Contacts of the helix formed by residues 104 - 116 (chain B) in PDB entry 3RKR
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 LYS 104 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B THR 4.5 7.5 + - - +
103B MET* 1.3 71.8 - - - +
105B PRO* 1.3 75.9 - - + +
106B ALA* 4.4 5.6 - - + +
107B GLU* 2.8 44.7 + - + +
108B TRP 2.9 10.4 + - - -
120C TYR* 3.2 6.1 + - - -
124C ARG* 4.3 13.2 - - - +
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Residues in contact with PRO 105 (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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104B LYS* 1.3 86.3 - - + +
106B ALA* 1.3 51.5 + - - +
108B TRP* 3.1 5.9 + - + +
109B ASP* 2.8 38.6 + - - -
67C SER* 5.9 0.2 - - - -
117C LYS* 4.9 0.4 - - - +
120C TYR* 3.1 13.9 - - + +
121C LEU* 4.3 13.9 - - + -
124C ARG* 3.5 28.9 - - - +
241C SO4 3.3 39.0 - - - +
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Residues in contact with ALA 106 (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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104B LYS* 3.2 3.8 - - + +
105B PRO* 1.3 77.9 - - - +
107B GLU* 1.3 59.7 + - + +
109B ASP* 3.5 10.5 + - - +
110B ALA* 3.1 28.4 + - - +
241C SO4 4.3 4.1 + - - +
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Residues in contact with GLU 107 (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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95B TRP* 3.0 44.2 + - + +
102B THR 4.4 1.2 - - - +
103B MET* 3.7 10.9 - - + +
104B LYS* 2.8 51.5 + - + +
106B ALA* 1.3 77.2 - - + +
108B TRP* 1.3 66.1 + - - +
110B ALA* 3.4 5.6 + - - +
111B LEU* 3.1 24.8 + - - +
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Residues in contact with TRP 108 (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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100B LEU* 4.5 0.4 - - + -
103B MET* 3.8 14.2 - - - +
104B LYS 2.9 8.8 + - - +
105B PRO 3.1 7.4 + - - +
107B GLU* 1.3 76.7 - - - +
109B ASP* 1.3 80.8 + - - +
111B LEU* 3.2 3.3 + - - +
112B ILE* 3.0 53.8 + - + +
155B ALA* 3.7 24.0 - - + -
158B ALA* 5.0 1.3 - - + -
112C ILE* 5.7 2.3 - - + +
116C LEU* 3.9 33.4 - - + -
117C LYS* 3.5 42.7 - - + +
120C TYR* 3.5 40.4 - + + +
166C LEU* 3.6 30.7 - - + -
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Residues in contact with ASP 109 (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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105B PRO 2.8 19.7 + - - +
106B ALA* 3.7 7.7 - - - +
107B GLU 3.4 0.2 - - - -
108B TRP* 1.3 82.9 - - - +
110B ALA* 1.3 57.5 + - - +
112B ILE* 4.2 2.8 - - - +
113B ALA* 2.9 34.3 + - - +
117C LYS* 2.7 27.0 + - - +
241C SO4 3.1 23.4 + - - -
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Residues in contact with ALA 110 (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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65B SER* 5.6 3.1 - - - -
93B VAL* 3.9 5.0 - - + +
106B ALA 3.1 16.9 + - - +
107B GLU* 4.0 6.1 - - - +
109B ASP* 1.3 76.7 - - - +
111B LEU* 1.3 63.2 + - - +
113B ALA* 4.0 4.5 - - - +
114B VAL* 3.7 24.4 + - - +
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Residues in contact with LEU 111 (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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93B VAL* 3.7 17.0 - - + +
94B GLY 4.0 7.0 - - - +
95B TRP* 3.8 37.5 - - + +
103B MET* 4.5 6.3 - - + -
107B GLU 3.1 17.9 + - - +
108B TRP 3.8 2.5 - - - +
110B ALA* 1.3 77.4 - - - +
112B ILE* 1.3 63.6 + - + +
114B VAL* 3.5 1.4 + - - -
115B ASN* 2.9 42.2 + - - +
155B ALA* 3.6 28.9 - - + +
156B TYR* 3.9 15.7 - - + +
159B SER* 3.6 21.1 - - - +
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Residues in contact with ILE 112 (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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108B TRP* 3.0 60.5 + - + +
109B ASP* 4.2 2.9 - - - +
111B LEU* 1.3 81.1 - - + +
113B ALA* 1.3 66.0 + - - +
115B ASN* 4.9 0.2 - - - -
116B LEU* 2.9 37.9 + - + +
117B LYS* 3.0 14.2 + - + +
155B ALA 4.5 4.3 - - - +
158B ALA* 5.3 0.7 - - + -
159B SER* 4.1 24.9 - - - +
108C TRP* 5.7 2.2 - - + +
112C ILE* 4.7 15.5 - - + -
116C LEU* 4.4 12.8 - - + -
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Residues in contact with ALA 113 (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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64B LEU 4.0 5.0 - - - +
65B SER* 4.0 28.0 - - - +
109B ASP 2.9 21.0 + - - +
110B ALA* 4.0 4.9 - - - +
112B ILE* 1.3 78.9 - - - +
114B VAL* 1.3 57.0 + - - +
117B LYS* 3.7 15.5 - - + +
118B ALA* 2.9 29.8 + - - +
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Residues in contact with VAL 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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64B LEU* 4.6 7.6 - - + +
65B SER* 4.5 13.5 - - - +
91B ALA* 4.0 17.1 - - + +
92B GLY* 4.0 18.4 - - - +
93B VAL* 4.3 11.9 - - + +
110B ALA 3.7 14.8 + - - +
111B LEU 3.5 2.5 + - - +
112B ILE 3.3 0.2 - - - -
113B ALA* 1.3 76.4 - - - +
115B ASN* 1.3 77.0 + - - +
116B LEU 3.4 0.2 - - - -
118B ALA* 3.6 8.3 - - - +
119B PRO* 3.3 18.7 - - - +
240B NAP 3.8 36.1 - - + +
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Residues in contact with ASN 115 (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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91B ALA 5.1 2.2 - - - -
92B GLY* 3.3 7.8 - - - -
93B VAL 2.8 45.8 + - - -
111B LEU* 2.9 28.8 + - - +
114B VAL* 1.3 77.3 - - - +
116B LEU* 1.3 57.8 + - - +
119B PRO* 3.5 13.7 - - - +
156B TYR* 3.8 3.0 - - - -
159B SER* 3.1 38.3 + - - +
160B LYS* 3.8 23.3 + - - +
163B LEU* 4.3 12.0 - - - +
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Residues in contact with LEU 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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112B ILE* 2.9 25.8 + - + +
114B VAL 3.4 0.6 - - - -
115B ASN* 1.3 79.8 - - - +
117B LYS* 1.3 65.6 + - - +
118B ALA 3.5 0.7 - - - -
119B PRO* 3.5 7.6 - - - +
120B TYR 3.8 5.9 + - - -
158B ALA 5.1 0.2 - - - +
159B SER* 3.9 15.5 - - - +
162B GLY* 3.6 14.6 - - - +
163B LEU* 3.5 33.7 - - + +
166B LEU* 3.8 10.0 - - + +
108C TRP* 3.7 31.4 - - + -
112C ILE* 4.4 7.6 - - + -
116C LEU* 3.9 27.4 - - + -
158C ALA* 4.4 6.5 - - + +
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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
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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