Contacts of the helix formed by residues 128 - 147 (chain B) in PDB entry 3U53
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 PHE 128 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B LEU* 5.2 0.4 - - + -
82B TYR* 3.1 55.0 - + + -
83B VAL 5.8 0.9 - - - -
126B ALA 2.8 11.9 + - - +
127B GLN* 1.3 71.5 - - - +
129B LYS* 1.3 110.7 + - + +
130B GLU* 2.9 31.2 - - + -
131B MET* 3.4 17.9 + - + +
132B LYS* 3.1 26.5 + - - +
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Residues in contact with LYS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASN* 4.8 11.5 + - - -
127B GLN 3.4 1.8 + - - -
128B PHE* 1.3 102.3 - - + +
130B GLU* 1.3 72.9 + - + +
132B LYS* 3.4 11.8 + - - +
133B ALA* 3.0 24.5 + - - +
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ARG* 4.0 16.9 + - - +
80B LEU* 3.9 19.3 - - + +
81B ASN* 2.5 41.4 + - - +
82B TYR* 4.4 0.2 - - + -
128B PHE* 2.9 39.1 - - + -
129B LYS* 1.3 85.6 - - + +
131B MET* 1.3 61.1 + - - +
133B ALA* 3.5 5.4 + - - +
134B ALA* 3.0 23.7 + - - +
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Residues in contact with MET 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 5.7 1.3 - - + -
38B TRP 5.0 2.0 - - - +
39B THR* 4.5 10.3 - - - +
40B PRO* 3.8 24.5 - - + -
80B LEU* 3.8 16.7 - - + +
82B TYR* 6.1 0.9 - - + -
93B TYR* 3.1 48.7 - - + +
126B ALA* 4.1 19.7 - - + +
128B PHE* 3.4 22.6 + - + +
129B LYS 3.2 0.6 - - - -
130B GLU* 1.3 76.3 - - - +
132B LYS* 1.3 66.9 + - - +
134B ALA* 3.1 5.6 + - + +
135B LEU* 3.0 42.6 + - - +
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Residues in contact with LYS 132 (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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123B CYS* 3.5 51.3 - - + +
124B GLN* 4.8 4.4 - - - +
126B ALA* 4.9 0.9 - - + -
127B GLN* 3.4 26.6 + - - +
128B PHE 3.1 12.7 + - - +
129B LYS* 3.8 8.1 - - - +
131B MET* 1.3 75.8 - - - +
133B ALA* 1.3 57.4 + - - +
135B LEU* 3.3 5.5 + - - +
136B GLN* 2.8 45.3 + - - +
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Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ARG* 4.1 13.9 - - - +
129B LYS 3.0 17.0 + - - +
130B GLU* 3.5 7.6 - - - +
132B LYS* 1.3 78.3 - - - +
134B ALA* 1.3 56.6 + - - +
136B GLN* 3.2 12.5 + - - +
137B GLU* 2.8 41.0 + - - +
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 4.1 14.5 - - + +
76B PHE* 4.1 5.5 - - - -
78B ARG* 3.7 27.3 - - + +
80B LEU* 3.8 12.3 - - + -
93B TYR* 5.4 0.4 - - + -
130B GLU 3.0 14.9 + - - +
131B MET* 3.1 7.8 + - - +
133B ALA* 1.3 81.9 - - - +
135B LEU* 1.3 56.6 + - - +
137B GLU* 3.3 11.0 + - - +
138B GLY* 2.9 25.5 + - - -
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 3.9 34.1 - - + -
26B PHE* 4.2 22.9 - - + -
28B LEU* 4.7 7.4 - - + -
40B PRO* 4.9 6.7 - - + -
119B LEU* 3.5 19.0 - - + +
122B ALA* 4.1 31.4 - - + +
123B CYS* 4.4 2.5 - - - +
126B ALA* 4.3 11.0 - - + -
131B MET* 3.0 34.8 + - - +
132B LYS* 3.8 5.6 - - - +
134B ALA* 1.3 73.5 - - - +
136B GLN* 1.3 66.7 + - - +
138B GLY* 3.2 1.8 + - - -
139B HIS* 3.1 18.7 + - - +
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Residues in contact with GLN 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 3.8 17.6 - - + +
123B CYS* 3.6 27.7 - - - +
132B LYS* 2.8 30.7 + - - +
133B ALA* 3.5 9.2 - - - +
135B LEU* 1.3 79.9 - - - +
137B GLU* 1.3 61.8 + - - +
139B HIS* 3.4 3.5 + - - +
140B GLN* 3.2 23.0 + - - +
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B PHE* 4.0 11.2 - - + -
78B ARG* 2.8 43.8 + - - +
133B ALA* 2.8 33.5 + - - +
134B ALA* 3.6 10.8 - - - +
136B GLN* 1.3 75.0 - - - +
138B GLY* 1.3 59.7 + - - +
140B GLN* 3.3 14.9 + - - +
141B PHE* 2.9 30.7 + - - +
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Residues in contact with GLY 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 5.4 1.6 - - - -
26B PHE* 5.1 1.3 - - - -
