Contacts of the helix formed by residues 106 - 124 (chain D) 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 GLU 106 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C GLU* 2.7 13.7 + - - +
105D GLY* 1.3 63.8 + - - -
107D LEU* 1.3 66.3 + - - +
108D ALA 2.8 4.8 + - - -
109D LYS* 2.9 38.5 + - - +
110D HIS* 3.0 45.9 + - + +
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Residues in contact with LEU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C TYR* 3.3 32.1 - - + +
58C LEU* 3.8 14.8 - - + -
61C GLU* 3.8 25.4 - - + -
90C ASP* 5.5 0.7 - - - +
92C GLU* 2.8 37.6 + - + +
93C LEU* 3.6 27.6 - - + -
96C LEU* 4.1 14.6 - - + -
103D LEU* 3.8 4.4 - - + +
104D PRO* 2.9 17.7 + - + +
106D GLU* 1.3 71.3 - - - +
108D ALA* 1.3 62.5 + - - +
111D ALA* 3.0 20.6 + - - +
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Residues in contact with ALA 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D VAL* 4.6 8.1 - - + +
100D ARG* 4.6 18.6 - - - +
103D LEU* 3.7 29.3 - - + +
104D PRO 3.3 2.2 + - - -
105D GLY* 3.5 20.9 - - - +
106D GLU 2.8 3.6 + - - -
107D LEU* 1.3 74.1 - - - +
109D LYS* 1.3 66.4 + - - +
111D ALA* 2.8 15.6 + - - +
112D VAL* 2.9 18.2 + - - +
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Residues in contact with LYS 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D ARG* 4.2 27.9 - - - +
105D GLY* 3.5 22.8 - - - +
106D GLU* 2.9 38.3 + - - +
108D ALA* 1.3 77.6 - - - +
110D HIS* 1.3 54.0 + - + +
112D VAL* 4.1 7.3 - - - +
113D SER* 2.6 31.2 + - - -
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Residues in contact with HIS 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C TYR* 3.1 37.5 + - + +
61C GLU* 5.8 0.6 + - - -
106D GLU* 3.0 44.1 + - + +
108D ALA 2.9 0.2 + - - -
109D LYS* 1.3 80.7 - - + +
111D ALA* 1.3 66.8 + - - +
113D SER* 3.2 7.7 + - - -
114D GLU* 3.2 26.8 + - + +
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Residues in contact with ALA 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C VAL* 3.6 29.0 - - + +
57C TYR* 3.6 24.1 - - + -
99D VAL* 4.0 2.7 - - + -
103D LEU* 3.6 19.1 - - + -
107D LEU 3.0 17.7 + - - +
108D ALA 2.8 4.6 + - - +
110D HIS* 1.3 79.1 - - - +
112D VAL* 1.3 61.6 + - - +
114D GLU* 3.3 3.5 + - - +
115D GLY 3.0 18.2 + - - -
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Residues in contact with VAL 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C TYR* 3.0 26.9 + - - +
96D GLN* 3.6 20.9 - - - +
99D VAL* 4.0 14.6 - - + -
100D ARG* 4.0 43.3 - - + +
108D ALA 2.9 19.5 + - - +
109D LYS 4.2 4.5 - - - +
111D ALA* 1.3 76.2 - - - +
113D SER* 1.3 60.1 + - - +
116D THR* 3.0 33.7 + - - +
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Residues in contact with SER 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D LYS 2.6 23.4 + - - -
110D HIS* 3.2 10.9 + - - -
112D VAL* 1.3 78.3 - - - +
114D GLU* 1.3 58.9 + - - +
116D THR* 3.4 5.8 + - - -
117D LYS* 2.9 31.2 + - - +
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Residues in contact with GLU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ALA* 3.8 12.1 - - + +
57C TYR* 4.1 35.3 - - + +
110D HIS* 3.2 15.6 + - + +
111D ALA 3.7 6.3 - - - +
113D SER* 1.3 77.5 - - - +
115D GLY* 1.3 56.6 + - - +
117D LYS* 3.5 31.2 + - - +
118D ALA* 2.8 32.4 + - - +
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Residues in contact with GLY 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C TYR* 3.7 31.6 - - - -
