Contacts of the helix formed by residues 128 - 141 (chain A) in PDB entry 1B43
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 GLU 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 THR 4.1 1.2 + - - -
125A ARG* 3.0 54.7 + - + +
126A VAL 3.0 1.4 - - - +
127A ASN* 1.3 77.7 - - - +
129A MET* 1.3 73.6 + - + +
131A ILE* 3.8 8.0 + - - +
132A GLU* 3.1 29.4 + - - +
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Residues in contact with MET 129 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A VAL 4.3 4.7 + - - +
127A ASN 3.2 0.6 - - - -
128A GLU* 1.3 97.1 - - + +
130A LEU* 1.3 73.4 + - + +
132A GLU* 3.1 38.6 - - - +
133A ASP* 3.0 34.3 + - - +
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Residues in contact with LEU 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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31A ILE* 4.1 19.5 - - + -
32A TYR* 4.5 0.7 - - + -
35A LEU* 3.9 30.1 - - + -
53A ILE* 6.1 4.0 - - + -
56A HIS* 3.7 37.0 - - + +
104A TRP* 3.9 25.4 - - + -
105A ARG* 6.1 3.1 - - - +
108A LEU* 5.4 2.2 - - + -
127A ASN* 3.0 30.2 + - + +
129A MET* 1.3 84.7 - - + +
131A ILE* 1.3 50.8 + - - +
133A ASP* 3.2 4.2 + - - +
134A ALA* 2.8 34.9 + - - +
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Residues in contact with ILE 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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28A LEU* 4.4 13.2 - - + -
31A ILE* 4.5 12.3 - - + -
78A PHE* 3.7 27.1 - - + -
79A ASP* 5.8 11.4 - - + +
124A THR* 5.8 6.3 - - + +
127A ASN* 2.9 33.1 + - + +
128A GLU* 4.0 6.5 - - - +
130A LEU* 1.3 74.3 - - + +
132A GLU* 1.3 59.8 + - - +
134A ALA* 3.2 6.8 + - - +
135A LYS* 2.8 46.4 + - + +
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Residues in contact with GLU 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 GLU* 3.1 20.2 + - - +
129A MET* 3.1 40.8 - - - +
131A ILE* 1.3 77.4 - - - +
133A ASP* 1.3 65.9 + - - +
135A LYS* 4.1 6.6 - - - +
136A LYS* 3.2 22.5 + - - +
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Residues in contact with ASP 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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53A ILE 5.5 0.3 - - - +
56A HIS* 3.6 16.5 + - - +
57A LEU* 3.7 25.2 - - + +
129A MET* 3.0 20.6 + - - +
130A LEU* 3.5 7.6 - - - +
132A GLU* 1.3 82.2 - - - +
134A ALA* 1.3 64.5 + - - +
136A LYS* 3.3 4.4 + - - +
137A LEU* 2.9 25.8 + - - +
302A PHE* 3.9 21.7 - - + -
307A HIS* 4.7 8.0 + - - -
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Residues in contact with ALA 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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27A ALA* 6.0 0.2 - - + -
31A ILE* 3.9 10.5 - - + -
56A HIS* 5.3 0.2 - - + -
57A LEU* 4.5 2.0 - - - +
60A LEU* 3.5 30.7 - - + -
78A PHE* 3.8 20.0 - - + -
130A LEU 2.8 14.3 + - - +
131A ILE 3.2 7.8 + - - +
133A ASP* 1.3 77.2 - - - +
135A LYS* 1.3 64.3 + - - +
137A LEU* 3.3 1.3 + - - +
138A LEU* 3.0 30.4 + - - +
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Residues in contact with LYS 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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78A PHE* 3.7 30.3 - - + -
131A ILE* 2.8 43.3 + - + +
