Contacts of the helix formed by residues 128 - 142 (chain B) in PDB entry 5BZZ
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 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B CYS* 3.4 6.5 - - - -
126B ALA* 4.1 19.5 - - + +
127B GLY* 1.3 75.3 - - - +
129B GLY* 1.3 54.3 + - - +
130B ARG 3.6 0.4 - - - -
132B GLY* 2.8 32.1 + - - -
155B TYR* 2.9 11.4 + - - -
159B ARG* 5.4 0.7 - - + -
160B THR* 5.0 7.6 - - + -
164B LYS* 3.4 22.6 + - - +
165B GLY* 2.8 29.2 - - - +
167B THR* 3.2 27.4 + - - +
168B ILE* 6.1 0.2 - - - +
401B TLA 3.8 17.1 + - - +
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Residues in contact with GLY 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LYS* 1.3 80.1 - - - +
130B ARG* 1.3 56.8 + - - +
132B GLY* 3.3 1.0 + - - -
133B VAL* 2.9 33.3 + - - +
165B GLY 4.1 10.1 - - - -
166B VAL* 3.8 6.6 - - - +
167B THR 5.6 0.2 - - - -
171B GLN* 3.4 20.9 - - - -
401B TLA 2.9 18.3 + - - -
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Residues in contact with ARG 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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70B LEU* 3.4 19.0 + - + -
71B CYS* 3.8 3.0 - - - +
73B GLU* 2.8 37.6 + - - -
90B PHE* 2.7 61.4 + - + -
91B GLU 3.6 15.3 - - - +
92B ASP* 3.4 14.3 + - - +
124B CYS* 3.9 13.7 - - + +
125B LYS* 3.3 13.9 - - - +
129B GLY* 1.3 70.9 - - - +
131B THR* 1.3 67.2 + - - +
132B GLY 3.3 0.2 + - - -
133B VAL* 3.3 4.9 + - - +
134B MET* 3.3 26.5 + - - +
171B GLN* 3.9 14.1 - - - +
401B TLA 3.1 40.7 + - - +
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Residues in contact with THR 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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34B ALA* 3.7 13.5 - - + -
70B LEU* 3.7 10.0 - - - +
122B ILE* 3.5 24.2 - - + +
123B HIS 3.5 2.9 + - - -
124B CYS* 2.9 38.9 + - - -
127B GLY* 3.5 7.7 - - - -
130B ARG* 1.3 76.9 - - - +
132B GLY* 1.3 56.8 + - - +
134B MET* 3.4 2.9 + - - +
135B ILE* 2.9 52.1 + - + +
155B TYR* 3.9 7.6 - - - +
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Residues in contact with GLY 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LYS 2.8 21.0 + - - -
129B GLY 3.5 1.3 - - - -
131B THR* 1.3 74.7 - - - +
133B VAL* 1.3 58.4 + - - +
136B CYS* 3.0 36.4 + - - +
155B TYR* 3.4 26.4 + - - -
166B VAL* 3.8 9.6 - - - -
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Residues in contact with VAL 133 (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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90B PHE* 5.1 0.2 - - + -
96B PRO* 3.7 34.5 - - + -
101B ILE* 5.0 5.4 - - + -
129B GLY 2.9 23.6 + - - +
130B ARG* 3.3 8.3 + - - +
132B GLY* 1.3 72.1 - - - +
134B MET* 1.3 63.4 + - + +
136B CYS* 3.8 1.2 - - - +
137B ALA* 2.8 31.8 + - + +
166B VAL* 3.9 4.2 - - + +
171B GLN* 3.6 41.3 - - + +
174B TYR* 4.7 4.9 - - + -
175B VAL* 3.8 21.3 - - + +
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Residues in contact with MET 134 (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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70B LEU* 3.6 21.1 - - + -
88B TYR* 4.9 0.7 - - + -
90B PHE* 3.8 19.5 - - + -
96B PRO* 4.3 16.2 - - - -
100B LEU* 4.3 14.4 - - + +
101B ILE* 4.2 18.8 - - + -
104B PHE* 3.2 66.3 - - + -
122B ILE* 4.9 1.1 - - + -
130B ARG 3.3 13.8 + - - +
131B THR 3.7 5.8 - - - +
132B GLY 3.2 0.4 - - - -
133B VAL* 1.3 77.9 - - - +
135B ILE* 1.3 60.9 + - - +
137B ALA* 3.5 3.8 + - - +
138B TYR* 2.9 28.4 + - - +
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Residues in contact with ILE 135 (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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28B ILE* 4.1 17.5 - - + -
32B ILE* 4.1 27.8 - - + -
34B ALA* 3.7 19.3 - - + -
104B PHE* 5.2 1.3 - - + -
108B LEU* 5.8 1.8 - - + -
