Contacts of the helix formed by residues 135 - 155 (chain A) in PDB entry 2B6U
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 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A THR* 4.1 2.5 - - - -
132A PHE* 3.6 37.7 - - + +
133A LEU* 2.8 26.2 + - + +
134A LYS* 1.3 75.4 - - - +
136A PRO* 1.4 69.4 - - + +
137A VAL* 3.0 21.3 - - + -
138A PHE* 2.9 20.6 + - + +
139A ALA* 2.9 10.9 + - - +
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Residues in contact with PRO 136 (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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56A THR* 4.4 7.4 - - + -
59A ILE* 4.8 12.7 - - + +
135A LYS* 1.4 89.1 - - + +
137A VAL* 1.4 60.3 + - + +
139A ALA* 3.5 11.6 - - + +
140A LYS* 3.1 24.9 + - - +
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Residues in contact with VAL 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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135A LYS* 4.2 13.5 - - + -
136A PRO* 1.4 79.2 - - + +
138A PHE* 1.4 75.9 + - + +
140A LYS* 3.3 9.1 + - - +
141A THR* 2.6 35.0 + - - -
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Residues in contact with PHE 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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132A PHE* 3.6 32.1 - - + -
133A LEU 2.9 23.6 - - - -
134A LYS* 3.7 20.1 - - + -
135A LYS* 2.9 16.9 + - + +
137A VAL* 1.4 93.1 - - + +
139A ALA* 1.4 60.0 + - - +
141A THR* 3.1 13.8 + - + -
142A VAL* 3.0 31.0 + - - +
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Residues in contact with ALA 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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56A THR* 3.6 37.5 - - + +
59A ILE* 3.8 23.6 - - + +
115A LEU* 5.6 1.5 - - - +
134A LYS* 4.6 4.3 - - - +
135A LYS 2.9 5.5 + - - +
136A PRO 3.5 10.8 - - - +
138A PHE* 1.4 74.5 - - - +
140A LYS* 1.4 64.4 + - - +
142A VAL* 3.5 8.9 + - - +
143A SER* 3.1 26.0 + - - -
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Residues in contact with LYS 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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59A ILE* 5.2 4.0 - - - +
136A PRO 3.1 12.0 + - - +
137A VAL* 3.4 12.1 - - - +
138A PHE 3.3 0.2 - - - -
139A ALA* 1.4 77.8 - - - +
141A THR* 1.4 65.0 + - - +
143A SER* 3.2 6.8 + - - -
144A ILE* 3.0 42.8 + - + +
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Residues in contact with THR 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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137A VAL 2.6 22.8 + - - -
138A PHE* 3.1 16.9 + - + -
140A LYS* 1.4 76.7 - - - +
142A VAL* 1.4 60.0 - - + +
144A ILE* 3.2 9.5 + - - +
145A PHE* 2.9 28.8 + - + +
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Residues in contact with VAL 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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115A LEU* 3.3 52.3 - - + -
118A PHE* 6.5 0.2 - - + -
134A LYS* 3.6 24.5 - - - +
138A PHE 3.0 11.0 + - - +
139A ALA 3.8 6.5 - - - +
140A LYS 3.3 0.2 - - - -
141A THR* 1.4 78.0 - - + +
143A SER* 1.4 62.7 + - - +
145A PHE* 3.5 28.9 - - + -
146A ILE* 2.9 33.6 + - - +
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Residues in contact with SER 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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59A ILE* 4.1 18.2 + - - +
60A TYR* 4.8 3.1 - - - -
62A LYS* 6.2 0.2 - - - -
63A ASN* 3.2 35.3 + - - +
115A LEU* 4.8 4.9 - - - +
139A ALA 3.1 17.5 + - - -
140A LYS* 3.2 7.2 + - - -
142A VAL* 1.4 76.7 - - - +
144A ILE* 1.4 60.2 + - - +
145A PHE 3.2 0.2 - - - -
146A ILE* 3.3 8.5 - - - +
147A TRP* 3.0 26.5 + - - +
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Residues in contact with ILE 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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140A LYS* 3.0 40.1 + - + +
141A THR* 3.4 9.6 - - - +
143A SER* 1.4 75.3 - - - +
145A PHE* 1.4 53.7 + - - +
147A TRP* 3.4 27.5 + - + +
148A PHE* 2.8 36.7 + - + +
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Residues in contact with PHE 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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111A VAL* 4.1 15.0 - - + -
114A GLY 6.3 1.1 - - - -
115A LEU 6.1 1.3 - - - -
141A THR* 2.9 17.8 + - + +
142A VAL* 3.3 31.0 - - + +
144A ILE* 1.4 74.6 - - - +
146A ILE* 1.4 61.9 - - + +
148A PHE* 3.0 6.5 + - - +
149A PHE* 2.9 78.0 + + - -
