Contacts of the helix formed by residues 128 - 142 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A CYS* 3.3 6.3 - - - -
126A ALA* 4.0 20.9 - - + +
127A GLY* 1.3 74.9 - - - +
129A GLY* 1.3 62.2 + - - +
130A ARG 3.5 0.9 - - - -
132A GLY* 2.8 27.0 + - - -
155A TYR* 2.9 12.4 + - - -
159A ARG* 5.5 0.7 - - + -
160A THR* 5.3 5.8 - - + -
164A LYS* 3.4 19.1 + - - +
165A GLY* 2.7 35.2 + - - +
167A THR* 3.4 24.6 + - - +
401A TLA 4.2 13.1 + - - +
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Residues in contact with GLY 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LYS* 1.3 80.9 - - - +
130A ARG* 1.3 58.4 + - - +
132A GLY* 3.2 1.4 + - - -
133A VAL* 2.9 33.4 + - - +
165A GLY 4.1 11.0 - - - -
166A VAL* 3.8 6.7 - - - +
167A THR 5.6 0.2 - - - -
171A GLN* 3.3 23.1 - - - -
401A TLA 3.2 13.0 + - - -
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Residues in contact with ARG 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 3.4 20.0 + - + -
71A CYS* 3.8 3.6 - - - +
73A GLU* 2.9 36.2 + - - -
90A PHE* 2.7 62.6 + - + -
91A GLU 3.5 14.4 - - - +
92A ASP* 3.3 17.0 + - - +
124A CYS* 3.9 14.5 - - + +
125A LYS* 4.3 6.9 - - - +
129A GLY* 1.3 71.5 - - - +
131A THR* 1.3 66.5 + - - +
133A VAL* 3.3 12.5 + - - +
134A MET* 3.3 19.8 + - - +
171A GLN* 3.9 5.6 - - - +
401A TLA 2.9 55.0 + - - +
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Residues in contact with THR 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ALA* 3.7 13.2 - - + -
70A LEU* 3.7 9.8 - - - +
122A ILE* 3.5 24.0 - - + +
123A HIS* 3.6 3.3 - - - -
124A CYS* 2.9 37.3 + - - -
127A GLY* 3.5 7.4 - - - -
130A ARG* 1.3 77.5 - - - +
132A GLY* 1.3 57.6 + - - +
134A MET* 3.4 1.7 + - - +
135A ILE* 2.9 52.4 + - + +
155A TYR* 3.9 7.2 - - - +
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Residues in contact with GLY 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LYS 2.8 20.6 + - - -
129A GLY 3.5 1.6 - - - -
130A ARG 3.2 0.2 - - - -
131A THR* 1.3 75.1 - - - +
133A VAL* 1.3 58.7 + - - +
135A ILE* 4.3 0.2 - - - +
136A CYS* 2.9 36.4 + - - +
155A TYR* 3.4 25.7 + - - -
166A VAL* 3.8 9.4 - - - -
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Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A PHE* 5.1 0.4 - - + -
96A PRO* 3.7 20.4 - - + -
101A ILE* 5.0 3.1 - - + -
129A GLY 2.9 23.5 + - - +
130A ARG* 3.6 8.3 - - - +
132A GLY* 1.3 71.7 - - - +
134A MET* 1.3 80.3 + - + +
136A CYS* 3.8 1.2 - - - +
137A ALA* 2.8 32.4 + - + +
166A VAL* 3.9 4.2 - - + +
171A GLN* 3.6 40.2 - - + +
174A TYR* 4.7 5.2 - - + -
175A VAL* 3.9 21.3 - - + +
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Residues in contact with MET 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 3.6 21.8 - - + -
90A PHE* 3.8 13.7 - - + -
96A PRO* 3.3 37.9 - - + -
100A LEU* 4.8 5.2 - - - -
101A ILE* 3.6 21.3 - - + -
104A PHE* 3.6 46.9 - - + -
122A ILE* 4.9 1.1 - - + -
130A ARG 3.3 13.8 + - - +
131A THR 3.7 6.3 - - - +
133A VAL* 1.3 91.8 - - + +
135A ILE* 1.3 59.9 - - - +
137A ALA* 3.5 3.4 + - - +
138A TYR* 2.9 28.8 + - - +
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 4.1 13.2 - - + -
32A ILE* 4.1 25.6 - - + -
34A ALA* 3.7 20.9 - - + -
122A ILE* 3.7 24.0 - - + -
131A THR* 2.9 41.1 + - + +
