Contacts of the helix formed by residues 114 - 130 (chain B) in PDB entry 2UZ8
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 THR 114 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B TYR 4.6 6.3 - - - +
60B LEU* 3.3 23.3 - - - +
62B GLY 4.8 0.2 - - - +
67B GLU* 4.4 15.3 - - - +
71B VAL* 3.8 15.0 - - + +
109B THR* 3.6 26.8 - - - +
112B ASN* 3.7 6.7 - - + +
113B PHE* 1.3 82.3 - - - +
115B LEU* 1.3 67.2 + - - +
116B ALA* 3.4 18.7 + - - +
117B ASP* 3.1 29.4 + - - +
118B ILE* 3.5 7.4 + - - +
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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
----------------------------------------------------------
10B LEU* 3.8 32.8 - - + -
48B ALA* 3.9 29.4 - - + +
49B ALA* 4.0 1.8 - - - +
52B VAL* 4.0 10.5 - - + -
60B LEU* 2.8 31.1 + - + +
61B LEU* 3.8 22.4 - - + -
71B VAL* 4.8 1.6 - - + -
75B LEU* 4.0 22.2 - - + -
114B THR* 1.3 70.4 - - - +
116B ALA* 1.3 63.0 + - - +
118B ILE* 3.1 12.4 + - + -
119B LEU* 3.0 34.1 + - + +
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Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 4.3 12.9 - - - +
74B TRP* 3.6 32.4 - - + +
75B LEU* 4.0 12.6 - - + +
108B LEU* 3.6 7.7 - - + +
109B THR* 4.0 10.1 - - + -
114B THR* 3.1 13.8 + - - +
115B LEU* 1.3 78.1 - - - +
117B ASP* 1.3 55.9 + - - +
119B LEU* 4.3 1.0 - - - +
120B LEU* 3.0 32.1 + - - +
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Residues in contact with ASP 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B TYR* 3.7 13.9 - - - +
108B LEU* 2.9 27.7 + - - +
109B THR 4.8 0.2 + - - -
112B ASN 3.9 0.9 - - - +
113B PHE* 3.7 12.1 - - + -
114B THR* 3.1 34.9 + - - +
116B ALA* 1.3 71.6 - - - +
118B ILE* 1.3 67.4 + - - +
120B LEU 3.5 0.2 + - - -
121B TYR* 3.0 25.8 + - - +
145B TRP* 2.9 35.8 + - - +
149B ILE* 4.0 17.3 - - + -
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Residues in contact with ILE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 4.0 24.2 - - + -
13B SER* 5.0 4.7 - - - +
14B LEU* 5.2 2.2 - - + -
60B LEU* 4.8 11.7 - - + -
113B PHE* 3.4 36.3 - - + -
114B THR 3.5 2.6 + - - +
115B LEU* 3.1 21.4 + - + +
117B ASP* 1.3 77.7 - - - +
119B LEU* 1.3 60.6 + - + +
121B TYR* 3.2 4.7 + - - +
122B TYR* 3.0 63.5 + - + +
149B ILE* 5.0 0.7 - - - -
155B ILE* 4.2 20.6 - - + -
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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
----------------------------------------------------------
6B GLU* 3.7 19.5 - - + +
10B LEU* 4.5 13.5 - - + -
44B LEU* 4.4 13.5 - - + -
45B THR* 4.2 17.0 - - + -
48B ALA* 3.8 23.1 - - + -
75B LEU* 3.9 23.1 - - + -
78B ARG* 2.9 38.2 + - + +
115B LEU* 3.0 30.4 + - + +
116B ALA 4.3 2.0 - - - +
118B ILE* 1.3 80.8 - - + +
120B LEU* 1.3 58.1 + - - +
122B TYR* 3.9 9.1 - - + -
123B GLY 3.0 11.4 + - - -
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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
----------------------------------------------------------
74B TRP* 4.5 6.5 - - + +
77B TYR* 3.8 26.9 - - + -
78B ARG* 4.6 10.7 - - + +
82B VAL* 3.8 17.5 - - + -
98B LEU* 4.1 13.5 - - + -
108B LEU* 3.7 32.5 - - + -
116B ALA 3.0 20.1 + - - +
117B ASP 4.1 0.4 - - - +
119B LEU* 1.3 75.1 - - - +
121B TYR* 1.3 61.1 - - - +
123B GLY 4.4 0.2 - - - +
124B LEU* 2.8 46.7 + - + +
145B TRP* 3.8 20.2 - - + -
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Residues in contact with TYR 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ASP 3.0 18.4 + - - +
118B ILE 3.4 2.0 - - - +
120B LEU* 1.3 73.7 - - - +
122B TYR* 1.3 93.2 + + - +
124B LEU 3.9 0.5 - - - -
125B HIS* 3.0 36.7 + + - +
145B TRP* 3.6 10.2 - - + -
146B PHE* 3.4 47.4 - + - -
149B ILE* 3.6 22.7 - - + -
150B GLN* 3.7 22.5 + - + +
155B ILE* 3.7 22.9 - - + -
156B ARG* 3.3 32.3 - - - +
159B LEU* 4.1 9.4 - - + +
160B SER 4.9 0.3 + - - -