122B ILE* 4.4 16.4 - - + -
131B THR* 2.9 43.2 + - + +
132B GLY 4.3 2.0 - - - +
134B MET* 1.3 74.6 - - - +
136B CYS* 1.3 53.1 + - - +
138B TYR* 3.3 6.5 + - + +
139B LEU* 2.8 54.7 + - + +
155B TYR* 4.2 12.6 - - + -
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Residues in contact with CYS 136 (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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132B GLY 3.0 25.0 + - - +
133B VAL 3.8 2.5 - - - +
135B ILE* 1.3 73.5 - - - +
137B ALA* 1.3 65.7 + - - +
139B LEU* 3.4 7.1 + - - +
140B LEU* 2.9 31.7 + - - +
151B ALA* 3.3 39.6 - - + +
152B LEU* 3.9 12.1 - - - -
155B TYR* 3.6 20.0 - - - -
175B VAL* 4.0 18.4 - - + -
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Residues in contact with ALA 137 (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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101B ILE* 3.7 32.1 - - + -
105B CYS* 3.9 4.7 - - - -
133B VAL* 2.8 22.1 + - + +
134B MET* 3.6 6.7 - - - +
136B CYS* 1.3 75.8 - - - +
138B TYR* 1.3 51.3 + - - +
140B LEU* 3.2 10.0 + - - +
141B HIS* 2.6 35.5 + - - +
175B VAL* 4.6 4.7 - - + +
178B TYR* 3.8 16.3 - - + -
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Residues in contact with TYR 138 (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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32B ILE* 3.9 28.0 - - + -
104B PHE* 4.6 0.7 - - + -
105B CYS* 3.6 40.2 - - - -
108B LEU* 3.4 27.6 - - + -
109B ASP* 2.8 36.7 + - + -
112B LEU* 3.9 18.6 - - + +
134B MET 2.9 19.0 + - - +
135B ILE* 3.5 5.4 - - - +
137B ALA* 1.3 76.4 - - - +
139B LEU* 1.3 58.1 + - + +
141B HIS* 3.1 7.8 + + - +
142B ARG* 2.7 59.8 + - + +
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Residues in contact with LEU 139 (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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28B ILE* 3.9 7.6 - - + -
29B TYR* 3.8 26.2 - - + -
32B ILE* 3.8 26.0 - - + -
135B ILE* 2.8 45.4 + - + +
136B CYS* 4.0 7.0 - - - +
138B TYR* 1.3 77.5 - - + +
140B LEU* 1.3 58.9 + - - +
142B ARG* 3.7 3.3 + - + +
143B GLY 3.5 1.2 + - - -
144B LYS* 2.9 44.0 + - + +
145B PHE* 3.3 36.9 + - + -
151B ALA 6.0 0.2 - - - +
154B PHE* 5.1 1.6 - - + -
155B TYR* 6.4 1.1 - - + -
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Residues in contact with LEU 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 CYS 2.9 24.9 + - - +
137B ALA* 3.4 6.5 - - - +
139B LEU* 1.3 76.5 - - - +
141B HIS* 1.3 64.7 + - - +
142B ARG 3.2 0.2 - - - -
143B GLY* 3.0 14.6 + - - -
145B PHE* 3.6 27.3 - - + +
146B LEU 4.4 1.8 - - - -
147B LYS 3.7 29.2 - - - +
148B ALA* 4.0 5.4 - - - +
151B ALA* 4.1 6.1 - - + -
175B VAL* 3.5 30.7 - - + +
178B TYR* 5.7 0.2 - - + -
179B SER* 4.0 23.1 - - - +
182B LEU* 3.8 19.8 - - + +
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Residues in contact with HIS 141 (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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102B LYS* 5.4 3.1 - - + -
105B CYS* 3.6 26.8 - - + +
106B GLU* 4.2 20.3 - - + +
109B ASP* 4.1 18.2 + - - -
137B ALA 2.6 18.4 + - - +
138B TYR* 3.1 27.8 - + - +
140B LEU* 1.3 73.3 - - - +
142B ARG* 1.3 60.8 + - + +
143B GLY 3.4 1.0 + - - -
178B TYR* 3.0 25.3 + - + -
182B LEU* 3.7 22.5 - - + +
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Residues in contact with ARG 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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19A ASP 5.3 6.1 + - - -
109B ASP* 3.1 30.1 + - - -
113B SER* 5.9 4.0 - - - -
138B TYR* 2.7 50.6 + - + +
139B LEU* 4.1 9.2 - - + +
140B LEU 3.2 0.4 - - - -
141B HIS* 1.3 72.9 - - + +
143B GLY* 1.3 58.9 + - - +
144B LYS* 3.1 16.6 + - + +
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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