Contacts of the helix formed by residues 104 - 123 (chain B) in PDB entry 5T8Y
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 ASP 104 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LYS* 1.3 73.5 - - - +
105B TYR* 1.3 66.8 + - - +
106B HIS* 3.1 35.3 + - - +
107B ASP* 2.9 39.6 + - - +
108B VAL* 3.3 9.2 + - - +
289B HIS* 2.8 17.6 + - - +
290B VAL 3.9 4.3 - - - +
291B SER* 3.1 40.0 - - - +
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Residues in contact with TYR 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ALA* 3.7 17.5 - - + -
103B LYS 3.2 5.5 + - - +
104B ASP* 1.3 74.3 + - - +
106B HIS* 1.3 95.4 + + - +
107B ASP 3.1 2.5 - - - -
108B VAL* 3.8 10.1 - - + -
109B LEU* 3.0 35.1 + - + +
168B TYR* 3.4 60.3 - + + -
261B MET* 6.0 0.4 - - - -
291B SER* 3.6 20.4 - - - -
503B B12 3.9 43.3 - - + +
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Residues in contact with HIS 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ASP* 3.1 25.2 + - - +
105B TYR* 1.3 121.6 - + - +
107B ASP* 1.3 59.7 + - - +
109B LEU* 5.1 0.8 - - - +
110B ARG* 3.2 23.6 + - - +
291B SER* 5.7 1.1 - - - -
294B TRP* 6.4 2.2 - - + -
508B PO4 3.4 29.6 + - - -
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Residues in contact with ASP 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LYS* 4.0 26.1 - - - +
104B ASP* 2.9 30.4 + - - +
106B HIS* 1.3 83.5 - - - +
108B VAL* 1.3 64.5 + - - +
109B LEU 3.4 0.2 - - - -
110B ARG* 3.7 4.4 - - - +
111B GLU* 3.1 24.4 + - - +
289B HIS* 5.7 3.8 + - - -
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Residues in contact with VAL 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 3.7 26.5 - - + -
103B LYS* 4.2 20.2 - - + +
104B ASP 3.3 12.9 + - - +
105B TYR* 4.1 8.3 - - - +
107B ASP* 1.3 77.4 - - - +
109B LEU* 1.3 64.5 + - + +
111B GLU* 3.3 7.4 + - - +
112B LYS* 3.2 33.6 + - - +
258B HIS* 5.9 0.2 - - - +
260B GLU* 3.5 38.8 - - + +
261B MET* 4.6 11.2 - - + -
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 4.6 2.2 - - + +
75B LEU* 3.8 34.5 - - + -
105B TYR* 3.0 27.2 + - + +
106B HIS* 5.1 0.9 - - - +
108B VAL* 1.3 80.4 - - + +
110B ARG* 1.3 64.1 + - - +
112B LYS* 3.4 6.5 + - - +
113B LEU* 3.0 31.1 + - - +
168B TYR* 3.7 32.3 - - + +
169B LEU 3.3 35.9 - - - +
170B ALA* 3.6 14.8 - - + +
503B B12 5.3 0.2 - - - +
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Residues in contact with ARG 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B HIS 3.2 22.7 + - - +
107B ASP* 3.5 6.7 + - - +
108B VAL 3.3 0.6 - - - -
109B LEU* 1.3 78.3 - - - +
111B GLU* 1.3 61.4 + - - +
113B LEU* 3.5 10.1 + - - +
114B ASP* 2.3 72.3 + - - +
117B GLU* 4.8 3.4 + - - -
131B SER* 4.2 24.2 + - - -
132B MET 5.4 7.4 - - - -
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Residues in contact with GLU 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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107B ASP 3.1 17.1 + - - +
108B VAL* 3.5 6.2 - - - +
109B LEU 3.2 0.2 - - - -
110B ARG* 1.3 77.6 - - - +
112B LYS* 1.3 90.7 + - - +
114B ASP* 3.5 8.8 + - - +
115B LEU* 3.1 47.1 + - + +
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Residues in contact with LYS 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE* 2.3 52.5 + - + +
18B GLY* 4.3 6.2 - - - -
19B VAL* 4.7 5.8 - - + -
73B ILE* 4.2 14.8 - - + -
75B LEU* 4.4 18.6 - - + -
108B VAL* 3.2 27.5 + - - +
109B LEU* 3.7 7.6 - - - +
111B GLU* 1.3 94.7 + - - +
113B LEU* 1.3 65.0 + - - +
115B LEU* 3.2 9.4 + - + +
116B LEU* 3.1 27.8 + - - +
258B HIS* 5.6 3.5 + - - -
260B GLU* 5.5 3.3 + - - -
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL 5.3 0.7 - - - +
73B ILE* 3.8 26.9 - - + -
109B LEU 3.0 22.6 + - - +
110B ARG* 3.9 10.8 - - - +
112B LYS* 1.3 76.4 - - - +
114B ASP* 1.3 58.5 + - - +
116B LEU* 3.3 13.9 + - + +
117B GLU* 2.9 33.3 + - - +
131B SER* 3.7 30.1 - - - +
132B MET 4.3 11.0 - - - +
170B ALA* 3.9 14.6 - - + -
171B GLU 3.8 16.2 - - - +
172B MET* 4.0 22.5 - - + +
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Residues in contact with ASP 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ARG* 2.3 60.2 + - - +
