Contacts of the helix formed by residues 79 - 87 (chain H) in PDB entry 1KD1
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 GLN 79 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13H GLU* 4.2 1.9 + - - +
51H ALA* 4.4 2.2 - - - +
53H ASP* 3.8 9.0 - - - +
77H VAL* 3.5 20.4 - - - +
78H GLU* 1.3 82.4 - - + +
80H GLN* 1.3 62.9 + - - +
81H ASP* 4.4 2.0 - - + +
82H ASP* 2.9 39.0 + - + +
83H LEU* 3.6 9.5 + - - +
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Residues in contact with GLN 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A U 2.7 45.8 + - - +
51H ALA* 3.9 7.9 - - + -
53H ASP* 2.8 42.9 + - - +
54H VAL* 3.9 2.6 - - - +
79H GLN* 1.3 71.8 - - - +
81H ASP* 1.3 64.7 + - - +
82H ASP 3.2 0.4 - - - -
83H LEU 3.5 0.7 + - - -
84H GLY 3.2 11.8 + - - -
92H GLY* 4.7 6.4 - - - -
93H SER 3.1 46.5 + - - +
94H ALA* 4.2 3.8 - - - +
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Residues in contact with ASP 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H GLN* 3.4 2.3 - - + +
80H GLN* 1.3 81.8 + - - +
82H ASP* 1.3 67.2 + - - +
84H GLY 3.7 0.9 - - - -
85H HIS* 3.0 27.9 + - - +
91H VAL 4.5 2.3 - - - +
92H GLY* 3.5 23.7 + - - -
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Residues in contact with ASP 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H GLU* 5.1 2.8 - - - +
17H LEU* 4.3 21.4 - - + +
77H VAL* 4.8 2.5 - - + -
79H GLN* 2.9 41.2 + - + +
80H GLN 3.2 0.4 - - - -
81H ASP* 1.3 82.0 - - - +
83H LEU* 1.3 54.7 + - - +
85H HIS* 3.6 5.5 - - - +
86H ALA* 2.7 38.3 + - - +
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Residues in contact with LEU 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H LEU* 4.2 9.3 - - + +
20H LEU* 3.5 24.7 - - + -
49H PHE* 3.4 53.8 - - + +
50H VAL 4.1 0.9 - - - +
51H ALA* 4.0 9.0 - - + +
77H VAL* 4.6 7.6 - - + +
79H GLN 3.6 10.2 + - - +
80H GLN* 3.5 2.8 + - - +
81H ASP 3.4 0.2 - - - -
82H ASP* 1.3 78.4 - - - +
84H GLY* 1.3 63.8 + - - +
86H ALA* 3.8 0.2 - - - +
87H ALA* 2.9 25.8 + - - +
93H SER* 3.6 24.9 - - - +
94H ALA 3.9 4.5 - - - +
95H ALA* 3.8 10.1 - - - -
96H ALA* 3.7 10.8 - - + +
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Residues in contact with GLY 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H GLN 3.2 8.3 + - - -
81H ASP 3.6 0.6 + - - -
82H ASP 3.2 0.4 - - - -
83H LEU* 1.3 80.6 - - - +
85H HIS* 1.3 58.9 + - - +
87H ALA* 3.2 8.8 + - - +
88H GLY 3.3 0.2 + - - -
89H LEU* 2.8 26.7 + - - +
91H VAL 3.5 21.1 - - - -
92H GLY* 3.8 2.0 - - - -
93H SER* 3.7 23.4 - - - +
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Residues in contact with HIS 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H GLU* 4.5 13.2 + - - -
24H ARG* 4.2 9.5 + - - -
81H ASP 3.0 19.0 + - - +
82H ASP* 3.6 5.4 - - - +
84H GLY* 1.3 71.9 - - - +
86H ALA* 1.3 62.8 + - - +
88H GLY* 2.9 19.2 + - - -
89H LEU 3.5 15.7 + - - +
91H VAL 4.1 0.8 + - - -
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Residues in contact with ALA 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H LEU* 3.6 28.9 - - + +
20H LEU* 3.8 11.1 - - + +
21H GLU* 3.7 34.1 + - + +
24H ARG* 3.1 23.9 + - - -
82H ASP 2.7 21.0 + - - +
83H LEU 3.8 3.1 - - - +
85H HIS* 1.3 76.2 - - + +
87H ALA* 1.3 56.3 + - - +
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Residues in contact with ALA 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H LEU* 4.1 15.0 - - + +
24H ARG* 3.9 14.7 - - - +
29H VAL* 4.4 7.4 - - + +
31H LYS* 3.7 40.6 + - + -
83H LEU 2.9 18.0 + - - +
84H GLY* 3.5 7.9 - - - +
85H HIS 3.1 0.2 - - - -
86H ALA* 1.3 75.3 - - - +
88H GLY* 1.3 59.1 + - - +
89H LEU* 3.5 2.0 - - + +
93H SER* 5.4 2.2 - - - -
96H ALA* 4.7 11.4 - - + -
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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