132A GLU* 4.1 6.5 - - - +
134A ALA* 1.3 72.3 - - - +
136A LYS* 1.3 62.4 + - - +
138A LEU* 3.5 3.0 + - - +
139A GLU* 3.1 29.6 + - - +
145A ILE* 4.0 24.0 - - + +
147A GLN* 2.5 35.8 + - - +
81B GLU* 5.5 0.2 + - - -
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Residues in contact with LYS 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 GLU 3.2 17.3 + - - +
133A ASP* 3.6 6.3 - - - +
134A ALA 3.2 0.4 - - - -
135A LYS* 1.3 79.6 - - - +
137A LEU* 1.3 63.2 + - - +
139A GLU* 3.7 6.1 - - - +
140A LEU* 3.1 32.7 + - + +
302A PHE* 3.7 43.6 - - + +
306A GLU* 4.4 7.5 + - - -
95B GLU* 5.5 11.4 - - - +
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Residues in contact with LEU 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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57A LEU* 3.4 39.0 - - + +
60A LEU* 3.7 20.4 - - + -
61A PHE* 3.9 9.0 - - + +
133A ASP 2.9 16.6 + - - +
134A ALA* 3.9 2.5 - - - +
136A LYS* 1.3 73.6 - - - +
138A LEU* 1.3 68.2 + - - +
140A LEU* 3.2 4.3 + - + +
141A MET* 3.0 47.9 + - + +
299A ILE* 4.8 8.3 - - + -
302A PHE* 3.8 16.4 - - + -
303A LEU* 4.0 31.6 - - + -
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Residues in contact with LEU 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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60A LEU* 4.1 33.2 - - + +
64A THR* 4.4 0.2 - - - +
76A TYR* 3.5 57.2 - - + -
78A PHE* 3.9 17.0 - - + -
134A ALA 3.0 20.6 + - - +
135A LYS 4.1 0.7 - - - +
137A LEU* 1.3 75.2 - - - +
139A GLU* 1.3 55.9 + - - +
141A MET* 3.3 6.7 + - - +
142A GLY 3.0 8.0 + - - -
143A ILE* 2.9 45.8 + - + +
145A ILE* 3.8 17.9 - - + -
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Residues in contact with GLU 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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135A LYS* 3.1 19.9 + - - +
136A LYS* 3.7 6.8 - - - +
138A LEU* 1.3 75.6 - - - +
140A LEU* 1.3 66.7 + - + +
142A GLY* 3.0 13.9 + - - -
143A ILE 4.7 4.5 - - - -
145A ILE* 5.0 10.4 - - + +
293A ASP 5.5 0.3 - - - +
88B LYS* 5.1 18.2 + - + +
91B GLU* 2.9 45.7 - - - +
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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 LYS* 3.1 30.1 + - + +
137A LEU* 3.2 6.0 + - + +
139A GLU* 1.3 76.8 - - + +
141A MET* 1.3 57.0 - - - +
142A GLY 3.5 0.2 + - - -
293A ASP 4.4 0.7 - - - +
294A PRO* 3.1 4.5 - - - +
295A ASP* 2.7 58.6 + - + +
298A GLY* 3.5 30.7 - - - +
299A ILE* 3.6 16.8 - - + +
302A PHE* 4.0 23.8 - - + -
92B LYS* 6.0 4.0 - - - -
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Residues in contact with MET 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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60A LEU 3.6 26.7 - - - +
61A PHE* 3.6 35.0 - - + +
64A THR* 4.1 14.4 - - + -
65A ILE* 4.0 13.2 - - + -
137A LEU* 3.0 39.9 + - + +
138A LEU* 3.5 11.9 - - - +
139A GLU 3.1 0.2 - - - -
140A LEU* 1.3 76.8 - - - +
142A GLY* 1.3 59.2 + - - +
143A ILE* 3.6 13.4 + - + +
292A ARG 3.7 5.5 - - - +
294A PRO* 3.6 16.5 - - - +
299A ILE* 3.9 17.7 - - + -
321A LEU* 3.8 16.3 - - + +
325A ILE* 4.3 2.3 - - - +
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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