Contacts of the helix formed by residues 139 - 155 (chain A) in PDB entry 4BHT
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 SER 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ASP* 2.4 33.6 + - - -
137A GLY 3.7 2.0 + - - -
138A LYS* 1.3 77.1 - - - +
140A GLU* 1.3 65.8 + - - +
141A GLY* 3.7 4.2 + - - -
142A GLU* 3.0 27.0 + - - -
143A VAL* 3.1 14.0 + - - +
174A ARG* 4.8 0.4 - - - -
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Residues in contact with GLU 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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138A LYS 4.1 0.2 + - - -
139A SER* 1.3 72.2 - - - +
141A GLY* 1.3 58.5 + - - +
143A VAL* 3.6 2.4 + - - +
144A MET* 3.0 27.1 + - + +
174A ARG* 3.8 32.2 + - - +
178A PHE* 4.1 22.5 - - + -
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Residues in contact with GLY 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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70A ASP* 5.1 0.7 - - - -
139A SER* 3.1 6.5 + - - -
140A GLU* 1.3 80.1 - - - +
142A GLU* 1.3 56.7 + - - +
144A MET* 3.3 10.0 + - - +
145A ARG* 2.9 49.8 + - - +
72B ASN* 5.3 10.0 - - - +
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Residues in contact with GLU 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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67A TRP* 3.8 18.5 - - + -
69A ASP* 3.3 11.2 - - - +
70A ASP* 2.7 48.5 + - - +
133A PHE* 4.9 1.3 - - - -
137A GLY 4.2 2.6 - - - +
138A LYS* 3.4 23.4 - - + +
139A SER* 3.0 29.0 + - - +
141A GLY* 1.3 71.8 - - - +
143A VAL* 1.3 61.4 + - - +
145A ARG* 3.4 14.6 + - - +
146A PHE* 2.8 30.5 + - - +
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Residues in contact with VAL 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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97A PHE* 5.4 0.7 - - + -
133A PHE* 4.3 15.5 - - + -
135A PRO* 4.7 7.2 - - + +
138A LYS* 3.8 20.6 - - + +
139A SER 3.1 15.9 + - - +
140A GLU 3.8 3.8 - - - +
142A GLU* 1.3 71.9 - - - +
144A MET* 1.3 59.8 + - - +
146A PHE* 3.3 6.1 + - - +
147A CYS* 2.8 34.6 + - - -
174A ARG* 3.7 22.7 - - - +
175A GLU* 3.4 38.6 - - + +
178A PHE* 4.4 4.7 - - + -
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Residues in contact with MET 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 GLU* 3.0 19.3 + - + +
141A GLY* 3.6 9.0 - - - +
143A VAL* 1.3 75.1 - - - +
145A ARG* 1.3 74.0 + - + +
147A CYS* 3.2 3.1 + - - +
148A GLN* 2.9 58.7 + - - +
178A PHE* 3.5 41.7 - - + -
68B VAL* 4.5 22.2 - - + -
74B ILE* 6.2 4.5 - - + -
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Residues in contact with ARG 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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67A TRP* 4.5 7.9 - - + +
68A VAL* 2.8 39.9 + - - +
69A ASP 3.5 12.7 + - - -
70A ASP* 2.8 26.5 + - - +
141A GLY* 2.9 38.6 + - - +
142A GLU* 3.5 11.1 - - - +
144A MET* 1.3 88.5 - - + +
146A PHE* 1.3 57.2 + - - +
148A GLN* 3.3 11.3 + - - +
149A ALA* 2.9 31.1 + - - +
68B VAL* 5.9 6.2 - - + +
72B ASN* 4.7 10.3 + - - -
145B ARG* 4.9 17.3 - - - +
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Residues in contact with PHE 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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65A VAL* 3.6 22.0 - - + -
67A TRP* 3.6 30.0 - + + +
77A ASN* 4.2 4.0 - - + -
97A PHE* 3.6 33.2 - + - -
131A SER* 3.4 26.7 - - - -
133A PHE* 3.4 53.2 - + + -
142A GLU 2.8 18.5 + - - +
143A VAL 3.6 3.4 - - - +
145A ARG* 1.3 77.6 - - - +
147A CYS* 1.3 58.3 + - - +
149A ALA* 3.3 1.6 + - - +
150A LEU* 3.0 40.5 + - + +
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Residues in contact with CYS 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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97A PHE* 4.1 23.8 - - - -
143A VAL* 2.8 34.0 + - - +
144A MET 3.5 4.0 - - - +
146A PHE* 1.3 72.6 - - - +
148A GLN* 1.3 67.7 + - - +
150A LEU* 3.4 5.5 + - - +
151A MET* 2.9 30.1 + - - +
175A GLU* 4.2 15.0 - - - -