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Residues in contact with ILE 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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63A ASN* 3.6 22.0 - - + +
107A TYR 4.2 2.5 - - - +
108A VAL* 3.5 25.6 - - + +
111A VAL* 3.5 42.4 - - + +
112A LEU* 3.4 30.1 - - + +
115A LEU* 4.2 11.9 - - + -
142A VAL 2.9 21.8 + - - +
143A SER* 3.3 12.3 - - - +
145A PHE* 1.4 78.3 - - + +
147A TRP* 1.4 62.0 + - - +
149A PHE* 3.3 0.5 + - - +
150A LEU* 2.8 34.4 + - - +
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Residues in contact with TRP 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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62A LYS* 6.1 3.8 - - - -
63A ASN* 3.0 40.1 + - - -
66A VAL* 5.3 13.9 - - + +
67A ALA* 5.5 2.8 - - - +
108A VAL* 3.9 11.5 - - + +
143A SER 3.0 12.6 + - - +
144A ILE* 3.4 31.0 - - + +
146A ILE* 1.4 77.6 - - - +
148A PHE* 1.3 58.0 + - - +
150A LEU* 3.5 12.3 - - + +
151A PHE* 2.9 51.5 + + + -
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Residues in contact with PHE 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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144A ILE* 2.8 21.4 + - + +
145A PHE* 3.0 9.8 + - - +
147A TRP* 1.3 77.0 - - - +
149A PHE* 1.3 75.5 + + + +
151A PHE* 3.4 10.5 + + + +
152A PHE* 3.0 44.1 + + + +
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Residues in contact with PHE 149 (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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111A VAL* 3.7 31.0 - - + -
145A PHE* 2.9 59.1 + + - +
146A ILE 4.0 0.2 - - - +
148A PHE* 1.3 91.8 - + + +
150A LEU* 1.4 64.8 - - - +
152A PHE* 3.1 13.4 + - + +
153A ILE* 3.1 15.5 + - - +
194A PHE* 3.7 32.8 - + + -
195A ILE* 4.2 11.1 - - + +
199A VAL* 5.7 2.9 - - + -
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Residues in contact with LEU 150 (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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67A ALA* 5.5 0.9 - - + -
104A GLU* 2.8 57.7 - - + +
107A TYR* 3.9 13.0 + - - +
108A VAL* 3.3 29.8 - - + -
146A ILE 2.8 17.9 + - - +
147A TRP* 3.5 21.5 - - + +
149A PHE* 1.4 73.6 - - - +
151A PHE* 1.4 88.9 + - + +
153A ILE* 2.9 13.4 - - - +
154A SER* 2.7 32.6 + - - +
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Residues in contact with PHE 151 (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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104A GLU* 4.0 21.3 - - - -
147A TRP* 2.9 41.3 + + + +
148A PHE* 3.7 12.1 - + + +
149A PHE 3.4 0.2 - - - -
150A LEU* 1.4 91.3 - - + +
152A PHE* 1.3 58.2 + - - +
154A SER* 4.3 4.9 - - - -
155A LEU* 2.8 58.8 + - + +
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Residues in contact with PHE 152 (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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148A PHE* 3.0 33.9 + + + +
149A PHE* 3.1 7.5 + - + +
151A PHE* 1.3 79.0 - - - +
153A ILE* 1.4 56.2 + - - +
155A LEU* 6.5 0.7 - - + -
156A PRO* 3.2 31.0 - - + +
187A MET* 5.2 3.9 - - + +
190A ASN* 4.7 17.2 - - - +
194A PHE* 3.8 27.6 - + + -
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Residues in contact with ILE 153 (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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103A TYR* 3.7 34.5 - - + -
107A TYR* 3.7 36.1 - - + -
149A PHE 3.1 11.9 + - - +
150A LEU 2.9 21.5 - - - +
152A PHE* 1.4 78.2 - - - +
154A SER* 1.3 55.0 + - - +
155A LEU 3.5 0.2 - - - -
156A PRO* 3.6 3.8 - - - +
157A ASN* 2.7 30.9 + - - +
187A MET* 5.4 1.4 - - - +
191A ILE* 3.6 37.4 - - + +
194A PHE* 4.2 2.6 - - + -
195A ILE* 3.7 23.8 - - + -
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Residues in contact with SER 154 (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 VAL* 3.8 25.4 - - - +
103A TYR* 3.9 13.0 + - - -
104A GLU* 3.2 40.8 + - - +
150A LEU* 2.7 22.7 + - - -
151A PHE* 4.2 5.8 - - - -
153A ILE* 1.3 81.0 - - - +
155A LEU* 1.3 62.9 - - - +
157A ASN* 3.0 20.3 + - - +
158A MET 4.4 1.0 + - - -
164A GLU* 5.4 0.2 - - - +
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Residues in contact with LEU 155 (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 VAL* 5.2 2.5 - - - -
151A PHE* 2.8 47.4 + - + +
152A PHE* 6.5 0.7 - - + -
154A SER* 1.3 70.3 - - - +
156A PRO* 1.4 59.2 - - + +
157A ASN 2.9 11.8 + - - -
158A MET* 2.9 35.5 + - + +
159A ILE* 3.4 25.8 + - + +
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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