Contacts of the helix formed by residues 113 - 131 (chain B) in PDB entry 4DKE
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 HIS 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A HIS 3.3 11.7 + - - +
57A TYR* 3.1 36.0 + - - -
58A PHE 4.5 4.6 - - - -
59A PRO* 5.2 1.8 - - - +
57B TYR* 3.4 19.6 + - + -
58B PHE* 4.6 6.2 - + - -
109B LEU* 3.7 38.5 - - + +
110B LEU 2.8 15.4 + - - +
111B GLU 3.1 0.9 + - - +
112B GLY* 1.3 78.3 - - - +
114B PRO* 1.3 70.2 - - + +
115B SER* 2.9 47.5 + - - -
116B TRP* 2.8 28.7 + - + +
117B LYS* 4.1 1.6 + - - +
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Residues in contact with PRO 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A TYR* 3.4 31.6 - - + +
114A PRO* 3.8 20.0 - - + -
53B TYR* 3.8 15.1 - - + -
57B TYR* 4.1 22.4 - - + -
112B GLY 4.7 0.4 - - - +
113B HIS* 1.3 99.9 - - + +
115B SER* 1.3 58.1 + - - +
116B TRP 3.0 6.4 + - - -
117B LYS* 4.0 10.5 + - + +
118B TYR 4.0 4.0 + - - -
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Residues in contact with SER 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 2.6 44.0 + - - -
54B MET* 3.8 14.8 - - - -
57B TYR* 3.6 6.1 - - - +
58B PHE* 4.5 1.3 - - - -
109B LEU* 4.3 6.7 - - - -
113B HIS* 2.9 23.6 + - - -
114B PRO* 1.3 75.3 - - - +
116B TRP* 1.3 58.0 + - - +
117B LYS 3.5 0.2 - - - -
118B TYR* 3.7 2.6 - - - +
119B LEU* 3.0 35.2 + - - +
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Residues in contact with TRP 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B GLN* 3.3 57.6 + - + +
109B LEU* 3.6 10.1 - - + -
110B LEU 3.9 9.4 - - - -
111B GLU* 3.1 41.5 - - + +
113B HIS* 2.8 27.2 + - + +
114B PRO 3.0 0.6 - - - -
115B SER* 1.3 75.4 - - - +
117B LYS* 1.3 67.3 + - + +
119B LEU* 3.4 0.5 + - - +
120B GLN* 3.1 17.7 + - - +
99I GLY* 3.6 4.7 - - - -
100I SER* 3.3 56.3 - + - -
91M SER 4.0 11.9 - - - -
92M PHE* 3.2 43.0 + + - -
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Residues in contact with LYS 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B HIS 4.1 1.3 + - - +
114B PRO 4.0 7.0 + - - +
116B TRP* 1.3 77.5 - - + +
118B TYR* 1.3 67.3 + - - +
120B GLN* 3.0 5.2 + - + +
121B GLU* 2.6 53.4 + - + +
28M ASP* 5.0 19.0 + - - -
30M SER* 6.2 2.2 - - - -
92M PHE* 3.9 31.9 - - + -
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Residues in contact with TYR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LYS* 2.7 47.0 + - - -
45B LEU* 3.5 16.5 - - - +
49B SER* 3.9 9.8 - - - -
50B ARG* 4.1 5.5 + - - +
53B TYR* 3.0 69.5 - + + -
54B MET* 4.4 7.9 - - + -
114B PRO 4.0 1.8 + - - -
115B SER 3.5 7.7 + - - +
116B TRP 3.3 0.6 - - - -
117B LYS* 1.3 80.3 - - - +
119B LEU* 1.3 60.9 + - + +
121B GLU* 3.2 10.1 + - - +
122B VAL* 2.9 51.0 + - + +
165B LEU* 3.9 19.3 - - + -
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B MET* 4.1 24.5 - - + -
102B THR* 3.7 41.5 - - + +
105B VAL* 3.6 33.2 - - + -
106B GLN* 4.1 18.8 - - + +
109B LEU* 4.0 15.3 - - + -
115B SER 3.0 23.2 + - - +
116B TRP 3.8 3.4 - - - +
118B TYR* 1.3 78.7 - - + +
120B GLN* 1.3 57.9 + - - +
122B VAL* 3.7 5.6 - - + +
123B GLU* 2.8 29.8 + - - +
165B LEU* 4.7 9.9 - - + -
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Residues in contact with GLN 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B GLN* 3.1 20.5 + - - +
116B TRP 3.1 10.6 + - - +
117B LYS* 3.0 12.0 + - + +
119B LEU* 1.3 74.0 - - - +
121B GLU* 1.3 55.7 + - + +
123B GLU* 2.8 23.7 + - - +
124B THR* 2.8 36.0 + - - +
100I SER* 3.0 30.9 + - - -
30M SER* 3.5 25.6 - - - +
31M THR* 3.5 24.4 - - + +
32M ALA* 4.6 3.6 - - - +
92M PHE* 3.4 19.1 - - + -
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Residues in contact with GLU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LYS* 2.8 34.0 + - - -
117B LYS* 2.6 50.5 + - + +
118B TYR* 3.5 10.6 - - - +
120B GLN* 1.3 80.1 - - + +
122B VAL* 1.3 63.5 + - - +
123B GLU 3.0 0.9 + - - -
124B THR* 3.0 19.5 + - - -
125B LEU* 3.2 22.7 + - + +