178A PHE* 3.8 20.2 - - + -
179A MET* 4.0 20.8 - - + +
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Residues in contact with GLN 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 MET* 2.9 54.9 + - + +
145A ARG* 3.8 8.9 - - - +
147A CYS* 1.3 77.5 - - + +
149A ALA* 1.3 57.2 + - - +
151A MET* 3.1 2.6 + - - +
152A THR* 2.9 32.4 + - - -
178A PHE* 5.0 7.6 + - + +
182A MET* 4.1 41.9 - - + +
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Residues in contact with ALA 149 (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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64A ARG 5.3 0.9 - - - +
65A VAL* 3.6 19.1 - - + +
66A VAL 3.6 24.9 - - - +
67A TRP* 4.4 4.9 - - + -
145A ARG 2.9 17.4 + - - +
146A PHE 3.7 1.3 - - - +
148A GLN* 1.3 74.1 - - - +
150A LEU* 1.3 67.2 + - - +
152A THR* 3.4 20.5 + - - +
153A GLU* 3.7 4.9 + - - +
185B LYS* 4.5 5.4 + - - -
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Residues in contact with LEU 150 (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 PHE* 3.6 14.4 - - + -
65A VAL* 3.6 14.1 - - + +
79A ALA* 3.9 19.7 - - + -
95A MET* 4.0 12.3 - - + -
97A PHE* 4.0 17.7 - - + -
131A SER* 4.3 1.6 - - - -
146A PHE* 3.0 42.3 + - + +
147A CYS* 3.6 6.5 - - - +
149A ALA* 1.3 75.2 - - - +
151A MET* 1.3 67.5 + - - +
153A GLU 3.3 3.6 + - - -
154A LEU* 2.9 54.5 + - + +
179A MET* 4.3 8.5 - - - -
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Residues in contact with MET 151 (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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147A CYS 2.9 21.6 + - - +
148A GLN 3.6 3.8 - - - +
150A LEU* 1.3 82.0 - - + +
152A THR* 1.3 67.0 + - - +
153A GLU 3.0 1.8 - - - -
154A LEU* 3.6 10.3 - - - +
155A TYR* 3.0 42.8 + - + +
158A LEU* 4.2 8.5 - - + -
179A MET* 3.8 49.4 - - + +
182A MET* 3.8 18.2 - - + -
183A MET* 3.9 32.3 - - + -
186A LEU* 3.9 2.8 - - - +
194A PHE* 4.1 9.2 - - + -
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Residues in contact with THR 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 GLN 2.9 15.2 + - - -
149A ALA* 3.5 13.5 - - - -
151A MET* 1.3 77.0 - - - +
153A GLU* 1.3 57.0 + - - +
155A TYR* 3.5 9.0 - - - -
156A ARG* 3.1 17.7 + - - -
182A MET* 4.0 11.1 - - - +
186A LEU* 3.9 9.1 - - - +
182B MET* 3.7 21.3 - - + +
185B LYS* 3.2 42.0 - - + +
186B LEU* 4.0 11.4 - - + +
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Residues in contact with GLU 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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61A ILE* 4.7 3.5 - - - +
63A PHE* 3.4 45.7 - - + +
64A ARG 5.0 2.5 - - - +
149A ALA 3.7 3.4 + - - +
150A LEU 3.3 4.0 + - - +
151A MET 3.0 0.2 - - - -
152A THR* 1.3 81.5 - - - +
154A LEU* 1.3 65.6 + - - +
155A TYR 3.2 1.7 + - - -
156A ARG* 3.2 38.9 + - - +
157A HIS* 2.8 26.7 + - - +
185B LYS* 3.9 20.2 - - - +
188B ASN* 6.1 0.2 - - - -
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Residues in contact with LEU 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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63A PHE* 4.1 12.8 - - + -
81A ARG* 3.7 31.0 - - + -
95A MET* 3.7 23.8 - - + -
150A LEU* 2.9 41.0 + - + +
151A MET* 3.3 9.4 + - - -
153A GLU* 1.3 79.5 - - - +
155A TYR* 1.3 63.4 + - - +
156A ARG 3.0 1.4 + - - -
157A HIS* 3.0 27.5 + - + +
158A LEU* 3.6 32.8 - - + +
165A PRO* 5.1 2.0 - - + -
179A MET* 5.6 0.4 - - - -
194A PHE* 5.3 1.1 - - + -
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Residues in contact with TYR 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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151A MET* 3.0 31.5 + - + +
152A THR 3.5 17.7 - - - -
153A GLU 3.2 0.8 + - - -
154A LEU* 1.3 76.3 - - - +
156A ARG* 1.3 93.6 + - + +
157A HIS 3.2 1.2 + - - -
158A LEU* 3.3 11.9 + - - +
183A MET* 3.4 39.4 - - + +
186A LEU* 3.8 36.1 - - + -
187A SER* 4.5 10.8 - - - -
155B TYR* 3.6 27.1 + + - -
186B LEU* 2.6 28.5 + - + -
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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