Contacts of the helix formed by residues 105 - 124 (chain H) in PDB entry 3WKJ
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 GLY 105 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G GLU* 3.8 5.4 - - - -
103H LEU 3.7 2.8 + - - -
104H PRO* 1.3 69.9 - - - +
106H GLU* 1.3 62.7 + - - -
108H ALA* 3.2 14.8 + - - +
109H LYS* 3.3 16.5 + - - +
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Residues in contact with GLU 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G GLU* 2.9 19.6 + - - +
105H GLY* 1.3 69.2 - - - -
107H LEU* 1.3 65.0 + - - +
109H LYS* 3.2 20.4 + - - +
110H HIS* 3.1 49.1 + - + +
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Residues in contact with LEU 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G TYR* 3.6 23.5 - - - +
58G LEU* 3.8 24.2 - - + -
61G GLU* 4.3 17.9 - - + -
90G ASP* 5.5 0.9 - - - +
92G GLU* 2.7 45.2 + - + +
93G LEU* 3.7 24.2 - - + -
96G LEU* 4.6 5.2 - - + -
103H LEU* 4.1 10.5 - - + -
104H PRO* 3.1 17.0 + - + +
106H GLU* 1.3 73.0 - - - +
108H ALA* 1.3 58.3 + - - +
111H ALA* 2.9 31.9 + - - +
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Residues in contact with ALA 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H VAL* 4.0 8.3 - - - +
100H ARG* 4.5 17.3 - - - +
103H LEU* 3.1 38.6 - - + +
104H PRO 3.8 0.8 + - - -
105H GLY 3.2 10.7 + - - +
106H GLU 3.2 0.2 - - - -
107H LEU* 1.3 80.6 - - - +
109H LYS* 1.3 55.9 + - + +
111H ALA* 3.5 2.9 + - - +
112H VAL* 2.8 37.3 + - - +
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Residues in contact with LYS 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100H ARG* 4.0 30.1 - - - +
105H GLY 3.3 10.9 + - - +
106H GLU* 3.2 29.3 + - - +
108H ALA* 1.3 79.0 - - + +
110H HIS* 1.3 59.9 + - + +
112H VAL* 3.1 8.7 + - + +
113H SER* 3.0 25.5 + - - -
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Residues in contact with HIS 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G TYR* 3.1 36.2 + + + +
106H GLU* 3.1 41.0 + - + +
109H LYS* 1.3 76.9 - - + +
111H ALA* 1.3 64.5 + - - +
113H SER* 3.1 10.3 + - - -
114H GLU* 3.0 30.7 + - + +
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Residues in contact with ALA 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G VAL* 3.9 19.5 - - + +
57G TYR* 3.7 18.1 - - + -
99H VAL* 3.9 9.0 - - + -
103H LEU* 3.6 24.2 - - + -
107H LEU 2.9 19.5 + - - +
108H ALA 3.6 4.5 - - - +
110H HIS* 1.3 76.4 - - - +
112H VAL* 1.3 58.5 + - - +
114H GLU* 3.4 2.9 + - - +
115H GLY* 2.9 26.9 + - - -
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Residues in contact with VAL 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G TYR* 3.6 10.9 + - - +
96H GLN* 3.2 28.5 - - + +
99H VAL* 3.8 17.9 - - + -
100H ARG* 3.7 40.8 - - + +
108H ALA 2.8 27.1 + - - +
109H LYS* 3.4 5.6 - - + +
111H ALA* 1.3 77.3 - - - +
113H SER* 1.3 61.2 + - - +
116H THR* 3.1 27.0 + - + +
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Residues in contact with SER 113 (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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109H LYS 3.0 12.6 + - - -
110H HIS* 3.1 15.9 + - - -
112H VAL* 1.3 76.3 - - - +
114H GLU* 1.3 75.0 + - - +
116H THR* 3.9 5.2 + - - -
117H LYS* 3.1 31.4 + - - +
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Residues in contact with GLU 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G ALA* 3.9 11.6 - - + +
57G TYR* 4.0 37.4 - - + +
110H HIS* 3.0 18.5 + - + +
111H ALA 3.8 3.4 - - - +
113H SER* 1.3 79.1 + - - +
115H GLY* 1.3 58.7 + - - +
117H LYS* 3.0 37.3 + - - +
118H ALA* 2.8 33.1 + - - +
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Residues in contact with GLY 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G TYR* 3.6 36.2 - - - -
53G ALA* 4.0 10.7 - - - +
54G VAL* 4.8 0.4 - - - -
111H ALA 2.9 11.6 + - - -
112H VAL 3.8 0.2 - - - -
113H SER 3.2 0.4 - - - -
114H GLU* 1.3 79.1 - - - +
