 4.1 24.7 - - + +
88A GLU 3.0 19.8 + - - +
89A VAL* 3.1 12.1 + - + +
91A HIS* 1.3 77.5 - - + +
93A LEU* 1.3 59.9 + - - +
95A SER* 4.0 6.1 - - - -
96A VAL* 2.8 41.5 + - + +
97A ASP 3.6 0.7 + - - -
104A ILE* 3.8 25.6 - - + -
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Residues in contact with LEU 93 (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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57A LEU 4.8 1.3 - - - +
59A ARG* 4.0 42.0 - - + +
62A LEU* 4.0 14.8 - - + -
89A VAL* 2.7 26.9 + - + +
90A ASP* 3.9 4.9 - - - +
92A ILE* 1.3 74.6 - - - +
94A GLN* 1.3 57.1 + - - +
97A ASP* 3.1 26.8 - - + +
102A GLY* 3.7 31.0 - - - +
103A TYR* 4.5 2.0 - - - -
104A ILE* 4.0 22.0 - - + +
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Residues in contact with GLN 94 (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 SER* 4.2 10.2 + - - +
90A ASP 3.2 11.1 + - - +
91A HIS* 3.2 9.2 + - - +
93A LEU* 1.3 79.5 - - - +
95A SER* 1.3 65.7 + - - +
97A ASP 4.4 7.6 - - - +
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Residues in contact with SER 95 (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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15A PHE* 3.5 33.1 + - - -
16A GLN* 4.7 0.9 - - - -
17A SER* 3.7 23.8 + - - -
91A HIS* 3.0 26.9 + - - -
92A ILE* 4.0 0.7 - - - -
94A GLN* 1.3 80.5 - - - +
96A VAL* 1.3 76.3 + - - +
97A ASP 3.5 0.6 - - - -
98A PHE* 3.2 23.7 - - - -
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Residues in contact with VAL 96 (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 MET* 4.4 19.5 - - + +
15A PHE* 4.0 13.5 - - + -
92A ILE* 2.8 27.8 + - + +
95A SER* 1.3 84.8 + - - +
97A ASP* 1.3 60.4 + - - +
98A PHE* 2.8 27.9 + - - -
104A ILE* 3.8 31.2 - - + -
108A GLU* 3.6 21.8 - - - +
109A PHE* 4.6 0.4 - - - +
112A VAL* 4.0 19.3 - - + -
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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