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Residues in contact with TYR 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MSE 5.4 7.9 - - - +
6B GLU* 3.5 38.3 - - + +
9B LEU* 3.7 27.8 + - + +
10B LEU* 4.0 21.3 - - + -
13B SER* 2.8 20.3 + - - -
78B ARG* 4.4 0.7 - - - -
118B ILE* 3.0 36.8 + - + +
119B LEU* 4.0 5.2 - - + +
121B TYR* 1.3 97.6 - + - +
123B GLY* 1.3 62.0 + - - +
125B HIS* 3.7 14.0 + - - +
126B ARG* 5.0 1.4 + - - +
155B ILE* 2.7 31.7 + - + +
159B LEU* 3.6 15.2 - - + +
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Residues in contact with GLY 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLU* 5.1 0.2 - - - -
78B ARG* 3.6 32.7 - - - +
82B VAL* 3.6 18.5 - - - +
83B ASP* 5.3 0.2 - - - -
119B LEU 3.0 13.3 + - - -
120B LEU 3.7 1.1 - - - -
121B TYR 3.2 0.4 - - - -
122B TYR* 1.3 77.4 - - - +
124B LEU* 1.3 57.9 + - - +
125B HIS 3.4 0.4 + - - -
126B ARG* 4.2 8.8 - - - +
127B PHE* 3.9 10.0 - - - -
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TYR* 5.8 1.3 - - - +
82B VAL* 3.9 28.0 - - + -
91B ILE* 5.5 1.1 - - + -
94B LEU* 4.7 12.1 - - + -
95B LEU* 4.4 20.6 - - + -
98B LEU* 3.8 28.5 - - + -
120B LEU* 2.8 39.9 + - + +
121B TYR 4.4 1.3 - - - +
123B GLY* 1.3 71.8 - - - +
125B HIS* 1.3 65.2 + - - +
126B ARG 3.2 2.9 - - - -
127B PHE* 2.9 28.5 + - + +
128B ILE* 3.0 26.3 + - + +
142B VAL* 5.0 0.7 - - + -
145B TRP* 4.2 9.9 - - + -
146B PHE* 4.7 3.1 - - + -
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Residues in contact with HIS 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B TYR* 3.0 30.9 + + - +
122B TYR* 3.7 11.9 - - - +
123B GLY 3.4 1.8 - - - -
124B LEU* 1.3 76.5 - - - +
126B ARG* 1.3 60.4 + - - +
128B ILE* 4.1 0.3 - - - +
129B VAL* 3.0 48.6 + - + +
146B PHE* 3.7 27.4 - + - -
159B LEU* 3.8 25.9 - - + +
160B SER* 2.8 52.0 + - - -
162B VAL* 4.8 0.2 - - - +
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Residues in contact with ARG 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TYR 5.0 1.3 + - - +
123B GLY 4.2 7.9 - - - +
125B HIS* 1.3 82.8 + - - +
127B PHE* 1.3 102.6 + - + +
129B VAL* 3.8 5.9 - - - +
130B ASP* 3.6 27.0 + - - +
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Residues in contact with PHE 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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82B VAL* 4.2 21.1 - - + -
89B ASN* 6.0 2.9 - - + -
91B ILE* 3.6 52.8 - - + +
95B LEU* 5.3 4.3 - - + -
123B GLY 3.9 20.9 - - - -
124B LEU* 2.9 18.0 + - + +
126B ARG* 1.3 111.9 - - + +
128B ILE* 1.3 68.9 + - + +
130B ASP* 3.3 13.3 + - - +
131B LEU* 3.5 18.6 + - - +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 4.1 16.4 - - + -
124B LEU* 3.0 23.9 + - + +
125B HIS 4.1 0.2 - - - +
127B PHE* 1.3 74.3 - - + +
129B VAL* 1.3 65.9 + - - +
130B ASP 3.1 2.7 + - - -
131B LEU* 3.1 39.2 + - + +
136B LYS* 4.9 0.9 - - + +
142B VAL* 4.0 25.6 - - + -
143B SER* 6.1 1.3 - - - +
146B PHE* 3.6 48.0 - - + -
162B VAL* 4.2 9.6 - - + +
164B PHE* 3.9 17.9 - - + -
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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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125B HIS* 3.0 47.4 + - + +
126B ARG* 3.8 7.9 - - - +
128B ILE* 1.3 76.4 - - - +
130B ASP* 1.3 71.1 + - - +
131B LEU 3.5 5.9 + - - +
136B LYS* 5.6 1.0 + - - -
160B SER* 3.7 13.5 - - - +
162B VAL* 3.9 21.2 - - + +
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Residues in contact with ASP 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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126B ARG 3.6 16.5 + - - +
127B PHE* 3.3 9.0 + - - +
128B ILE 3.1 1.8 - - - -
129B VAL* 1.3 86.5 - - - +
131B LEU* 1.3 65.0 + - - +
132B THR* 3.7 4.9 + - - +
135B GLU* 4.5 2.1 - - - +
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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