Contacts of the helix formed by residues 104 - 118 (chain H) in PDB entry 1K73
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 ALA 104 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H ALA* 4.2 14.4 - - + +
22H VAL* 3.2 30.1 - - + -
23H ALA* 5.5 0.2 - - - -
101H ALA* 4.1 4.7 - - + -
102H GLY 2.9 8.5 - - - +
103H ALA* 1.3 78.5 - - - +
105H ALA* 1.3 55.8 + - - +
106H THR* 2.7 11.1 + - - +
107H VAL* 3.1 13.3 + - + +
108H LEU* 2.7 38.0 + - + +
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Residues in contact with ALA 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H GLU* 6.0 0.9 - - - +
101H ALA* 3.7 23.8 - - + +
103H ALA 4.4 2.0 - - - +
104H ALA* 1.3 76.2 - - - +
106H THR* 1.3 57.3 + - - +
108H LEU* 4.1 4.7 - - + +
109H GLU* 3.1 28.9 + - - +
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Residues in contact with THR 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H ALA* 2.7 2.9 + - - -
105H ALA* 1.3 77.0 - - - +
107H VAL* 1.3 73.6 + - + +
108H LEU 3.0 1.9 + - - -
109H GLU* 3.0 19.3 + - - +
110H GLU* 3.0 35.9 + - + +
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Residues in contact with VAL 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H ASP* 4.9 11.7 - - + +
19H ALA* 4.9 7.0 - - + -
103H ALA 5.5 1.6 - - - +
104H ALA* 3.1 16.1 + - + +
106H THR* 1.3 85.1 - - + +
108H LEU* 1.3 58.0 + - - +
110H GLU* 3.3 17.2 + - + +
111H ILE* 2.9 44.7 + - + +
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Residues in contact with LEU 108 (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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19H ALA* 5.0 6.7 - - + +
46H GLU* 4.5 20.4 - - + +
47H LEU* 3.2 46.0 - - + -
98H VAL* 4.4 12.6 - - + -
101H ALA* 3.2 30.5 - - + -
104H ALA* 2.7 26.0 + - + +
105H ALA* 4.1 4.5 - - + +
106H THR 3.0 0.2 + - - -
107H VAL* 1.3 68.7 - - - +
109H GLU* 1.3 62.2 + - - +
110H GLU 2.9 1.3 - - - -
111H ILE* 2.6 35.5 + - + +
112H ALA* 3.0 11.3 + - + +
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Residues in contact with GLU 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H ALA 3.1 18.6 + - - +
106H THR* 3.0 10.1 + - - +
108H LEU* 1.3 81.9 - - + +
110H GLU* 1.3 58.2 + - - +
112H ALA* 3.3 10.9 - - - +
113H ASP* 2.6 41.6 + - - +
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Residues in contact with GLU 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H THR* 3.2 25.9 - - + +
107H VAL* 3.4 25.5 - - - +
108H LEU 2.8 1.4 + - - -
109H GLU* 1.3 81.3 - - - +
111H ILE* 1.3 58.2 + - - +
112H ALA 3.1 1.8 - - - -
113H ASP* 3.1 13.9 + - + +
114H LYS* 2.8 43.5 + - - +
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Residues in contact with ILE 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H LEU* 3.7 22.7 - - + -
15H ASP* 3.7 19.5 - - + +
16H ALA* 3.6 27.1 - - + -
19H ALA* 3.8 16.4 - - + -
47H LEU* 4.7 15.5 - - + -
75H ILE* 4.1 15.3 - - + -
107H VAL* 2.9 32.4 + - + +
108H LEU* 2.6 17.4 + - - +
110H GLU* 1.3 72.1 - - - +
112H ALA* 1.3 61.8 + - - +
114H LYS* 3.2 13.3 + - + +
115H VAL* 3.0 31.5 + - + +
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Residues in contact with ALA 112 (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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46H GLU 5.7 0.4 - - - +
47H LEU* 4.7 10.5 - - + +
73H PRO* 4.1 30.9 - - + +
108H LEU* 3.0 10.7 + - + +
109H GLU* 3.3 16.2 - - - +
111H ILE* 1.3 78.6 - - - +
113H ASP* 1.3 58.2 + - - +
115H VAL* 3.6 5.9 + - - +
116H GLU* 3.1 34.0 + - + +
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Residues in contact with ASP 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109H GLU* 2.6 29.8 - - - +
110H GLU* 3.1 19.3 + - + +
112H ALA* 1.3 78.4 - - - +
114H LYS* 1.3 64.5 + - + +
116H GLU* 3.2 7.4 + - - +
117H GLU* 3.0 39.8 + - - +
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Residues in contact with LYS 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H LEU* 4.3 27.1 - - + +
15H ASP* 3.9 21.8 + - - +
110H GLU* 2.8 30.0 + - - +
111H ILE* 3.6 13.1 - - + +
113H ASP* 1.3 75.3 - - + +
115H VAL* 1.3 58.3 + - - +
117H GLU* 3.4 14.6 + - - +
118H LEU* 2.9 25.9 + - - +
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Residues in contact with VAL 115 (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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6H PHE* 3.8 25.6 - - + -
12H LEU* 4.3 10.5 - - + -
47H LEU* 6.1 1.3 - - + -
73H PRO* 6.6 0.2 - - + -
74H PHE 3.6 22.0 - - - +
75H ILE* 4.1 32.5 - - + -
111H ILE* 3.0 19.6 + - + +
112H ALA* 3.9 6.3 - - - +
114H LYS* 1.3 73.2 - - - +
116H GLU* 1.3 60.7 + - + +
117H GLU 2.9 1.6 - - - -
118H LEU* 2.6 32.9 + - + +
119H ARG 3.1 8.2 + - - +
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Residues in contact with GLU 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H PRO* 5.8 8.2 - - + +
112H ALA* 3.1 24.3 + - + +
113H ASP* 3.6 8.5 - - - +
115H VAL* 1.3 75.6 - - + +
117H GLU* 1.3 63.2 + - + +
119H ARG* 3.2 16.2 + - - +
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Residues in contact with GLU 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H ASP* 3.0 32.9 + - - +
114H LYS* 3.4 14.3 + - - +
115H VAL 2.9 0.2 - - - -
116H GLU* 1.3 75.3 - - + +
118H LEU* 1.3 58.8 + - - +
119H ARG* 2.7 14.5 + - - +
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Residues in contact with LEU 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H PHE* 4.1 19.1 - - + +
7H ASP 3.4 28.0 - - - +
8H VAL* 3.8 16.2 - - + -
9H PRO* 3.8 24.0 - - + -
12H LEU* 4.0 15.7 - - + -
114H LYS 2.9 13.6 + - - +
115H VAL* 2.6 19.0 + - + +
117H GLU* 1.3 70.6 - - - +
119H ARG* 1.3 69.6 + - - +
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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
------------------------------------------------------------
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