116H THR* 1.3 61.8 + - - +
118H ALA* 3.2 3.1 + - - +
119H VAL* 3.2 23.0 + - - +
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Residues in contact with THR 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G TYR* 3.8 8.7 - - + +
96H GLN* 3.5 24.2 - - - +
112H VAL* 3.1 20.5 + - + +
113H SER* 3.9 6.0 + - - -
115H GLY* 1.3 73.4 - - - +
117H LYS* 1.3 64.6 + - - +
119H VAL* 3.3 8.6 + - - +
120H THR* 3.1 27.6 + - - -
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Residues in contact with LYS 117 (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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113H SER* 3.1 22.2 + - - +
114H GLU* 3.0 33.0 + - - +
116H THR* 1.3 83.0 + - - +
118H ALA* 1.3 58.6 + - - +
120H THR* 3.1 7.2 + - - +
121H LYS* 3.0 38.8 + - + +
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Residues in contact with ALA 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ALA* 3.4 17.2 - - - +
23G LEU* 3.8 23.1 - - + -
49G VAL* 3.3 9.7 - - + +
53G ALA* 3.7 21.8 - - + -
114H GLU 2.8 16.7 + - - +
115H GLY 3.7 2.2 - - - +
117H LYS* 1.3 78.0 - - - +
119H VAL* 1.3 58.1 + - - +
121H LYS* 5.0 0.2 - - - -
122H TYR* 3.1 26.3 + - - +
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Residues in contact with VAL 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G GLY* 4.0 31.6 - - - +
49G VAL* 4.0 6.5 - - + -
50G TYR* 4.0 24.5 - - + +
92H SER* 4.7 8.1 - - - +
115H GLY 3.2 13.1 + - - +
116H THR* 3.7 10.5 - - - +
117H LYS 3.2 0.6 - - - -
118H ALA* 1.3 78.0 - - - +
120H THR* 1.3 58.5 + - - +
122H TYR* 3.8 4.6 - - + +
123H THR* 2.9 40.7 + - - +
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Residues in contact with THR 120 (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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116H THR* 3.1 14.4 + - - -
117H LYS* 3.1 11.0 + - - +
119H VAL* 1.3 75.7 - - - +
121H LYS* 1.3 55.9 + - - +
122H TYR 2.6 15.7 + - - -
123H THR* 3.0 14.3 + - - +
124H SER* 3.1 22.8 + - - +
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Residues in contact with LYS 121 (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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19G SER 5.3 1.1 - - - +
20G ARG* 2.6 29.1 - - - +
21G ALA 3.6 24.7 + - - +
22G GLY* 3.8 17.9 + - - +
117H LYS* 3.0 25.7 + - + +
118H ALA* 4.1 1.1 - - - -
120H THR* 1.3 76.5 - - - +
122H TYR* 1.3 51.7 + - - +
124H SER* 4.3 13.2 - - - -
125H SER 5.2 1.2 + - - -
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Residues in contact with TYR 122 (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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17G ARG* 3.0 63.8 + - + +
20G ARG* 3.8 29.1 + - + -
21G ALA* 3.7 8.1 - - + -
45G ALA* 4.4 20.3 + - + +
46G GLY* 5.3 2.7 - - - -
49G VAL* 4.1 21.3 - - + -
118H ALA 3.1 19.2 + - - +
119H VAL* 3.8 6.3 - - + +
120H THR 2.6 7.3 + - - -
121H LYS* 1.3 75.1 - - - +
123H THR* 1.3 72.6 + - - +
124H SER 3.0 5.8 + - - -
125H SER* 3.3 18.2 + - - -
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Residues in contact with THR 123 (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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119H VAL* 2.9 25.6 + - - +
120H THR* 3.0 5.6 + - - -
122H TYR* 1.3 86.5 - - - +
124H SER* 1.3 60.4 + - - +
125H SER* 3.1 2.2 + - - -
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Residues in contact with SER 124 (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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120H THR* 3.1 22.1 + - - +
121H LYS* 4.4 11.5 - - - -
122H TYR 3.0 0.8 - - - -
123H THR* 1.3 78.6 - - - +
125H SER* 1.3 69.7 + - - +
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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
------------------------------------------------------------
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