30M SER* 6.0 4.7 - - - -
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 4.1 12.5 - - + +
44B LYS* 4.7 11.2 - - + +
45B LEU* 4.3 22.0 - - + -
102B THR* 3.8 19.1 - - + -
118B TYR* 2.9 59.6 + - + +
119B LEU* 3.7 7.6 - - + +
121B GLU* 1.3 71.9 - - - +
123B GLU* 1.3 60.3 + - - +
125B LEU* 3.8 6.0 + - - -
126B LEU* 3.1 29.8 + - + +
165B LEU* 5.0 5.8 - - + -
168B CYS* 6.1 0.2 - - - -
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Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 4.2 11.1 - - + +
102B THR* 4.0 15.6 + - - +
103B GLU* 3.3 32.6 + - - +
106B GLN* 4.1 14.3 - - - +
119B LEU 2.8 15.7 + - - +
120B GLN* 2.8 33.5 + - - +
122B VAL* 1.3 76.2 - - - +
124B THR* 1.3 64.1 + - - +
126B LEU* 3.2 12.7 + - - +
127B LEU* 3.1 27.6 + - + +
98I LYS 5.5 0.2 - - - +
100I LYS* 4.1 14.7 + - - +
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Residues in contact with THR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B GLN* 2.8 23.3 + - - +
121B GLU* 3.0 9.3 + - - -
123B GLU* 1.3 71.0 - - - +
125B LEU* 1.3 63.0 + - + +
127B LEU* 2.7 41.7 + - + +
128B ASN* 3.1 19.2 + - - +
30M SER* 6.0 0.7 - - - -
31M THR* 4.1 24.3 - - + +
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B VAL* 3.8 8.4 - - + +
40B PHE* 4.2 24.7 - - + -
41B LEU* 3.8 24.9 - - + +
44B LYS* 3.6 32.5 - - + -
121B GLU* 3.2 20.1 + - + +
122B VAL* 4.9 0.2 - - - -
124B THR* 1.3 83.7 - - + +
126B LEU* 1.3 61.0 + - - +
127B LEU 3.5 0.2 + - - -
128B ASN* 3.6 25.6 + - - +
129B VAL* 3.5 18.4 + - - +
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 4.5 19.7 - - + -
94B TRP* 4.5 7.4 - - + -
95B VAL* 3.4 29.9 - - + +
98B SER* 3.3 38.6 - - - +
99B LEU* 3.5 13.7 - - + +
102B THR* 3.8 25.6 - - + -
122B VAL* 3.1 27.6 + - + +
123B GLU* 3.2 9.8 + - - +
124B THR 3.1 0.4 - - - -
125B LEU* 1.3 77.4 - - - +
127B LEU* 1.3 64.3 + - - +
129B VAL* 3.3 20.3 - - - +
130B GLN* 3.5 1.6 + - - +
168B CYS* 4.5 6.1 - - - -
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LEU* 4.1 18.4 - - + -
123B GLU* 3.1 25.8 + - + +
124B THR* 2.7 21.9 + - + +
126B LEU* 1.3 74.0 - - - +
128B ASN* 1.3 57.6 + - - +
129B VAL 3.0 1.8 - - - -
130B GLN* 2.7 48.7 + - + +
131B GLN* 3.2 10.0 + - - +
31M THR* 6.4 2.0 - - + -
53M PHE* 4.5 31.4 - - + -
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Residues in contact with ASN 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B VAL* 3.9 22.8 - - + +
124B THR* 3.1 21.8 + - - +
125B LEU* 3.6 24.6 - - - +
126B LEU 3.4 0.2 - - - -
127B LEU* 1.3 77.5 - - - +
129B VAL* 1.3 62.0 + - - +
131B GLN* 3.4 34.5 + - - +
132B GLY* 4.0 2.1 + - - -
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Residues in contact with VAL 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B GLU* 5.8 2.2 - - - +
37B VAL* 3.8 17.9 - - + -
38B THR* 4.3 16.8 - - + -
41B LEU* 4.6 8.7 - - + -
91B ARG* 5.6 1.6 - - + +
94B TRP* 4.6 7.9 - - + -
95B VAL* 4.1 15.5 - - + -
125B LEU 3.5 15.3 - - - +
126B LEU* 3.3 12.6 - - - +
127B LEU 3.0 0.6 - - - -
128B ASN* 1.3 75.9 - - - +
130B GLN* 1.3 58.8 + - - +
132B GLY* 2.9 18.2 + - - -
133B LEU* 3.1 28.7 - - + +
176B TYR* 4.3 16.8 - - - +
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Residues in contact with GLN 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B TYR* 4.5 15.8 + - + -
95B VAL* 4.2 23.3 - - + -
96B LEU* 3.2 27.3 - - - +
99B LEU* 4.1 11.5 - - + +
126B LEU 3.5 1.2 + - - -
127B LEU* 2.7 38.7 + - + +
129B VAL* 1.3 69.2 - - - +
131B GLN* 1.3 55.1 + - - +
132B GLY 2.9 5.8 - - - -
133B LEU* 3.0 32.3 + - + -
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Residues in contact with GLN 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B LEU* 3.2 8.9 + - - +
128B ASN* 3.6 30.6 + - - +
129B VAL 3.3 0.2 - - - -
130B GLN* 1.3 76.2 - - + +
132B GLY* 1.3 57.3 + - - +
133B LEU 3.3 2.5 + - - -
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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