Contacts of the helix formed by residues 153 - 161 (chain D) in PDB entry 2BHT
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 THR 153 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D GLY* 6.0 1.6 - - - -
43D ARG* 3.9 11.8 + - - +
149D ALA* 2.3 31.1 + - - +
151D TYR 3.3 1.2 - - - -
152D THR* 1.3 94.2 - - - +
154D THR* 1.3 74.3 + - - +
156D PRO* 3.1 5.7 - - - +
157D GLU* 3.0 40.7 + - - +
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Residues in contact with THR 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LYS* 4.9 2.5 - - + -
32D GLU* 4.7 7.4 - - - +
40D VAL* 6.0 0.2 - - + -
43D ARG* 3.1 27.8 + - - +
150D HIS* 2.6 42.7 + - + +
153D THR* 1.3 79.1 + - - +
155D GLY* 1.3 63.8 + - - +
157D GLU* 3.2 7.7 + - - +
158D ILE* 3.0 40.9 + - + +
178D THR* 4.9 1.8 - - + -
182D VAL* 4.1 8.7 - - + -
278D ILE* 4.4 12.1 - - + -
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Residues in contact with GLY 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D HIS 3.2 9.8 + - - -
154D THR* 1.3 78.9 - - - +
156D PRO* 1.3 67.4 - - - +
158D ILE* 3.3 1.9 + - - -
159D TRP* 2.9 21.0 + - - +
182D VAL* 4.1 10.6 - - - +
185D PHE* 3.7 14.4 - - - -
186D MET* 3.3 23.5 - - - +
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Residues in contact with PRO 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D TYR 3.2 26.9 - - - +
152D THR* 3.7 16.2 - - - +
153D THR 3.1 13.2 - - - +
155D GLY* 1.3 89.8 - - - +
157D GLU* 1.3 56.0 + - + +
159D TRP* 3.2 2.8 + - + +
160D GLN* 2.8 30.3 + - - +
185D PHE* 3.9 25.8 - - + -
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Residues in contact with GLU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D GLY* 4.1 0.7 - - - -
10D ASN* 3.0 30.9 + - - +
11D THR 3.4 0.3 + - - -
30D LYS* 2.6 22.0 + - - +
43D ARG* 2.5 34.5 + - - -
153D THR* 3.0 32.5 + - - +
154D THR* 3.3 6.8 - - - +
156D PRO* 1.3 75.1 - - + +
158D ILE* 1.3 53.5 + - - +
160D GLN* 2.8 8.7 + - - -
161D GLN* 2.5 55.5 + - + +
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Residues in contact with ILE 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LEU* 4.8 3.6 - - + -
30D LYS* 4.4 17.0 - - + -
154D THR* 3.0 24.9 + - + +
155D GLY* 3.7 4.0 - - - +
157D GLU* 1.3 78.9 - - - +
159D TRP* 1.3 57.7 + - - +
161D GLN* 4.0 6.3 - - - +
162D THR* 2.9 27.2 + - + +
166D ILE* 3.7 21.8 - - + +
169D PHE* 3.3 31.9 - - + -
182D VAL* 4.8 3.1 - - + -
186D MET* 3.5 19.1 - - + -
276D VAL* 3.9 17.5 - - + -
278D ILE* 3.8 15.9 - - + -
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Residues in contact with TRP 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D GLY 2.9 13.5 + - - +
156D PRO 3.5 7.2 - - - +
158D ILE* 1.3 79.0 - - - +
160D GLN* 1.3 62.1 + - - +
162D THR 3.5 0.5 + - - -
163D GLY 3.2 2.1 + - - -
164D GLY* 2.5 59.2 + - - +
166D ILE* 3.3 30.1 - - + -
185D PHE* 3.6 16.2 - + + -
186D MET* 3.3 24.0 - - - +
189D GLN* 3.8 37.8 + - + -
190D SER* 5.1 4.5 - - - -
191D LYS* 3.9 24.5 - - + -
193D VAL* 3.6 17.3 - - + -
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Residues in contact with GLN 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D PRO 2.8 15.4 + - - +
157D GLU* 2.8 7.4 + - - +
159D TRP* 1.3 78.1 - - - +
161D GLN* 1.3 74.5 + - - +
163D GLY* 3.2 12.6 + - - +
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Residues in contact with GLN 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET 4.3 9.2 + - - +
10D ASN 5.2 2.6 + - - -
11D THR 2.9 23.1 + - - +
12D PRO* 4.0 1.8 - - - +
13D LEU* 3.5 43.7 - - + +
28D TRP* 6.0 0.5 - - - -
30D LYS* 3.0 30.4 + - - -
157D GLU* 2.5 31.7 + - + +
158D ILE* 4.1 2.4 + - - -
160D GLN* 1.3 83.8 - - - +
162D THR* 1.3 60.2 + - - +
163D GLY 3.5 0.2 - - - -
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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