Contacts of the helix formed by residues 139 - 155 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B ASP* 2.5 30.4 + - - -
137B GLY 4.0 1.2 + - - -
138B LYS* 1.3 76.0 - - - +
140B GLU* 1.3 66.7 + - - +
141B GLY* 3.7 3.8 + - - -
142B GLU* 3.0 24.3 + - - +
143B VAL* 3.0 22.4 + - - +
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Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B LYS 3.9 0.2 + - - -
139B SER* 1.3 73.2 - - - +
141B GLY* 1.3 57.3 + - - +
143B VAL* 3.3 2.3 + - - +
144B MET* 2.8 28.7 + - + +
174B ARG* 3.9 40.4 + - - +
178B PHE* 3.9 21.7 - - + -
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Residues in contact with GLY 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ASN* 5.3 7.4 - - - -
70B ASP* 5.3 0.7 - - - -
139B SER* 3.1 6.2 + - - -
140B GLU* 1.3 77.5 - - - +
142B GLU* 1.3 64.4 + - - +
144B MET* 3.2 9.8 + - - +
145B ARG* 2.9 44.3 + - - +
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Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B TRP* 3.8 19.2 - - + -
69B ASP* 3.2 11.5 - - - +
70B ASP* 2.7 36.3 + - - +
133B PHE* 4.9 1.3 - - - -
137B GLY 4.4 2.1 - - - +
138B LYS* 3.3 25.9 - - + +
139B SER* 3.0 31.4 + - - +
141B GLY* 1.3 75.9 - - - +
143B VAL* 1.3 59.0 + - - +
145B ARG* 3.5 23.4 - - - +
146B PHE* 2.9 30.2 + - - +
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Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B PHE* 5.6 1.1 - - + -
133B PHE* 4.4 20.4 - - + -
135B PRO* 4.6 10.8 - - + +
138B LYS* 3.9 20.0 - - + +
139B SER 3.0 20.0 + - - +
140B GLU 3.6 4.0 - - - +
142B GLU* 1.3 76.9 - - - +
144B MET* 1.3 61.8 + - - +
146B PHE* 3.3 1.9 + - - +
147B CYS* 2.9 28.4 + - - -
174B ARG* 3.5 25.1 - - - +
175B GLU* 3.4 36.1 - - + +
178B PHE* 4.4 1.3 - - + -
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Residues in contact with MET 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A VAL* 4.8 18.4 - - + -
74A ILE* 6.5 1.1 - - + -
140B GLU 2.8 20.9 + - - +
141B GLY* 3.2 8.7 + - - +
143B VAL* 1.3 72.0 - - - +
145B ARG* 1.3 71.0 + - + +
147B CYS* 3.2 3.5 + - - +
148B GLN* 2.9 64.6 + - - +
178B PHE* 3.4 42.8 - - + -
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Residues in contact with ARG 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A VAL* 5.9 4.8 - - + +
72A ASN* 4.9 8.9 + - - -
145A ARG* 4.9 17.5 - - - +
67B TRP* 4.5 7.7 - - + +
68B VAL* 2.9 40.3 + - - +
69B ASP 3.6 7.5 + - - -
70B ASP* 3.0 26.2 + - - -
141B GLY* 2.9 32.4 + - - +
142B GLU* 3.5 17.2 - - - +
144B MET* 1.3 87.7 - - + +
146B PHE* 1.3 58.1 + - - +
148B GLN* 3.8 10.5 - - - +
149B ALA* 2.9 31.5 + - - +
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Residues in contact with PHE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B VAL* 3.7 21.8 - - + -
67B TRP* 3.8 25.5 - + + +
77B ASN* 4.2 6.5 - - + -
97B PHE* 3.5 35.4 - + - -
131B SER* 3.3 27.4 - - - -
133B PHE* 3.3 53.6 - + + -
142B GLU 2.9 17.1 + - - +
143B VAL 3.7 4.0 - - - +
145B ARG* 1.3 78.2 - - - +
147B CYS* 1.3 64.2 + - - +
149B ALA* 3.3 1.2 + - - +
150B LEU* 3.0 37.0 + - + +
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Residues in contact with CYS 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B PHE* 3.9 26.0 - - - -
143B VAL* 2.9 23.0 + - - +
144B MET 3.5 3.8 - - - +
146B PHE* 1.3 79.1 - - - +
148B GLN* 1.3 63.2 + - - +
150B LEU* 3.4 6.3 + - - +
151B MET* 3.1 29.0 + - - +
175B GLU* 4.0 32.8 - - - -
178B PHE* 3.7 19.7 - - + -
179B MET* 4.0 12.1 - - + +