76B PHE* 3.8 18.6 - - - -
95B LEU* 3.7 15.1 - - - +
134B ALA 2.9 16.7 + - - -
135B LEU* 3.2 3.7 + - - -
137B GLU* 1.3 77.4 - - - +
139B HIS* 1.3 56.4 - - - +
141B PHE* 3.3 5.0 + - - +
142B LEU* 3.0 33.0 + - - +
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Residues in contact with HIS 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 3.8 30.2 + - + +
26B PHE* 4.1 11.8 - + + -
119B LEU* 3.5 31.5 - - + +
135B LEU 3.1 9.0 + - - +
136B GLN 3.7 8.1 - - - +
138B GLY* 1.3 73.7 - - - +
140B GLN* 1.3 59.2 + - - +
142B LEU* 2.8 27.4 + - + +
143B CYS* 2.8 34.8 + - - -
156B SO4 3.0 43.9 + - - -
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Residues in contact with GLN 140 (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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136B GLN 3.2 9.6 + - - +
137B GLU* 3.4 19.9 - - + +
139B HIS* 1.3 79.7 + - - +
141B PHE* 1.3 64.0 + - - +
143B CYS* 3.5 7.3 + - - +
144B SER* 3.1 24.0 + - - -
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Residues in contact with PHE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 3.5 27.1 - - + -
74B GLU 3.4 21.8 - - - -
75B GLY* 3.6 23.1 - - - -
76B PHE* 3.8 23.3 - + + -
95B LEU* 3.7 15.9 - - + -
137B GLU 2.9 13.7 + - - +
138B GLY 3.4 7.2 - - - +
140B GLN* 1.3 78.9 - - - +
142B LEU* 1.3 64.8 + - + +
144B SER* 2.9 25.2 + - - -
145B ILE* 3.1 38.4 + - + +
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Residues in contact with LEU 142 (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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11B PHE* 3.8 49.6 - - + -
13B ARG* 4.6 15.1 + - - +
24B ILE* 4.3 24.7 - - + -
26B PHE* 4.7 1.8 - - + -
73B ILE* 4.5 11.4 - - + -
95B LEU* 3.9 20.6 - - + -
138B GLY 3.0 18.4 + - - +
139B HIS* 2.8 14.5 + - - +
141B PHE* 1.3 79.1 - - + +
143B CYS* 1.3 64.6 + - - +
145B ILE* 3.6 5.7 + - + +
146B GLU* 3.3 21.1 + - - +
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Residues in contact with CYS 143 (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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24B ILE* 6.0 1.8 - - - -
139B HIS* 2.8 49.7 + - - +
140B GLN* 4.0 6.3 - - - +
142B LEU* 1.3 71.7 - - - +
144B SER* 1.3 62.0 + - - +
146B GLU* 3.3 7.2 + - - +
147B ALA* 3.1 20.4 + - - +
156B SO4 4.9 3.4 - - - -
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Residues in contact with SER 144 (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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140B GLN* 3.1 17.9 + - - -
141B PHE* 2.9 15.2 + - - -
142B LEU 3.3 0.2 - - - -
143B CYS* 1.3 73.6 - - - +
145B ILE* 1.3 79.3 + - - +
147B ALA* 3.1 25.5 + - - +
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Residues in contact with ILE 145 (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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73B ILE* 5.5 5.4 - - + -
141B PHE* 3.1 49.1 + - + +
142B LEU* 4.0 6.5 - - + +
144B SER* 1.3 88.6 + - - +
146B GLU* 1.3 64.2 + - - +
147B ALA 3.3 9.2 + - - +
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Residues in contact with GLU 146 (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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13B ARG* 5.8 7.9 - - - +
142B LEU 3.3 12.1 + - - +
143B CYS* 3.7 9.9 - - - +
144B SER 3.1 0.8 - - - -
145B ILE* 1.3 81.1 - - - +
147B ALA* 1.3 63.7 + - - +
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Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B CYS 3.1 10.1 + - - +
144B SER* 3.1 18.6 + - - +
145B ILE 3.3 11.5 - - - +
146B GLU* 1.3 81.4 - - - +
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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
------------------------------------------------------------
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