Contacts of the helix formed by residues 133 - 148 (chain A) in PDB entry 2COJ
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 ASP 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A THR* 3.0 34.0 + - + +
25A PHE* 4.9 0.7 - - - -
132A PHE* 1.3 76.1 - - - +
134A LYS* 1.3 63.2 + - - +
135A GLU* 2.8 41.4 + - - +
136A GLU* 3.1 29.8 + - + +
137A LEU* 3.2 9.2 + - - +
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Residues in contact with LYS 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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117A MET* 3.5 38.9 - - + +
118A ASP* 2.5 35.4 + - - +
121A TYR* 3.7 33.5 - - + -
132A PHE* 3.3 14.5 + - + +
133A ASP* 1.3 72.9 + - - +
135A GLU* 1.3 64.3 + - + +
137A LEU* 3.6 2.3 + - - +
138A LEU* 3.1 24.1 + - - +
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Residues in contact with GLU 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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114A ASN* 3.9 17.1 - - - +
133A ASP* 2.8 14.1 + - - +
134A LYS* 1.3 76.8 - - + +
136A GLU* 1.3 67.6 + - + +
138A LEU* 3.3 13.9 + - - +
139A GLU* 3.0 23.4 + - - +
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Residues in contact with GLU 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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24A THR* 4.9 1.1 - - + -
25A PHE* 3.3 28.3 - - + +
26A LYS* 3.4 19.0 - - + +
27A ALA* 2.8 31.3 + - - +
28A LYS 4.5 0.5 + - - -
133A ASP* 3.1 30.8 + - + +
135A GLU* 1.3 78.7 - - - +
137A LEU* 1.3 57.8 + - - +
139A GLU* 3.3 5.0 + - - +
140A CYS* 2.9 32.9 + - - -
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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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25A PHE* 3.8 24.6 - - + -
58A LEU* 4.6 9.6 - - + -
117A MET* 3.8 13.9 - - + -
120A MET* 3.7 21.3 - - + -
132A PHE* 3.5 33.2 - - + -
133A ASP 3.2 9.5 + - - +
134A LYS 3.8 7.9 - - - +
135A GLU 3.3 0.2 - - - -
136A GLU* 1.3 78.4 - - - +
138A LEU* 1.3 58.4 + - - +
140A CYS* 3.1 3.0 + - - +
141A ILE* 2.8 46.1 + - + +
164A PRO* 5.5 0.9 - - + -
183A LEU* 4.6 15.0 - - + -
185A VAL* 4.7 2.2 - - + -
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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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98A LEU* 5.6 2.0 - - + -
110A LEU* 4.3 10.5 - - + -
113A PRO* 3.6 29.4 - - + -
114A ASN* 3.5 26.7 - - - +
117A MET* 4.0 18.1 - - + -
134A LYS 3.1 15.1 + - - +
135A GLU* 3.7 15.7 - - - +
136A GLU 3.3 0.2 - - - -
137A LEU* 1.3 80.6 - - - +
139A GLU* 1.3 57.0 + - - +
141A ILE* 3.1 11.5 + - + +
142A GLN* 2.8 47.8 + - - +
383A ILE* 4.6 9.0 - - + -
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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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27A ALA* 3.5 21.8 - - + -
135A GLU 3.0 16.5 + - - +
136A GLU* 3.7 4.9 - - - +
138A LEU* 1.3 73.5 - - - +
140A CYS* 1.3 66.5 + - - +
142A GLN* 3.0 20.8 + - - +
143A GLN* 2.9 51.7 + - + +
385A LEU* 5.8 0.3 - - - +
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Residues in contact with CYS 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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25A PHE* 4.2 10.8 - - + -
27A ALA* 3.7 20.9 - - - -
30A LEU* 3.6 33.9 - - + -
58A LEU* 3.9 21.7 - - + +
71A PRO* 4.2 11.9 - - - -
73A ILE* 4.3 3.8 - - - +
136A GLU 2.9 20.7 + - - +
137A LEU* 3.3 11.7 - - + +
139A GLU* 1.3 77.7 - - - +
141A ILE* 1.3 61.1 + - - +
143A GLN* 3.6 3.5 + - - +
144A LEU* 3.2 19.9 + - - +
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Residues in contact with ILE 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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58A LEU* 4.7 1.1 - - + -