132A GLY 4.3 2.2 - - - +
134A MET* 1.3 75.0 - - - +
136A CYS* 1.3 53.9 + - - +
138A TYR* 3.3 6.9 + - + +
139A LEU* 2.8 54.3 + - + +
155A TYR* 4.2 13.0 - - + -
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Residues in contact with CYS 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A GLY 2.9 24.7 + - - +
133A VAL 3.8 2.5 - - - +
135A ILE* 1.3 75.1 - - - +
137A ALA* 1.3 59.5 + - - +
139A LEU* 3.4 6.9 + - - +
140A LEU* 2.9 37.3 + - - +
151A ALA* 3.3 39.4 - - + +
152A LEU* 3.8 13.5 - - - -
155A TYR* 3.6 19.1 - - - -
175A VAL* 4.0 18.6 - - + -
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Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ILE* 3.7 31.2 - - + -
105A CYS* 3.9 4.7 - - - -
133A VAL* 2.8 22.0 + - + +
134A MET* 3.6 8.1 - - + +
136A CYS* 1.3 74.7 - - - +
138A TYR* 1.3 51.3 + - - +
140A LEU* 3.2 9.1 + - - +
141A HIS* 2.6 35.9 + - - +
175A VAL* 4.6 4.6 - - + +
178A TYR* 3.8 16.5 - - + -
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Residues in contact with TYR 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ILE* 3.9 28.3 - - + -
104A PHE* 4.6 0.7 - - + -
105A CYS* 3.6 39.8 - - - -
108A LEU* 3.4 23.8 - - + -
109A ASP* 2.7 40.1 + - + -
112A LEU* 3.9 21.5 - - + +
134A MET 2.9 17.8 + - - +
135A ILE* 3.5 5.4 - - - +
137A ALA* 1.3 77.0 - - - +
139A LEU* 1.3 57.4 + - + +
141A HIS* 3.1 9.2 - + - +
142A ARG* 2.7 50.0 + - + +
144A LYS* 5.3 3.8 - - - -
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 3.9 9.9 - - + -
29A TYR* 3.6 33.0 - - + -
32A ILE* 3.7 19.5 - - + -
135A ILE* 2.8 43.3 + - + +
136A CYS* 3.9 7.4 - - - +
138A TYR* 1.3 75.7 - - + +
140A LEU* 1.3 59.2 + - - +
142A ARG* 3.8 2.1 + - + +
143A GLY 3.5 1.2 + - - -
144A LYS* 2.9 47.3 + - + +
145A PHE* 3.3 36.0 + - + -
151A ALA 5.9 0.4 - - - +
154A PHE* 5.0 1.1 - - + -
155A TYR* 6.4 1.1 - - + -
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A CYS 2.9 23.5 + - - +
137A ALA* 3.4 5.8 - - - +
139A LEU* 1.3 76.5 - - - +
141A HIS* 1.3 59.7 + - - +
143A GLY* 3.0 19.8 + - - -
145A PHE* 3.6 27.4 - - + +
146A LEU 4.3 1.8 - - - -
147A LYS* 3.7 28.9 - - - +
148A ALA* 4.1 5.2 - - - +
151A ALA* 4.1 6.5 - - + -
175A VAL* 3.5 30.3 - - + +
178A TYR* 5.7 0.2 - - + -
179A SER* 4.0 23.8 - - - +
182A LEU* 3.7 21.2 - - + +
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Residues in contact with HIS 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LYS* 5.3 3.1 - - + -
105A CYS* 3.6 27.8 - - + +
106A GLU* 4.1 21.3 - - + +
109A ASP* 4.1 17.6 + - - -
137A ALA 2.6 18.6 + - - +
138A TYR* 3.1 28.3 - + - +
140A LEU* 1.3 74.5 - - - +
142A ARG* 1.3 62.3 + - + +
143A GLY 3.4 0.5 + - - -
178A TYR* 3.0 24.6 + - + -
182A LEU* 3.6 23.5 - - + +
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Residues in contact with ARG 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ASN* 6.0 1.6 - - - +
109A ASP* 3.9 21.1 + - - +
113A SER* 5.6 9.1 - - - -
138A TYR* 2.7 37.8 + - + +
139A LEU* 3.8 4.2 + - - +
140A LEU 3.2 0.4 - - - -
141A HIS* 1.3 73.8 - - + +
143A GLY* 1.3 59.0 + - - +
144A LYS* 3.2 35.6 + - + +
19B ASP 5.4 9.8 + - - -
20B GLY* 6.1 2.2 - - - -
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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