53C ALA* 3.9 13.4 - - - +
111D ALA 3.0 12.2 + - - -
112D VAL 3.9 1.8 - - - -
114D GLU* 1.3 74.9 - - - +
116D THR* 1.3 65.7 + - - +
118D ALA* 3.5 0.9 + - - +
119D VAL* 3.0 29.8 + - - +
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Residues in contact with THR 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C TYR* 3.7 6.1 - - - -
96D GLN* 3.8 15.9 + - - -
112D VAL* 3.0 20.6 + - - +
113D SER* 3.7 6.5 - - - -
115D GLY* 1.3 74.0 - - - +
117D LYS* 1.3 64.8 + - - +
119D VAL* 3.2 5.1 + - - +
120D THR* 3.0 42.0 + - + +
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Residues in contact with LYS 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D SER 2.9 18.4 + - - +
114D GLU* 3.5 30.3 + - - +
116D THR* 1.3 80.2 - - - +
118D ALA* 1.3 65.6 + - - +
120D THR* 3.0 7.5 + - - +
121D LYS* 3.0 26.7 + - + +
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Residues in contact with ALA 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ALA* 3.6 23.4 - - - +
23C LEU* 3.8 21.8 - - + -
49C VAL* 3.6 14.4 - - + +
53C ALA* 3.8 10.5 - - + -
114D GLU 2.8 20.8 + - - +
115D GLY 4.0 1.6 - - - +
117D LYS* 1.3 74.2 - - - +
119D VAL* 1.3 62.1 + - - +
121D LYS* 3.6 3.0 + - - +
122D TYR* 3.0 22.9 + - - +
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Residues in contact with VAL 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLY* 4.2 18.8 - - - +
49C VAL* 3.9 19.3 - - + -
50C TYR* 3.9 27.8 - - + +
92D SER* 4.6 9.6 - - - +
115D GLY 3.0 24.0 + - - +
116D THR* 3.6 4.7 - - - +
117D LYS 3.1 0.2 - - - -
118D ALA* 1.3 72.9 - - - +
120D THR* 1.3 56.6 + - + +
122D TYR* 2.7 25.6 + - + +
123D THR* 2.7 34.1 + - + +
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Residues in contact with THR 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D THR* 3.0 27.2 + - + +
117D LYS* 3.0 12.0 + - - +
119D VAL* 1.3 76.3 - - + +
121D LYS* 1.3 68.6 + - - +
123D THR* 2.9 26.8 + - - -
124D SER* 3.0 15.4 + - - -
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Residues in contact with LYS 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C SER 3.5 21.4 + - - -
20C ARG* 3.5 11.5 + - - +
21C ALA 3.7 19.3 - - - +
22C GLY* 4.1 8.1 - - - +
117D LYS* 3.0 15.9 + - + +
118D ALA* 3.8 4.9 - - - +
120D THR* 1.3 81.9 + - - +
122D TYR* 1.3 63.8 + - - +
124D SER* 3.2 21.7 + - - -
125D SER 3.8 5.2 - - - +
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Residues in contact with TYR 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ARG* 2.9 64.4 + - + -
20C ARG* 3.6 38.4 + - + -
21C ALA* 4.1 2.5 - - - -
45C ALA* 4.5 23.2 - - + +
46C GLY* 5.4 2.5 - - - -
49C VAL* 4.0 25.8 - - + -
118D ALA 3.0 14.5 + - - +
119D VAL* 2.7 15.8 + - + +
121D LYS* 1.3 72.4 - - - +
123D THR* 1.3 57.8 + - + -
124D SER 2.9 4.3 - - - -
125D SER* 2.6 31.0 + - - -
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Residues in contact with THR 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D VAL* 2.7 38.2 + - + +
120D THR* 2.9 20.2 + - - -
122D TYR* 1.3 74.3 - - + +
124D SER* 1.3 55.2 + - - +
125D SER* 2.8 12.7 + - - -
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Residues in contact with SER 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D THR 3.0 13.3 + - - -
121D LYS* 3.2 16.9 - - - -
122D TYR 2.9 1.4 + - - -
123D THR* 1.3 76.3 + - - +
125D SER* 1.3 70.4 + - - +
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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