98A LEU* 5.3 5.2 - - + -
110A LEU* 5.4 7.2 - - + -
117A MET* 4.0 24.0 - - + -
137A LEU* 2.8 39.8 + - + +
138A LEU* 3.4 12.3 - - + +
139A GLU 3.0 0.4 - - - -
140A CYS* 1.3 76.6 - - - +
142A GLN* 1.3 65.5 + - - +
143A GLN 3.1 0.4 - - - -
144A LEU* 3.1 6.3 + - + +
145A VAL* 2.9 31.4 + - + +
162A ILE* 3.9 28.0 - - + -
164A PRO* 4.4 17.0 - - + -
185A VAL* 4.3 16.6 - - + -
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Residues in contact with GLN 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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110A LEU* 3.1 24.5 - - + +
138A LEU* 2.8 39.3 + - - +
139A GLU* 3.0 25.9 + - - +
141A ILE* 1.3 77.0 - - - +
143A GLN* 1.3 53.3 + - - +
145A VAL* 3.7 2.6 - - - +
146A LYS* 2.7 37.7 + - - +
383A ILE* 4.1 17.7 - - - +
385A LEU* 2.9 55.1 - - + +
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Residues in contact with GLN 143 (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* 4.7 4.8 + - - +
30A LEU* 3.5 31.4 - - + +
32A VAL* 6.5 0.2 - - + -
73A ILE* 4.0 8.2 - - + +
139A GLU* 2.9 42.0 + - + +
140A CYS 3.6 6.3 - - - +
142A GLN* 1.3 75.3 - - - +
144A LEU* 1.3 63.8 + - - +
146A LYS* 3.6 22.1 - - - +
147A LEU* 3.1 23.2 + - - +
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Residues in contact with LEU 144 (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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56A HIS* 3.8 35.7 - - + +
57A MET* 4.1 4.0 - - - +
58A LEU* 4.0 15.9 - - + +
73A ILE* 3.8 15.2 - - + +
140A CYS 3.2 11.3 + - - +
141A ILE* 3.1 12.2 + - + +
143A GLN* 1.3 76.8 - - - +
145A VAL* 1.3 66.2 + - + +
147A LEU* 3.3 3.9 + - + +
148A ASP* 3.1 19.8 + - - +
185A VAL* 3.7 38.4 - - + +
187A LEU* 3.7 31.0 - - + -
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Residues in contact with VAL 145 (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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100A ALA* 4.2 13.5 - - + -
108A ILE* 4.5 9.6 - - + -
110A LEU* 5.1 4.3 - - + -
141A ILE* 2.9 21.3 + - + +
142A GLN* 3.8 5.6 - - - +
144A LEU* 1.3 72.1 - - + +
146A LYS* 1.3 59.5 + - - +
148A ASP 2.9 3.0 + - - -
149A GLN* 2.6 37.1 + - + -
152A VAL* 4.2 23.8 - - + -
160A LEU* 4.4 4.9 - - + -
162A ILE* 4.0 26.2 - - + -
187A LEU* 4.3 19.7 - - + -
385A LEU* 4.7 8.1 - - + -
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Residues in contact with LYS 146 (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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142A GLN 2.7 24.2 + - - +
143A GLN* 3.6 24.9 + - - +
145A VAL* 1.3 72.6 - - - +
147A LEU* 1.3 64.3 + - - +
149A GLN* 3.4 36.8 + - - +
385A LEU* 4.5 36.8 - - + +
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Residues in contact with LEU 147 (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 VAL* 4.4 17.0 - - + -
34A PRO* 5.4 5.8 - - + -
56A HIS* 3.6 42.6 - - + +
73A ILE* 3.7 21.8 - - + -
143A GLN 3.1 11.8 + - - +
144A LEU* 3.4 10.1 - - - +
145A VAL 3.1 0.2 - - - -
146A LYS* 1.3 82.1 - - - +
148A ASP* 1.3 62.4 + - - +
149A GLN* 3.5 3.5 + - - +
150A GLU 5.2 0.5 + - - -
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Residues in contact with ASP 148 (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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54A THR* 3.0 16.4 + - - -
55A ASP* 4.0 2.6 - - - +
56A HIS* 2.7 57.1 + - - +
144A LEU* 3.1 11.9 + - - +
145A VAL* 2.9 6.6 + - - -
147A LEU* 1.3 80.6 - - - +
149A GLN* 1.3 61.7 + - - +
150A GLU 3.3 3.1 - - - -
151A TRP* 3.1 40.1 + - + +
152A VAL* 4.0 3.6 + - - +
160A LEU* 4.5 2.9 - - - +
187A LEU* 4.0 12.9 - - + +
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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