111B GLU* 3.7 9.2 - - + +
112B LYS 3.2 0.2 - - - -
113B LEU* 1.3 77.3 - - - +
115B LEU* 1.3 59.9 + - + +
117B GLU* 3.3 12.8 + - - +
118B ASP* 2.8 40.5 + - - +
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B TYR* 3.8 21.6 + - - +
17B ILE* 3.9 35.4 - - + -
111B GLU* 3.1 42.2 - - + +
112B LYS* 3.2 9.6 + - + +
114B ASP* 1.3 80.5 - - + +
116B LEU* 1.3 56.5 + - - +
118B ASP* 3.3 9.7 + - + +
119B PHE* 2.9 27.9 + - - +
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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
----------------------------------------------------------
10B LEU* 3.8 22.7 - - + -
13B TYR* 3.9 20.0 - - + -
14B ALA* 4.0 21.3 - - + -
17B ILE* 4.0 9.0 - - + -
19B VAL* 4.8 5.4 - - + -
22B ILE* 5.3 3.6 - - + -
71B VAL* 5.5 1.1 - - + -
73B ILE* 4.1 25.6 - - + -
112B LYS 3.1 15.7 + - - +
113B LEU* 3.8 16.8 - - + +
114B ASP 3.3 0.2 - - - -
115B LEU* 1.3 73.6 - - - +
117B GLU* 1.3 64.9 + - - +
119B PHE* 3.4 6.3 + - - +
120B LEU* 3.2 28.1 + - - +
172B MET* 4.2 21.8 - - + -
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ARG* 4.8 1.9 + - - -
113B LEU 2.9 21.0 + - - +
114B ASP* 3.6 15.1 - - - +
115B LEU 3.2 0.2 - - - -
116B LEU* 1.3 74.3 - - - +
118B ASP* 1.3 61.0 + - - +
119B PHE 3.3 0.2 + - - -
120B LEU* 3.3 4.2 + - - +
121B LYS* 2.9 43.8 + - - +
129B THR* 3.4 28.5 + - - +
130B LYS* 3.9 4.3 - - - -
131B SER* 2.3 38.7 + - - +
172B MET* 3.6 15.5 - - - -
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Residues in contact with ASP 118 (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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114B ASP* 2.8 32.3 + - - +
115B LEU* 3.6 10.5 - - + +
117B GLU* 1.3 78.5 - - - +
119B PHE* 1.3 60.7 + - - +
121B LYS* 4.0 5.8 - - - +
122B SER* 3.1 25.3 + - - -
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Residues in contact with PHE 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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6B LEU* 4.1 8.3 - - + -
9B GLU* 3.7 20.4 - - + -
10B LEU* 3.9 28.9 - - + -
13B TYR* 3.8 34.1 - + + -
115B LEU 2.9 13.4 + - - +
116B LEU 3.4 7.6 - - - +
117B GLU 3.1 0.2 - - - -
118B ASP* 1.3 77.6 - - - +
120B LEU* 1.3 81.9 + - + +
122B SER* 2.4 26.6 + - - -
123B LYS* 3.3 46.2 + - + +
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Residues in contact with LEU 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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6B LEU* 4.0 28.7 - - + -
10B LEU* 4.5 15.3 - - + -
116B LEU 3.2 17.1 + - - +
117B GLU 3.9 3.1 - - - +
119B PHE* 1.3 99.9 - - + +
121B LYS* 1.3 64.4 - - + +
122B SER 3.3 0.5 + - - -
123B LYS* 3.4 9.1 + - - +
124B HIS 3.3 17.7 + - - +
127B ILE* 3.3 20.3 - - + +
129B THR* 4.1 20.2 - - + -
172B MET* 4.3 17.3 - - + -
174B THR* 4.4 3.8 - - + -
176B ILE* 3.9 19.7 - - + -
178B PHE* 5.1 0.9 - - + -
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Residues in contact with LYS 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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117B GLU* 2.9 33.5 + - - +
118B ASP* 4.0 7.2 - - - +
120B LEU* 1.3 81.7 - - + +
122B SER* 1.3 62.4 + - - +
123B LYS 3.5 0.2 + - - -
124B HIS 4.0 9.7 - - - +
125B GLU* 4.1 17.4 - - - +
127B ILE* 3.2 30.5 - - + +
128B ARG* 4.6 0.7 - - - +
129B THR* 3.3 29.5 + - - +
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Residues in contact with SER 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASP 3.1 14.4 + - - -
119B PHE* 2.4 27.9 + - - -
121B LYS* 1.3 78.7 - - - +
123B LYS* 1.3 68.4 + - - +
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Residues in contact with LYS 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.8 21.5 - - + +
9B GLU* 2.4 41.9 + - - +
119B PHE* 3.3 42.9 + - + +
120B LEU 3.4 6.1 + - - +
121B LYS 3.3 1.7 - - - +
122B SER* 1.3 88.5 + - - +
124B HIS* 1.3 81.4 + - + +
125B GLU* 3.8 5.0 + - - +
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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