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Residues in contact with GLN 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B MET* 2.9 53.4 + - + +
145B ARG* 3.8 9.9 - - - +
147B CYS* 1.3 73.8 - - + +
149B ALA* 1.3 65.3 + - - +
151B MET* 3.2 3.3 + - - +
152B THR* 3.0 26.6 + - - -
178B PHE* 4.7 7.8 + - + +
182B MET* 4.1 40.4 - - + +
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LYS* 4.5 5.2 + - - -
64B ARG 5.5 0.5 - - - +
65B VAL* 3.8 16.0 - - + +
66B VAL 3.5 24.7 - - - +
67B TRP* 4.3 6.7 - - + -
145B ARG 2.9 18.1 + - - +
146B PHE 3.7 4.0 - - - +
148B GLN* 1.3 75.8 - - - +
150B LEU* 1.3 63.7 + - - +
152B THR* 3.4 20.7 - - - +
153B GLU* 4.0 3.1 + - - +
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B PHE* 3.7 11.9 - - + -
65B VAL* 3.7 12.5 - - + +
79B ALA* 3.8 23.6 - - + -
95B MET* 4.0 13.0 - - + -
97B PHE* 4.0 14.1 - - + -
131B SER* 4.4 1.3 - - - -
146B PHE* 3.0 41.8 + - + +
147B CYS* 3.6 5.2 - - - +
149B ALA* 1.3 77.3 - - - +
151B MET* 1.3 67.3 + - + +
153B GLU* 3.1 8.8 + - - +
154B LEU* 2.9 51.5 + - + +
179B MET* 4.2 10.5 - - - -
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Residues in contact with MET 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B CYS 3.1 16.6 + - - +
148B GLN 3.2 4.0 + - - +
150B LEU* 1.3 72.3 - - - +
152B THR* 1.3 64.8 + - - +
153B GLU 3.1 2.2 - - - -
154B LEU* 3.6 19.3 - - - +
155B TYR* 2.9 42.3 + - + +
158B LEU* 3.9 9.9 - - + -
179B MET* 3.6 39.5 - - + +
182B MET* 3.8 16.8 - - + -
183B MET* 3.7 32.8 - - + -
186B LEU* 3.6 3.0 - - + +
194B PHE* 3.9 17.7 - - + -
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Residues in contact with THR 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A MET* 3.7 22.9 - - + +
185A LYS* 3.2 39.9 - - + +
186A LEU* 3.8 10.7 - - + +
148B GLN 3.0 14.6 + - - -
149B ALA* 3.4 15.4 - - - +
151B MET* 1.3 78.7 - - - +
153B GLU* 1.3 56.3 + - - +
155B TYR* 3.6 8.5 - - - -
156B ARG* 3.2 18.0 + - - -
182B MET* 3.9 10.4 - - - +
186B LEU* 3.9 9.8 - - - +
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Residues in contact with GLU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LYS* 3.9 22.2 - - - +
188A ASN* 6.1 0.3 - - - -
61B ILE* 4.6 5.2 - - - +
63B PHE* 3.3 44.5 - - + +
64B ARG 5.2 2.7 - - - +
149B ALA 4.0 2.2 + - - +
150B LEU 3.1 3.8 + - - +
151B MET 3.1 0.2 - - - -
152B THR* 1.3 80.1 - - - +
154B LEU* 1.3 65.1 + - - +
155B TYR 3.3 1.7 + - - -
156B ARG* 3.2 39.0 + - - +
157B HIS* 2.9 26.7 + - - +
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Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ILE* 5.7 0.2 - - + -
63B PHE* 4.0 16.6 - - + -
81B ARG* 3.9 26.5 - - + -
95B MET* 3.8 20.9 - - + -
150B LEU* 2.9 37.2 + - + +
151B MET* 3.3 11.6 + - - -
153B GLU* 1.3 77.7 - - - +
155B TYR* 1.3 65.8 + - - +
156B ARG 3.0 1.4 + - - -
157B HIS* 3.0 28.0 + - + -
158B LEU* 3.5 36.6 - - + +
165B PRO* 5.2 2.0 - - + -
179B MET* 5.6 0.2 - - - -
194B PHE* 5.2 1.8 - - + -
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Residues in contact with TYR 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A TYR* 3.6 26.3 + - - -
186A LEU* 2.5 28.9 + - + -
151B MET* 2.9 30.9 + - + +
152B THR 3.6 17.3 - - - -
153B GLU 3.3 1.1 + - - -
154B LEU* 1.3 75.3 - - - +
156B ARG* 1.3 94.1 + - + +
157B HIS 3.2 1.2 + - - -
158B LEU* 3.3 12.3 + - - +
183B MET* 3.3 40.6 - - + +
186B LEU* 3.7 33.2 - - + -
187B SER* 4.5 13.7 - - - -
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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