Contacts of the helix formed by residues 142 - 151 (chain K) in PDB entry 2BM8
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 LEU 142 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140K SER 4.3 2.2 + - - +
141K ASP* 1.3 77.5 + - - +
143K THR* 1.3 62.0 + - + +
144K THR 3.1 5.4 - - - -
145K PHE* 3.2 25.4 + - + +
146K GLU* 4.0 2.4 + - - -
164K ASN* 4.4 11.4 - - - +
167K ASN* 4.1 26.0 - - + +
168K ILE* 4.0 26.9 - - + -
170K LYS* 6.4 2.7 - - - -
171K TRP* 4.1 34.6 + - + -
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Residues in contact with THR 143 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141K ASP* 2.8 25.2 + - - +
142K LEU* 1.3 75.5 - - + +
144K THR* 1.3 63.6 + - - +
146K GLU* 3.2 26.2 + - + +
147K HIS 5.0 0.2 + - - -
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Residues in contact with THR 144 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115K ILE* 4.6 9.4 - - + -
136K GLN 5.0 1.3 - - - +
137K GLY* 3.7 26.2 - - - -
138K ASP* 3.4 24.0 + - - +
141K ASP* 3.5 25.3 + - - +
143K THR* 1.3 79.4 + - - +
145K PHE* 1.3 72.8 + - + +
147K HIS* 3.0 26.9 + - + -
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Residues in contact with PHE 145 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88K LEU* 4.0 21.5 - - + -
115K ILE* 4.0 21.5 - - + -
138K ASP 4.5 1.3 - - - -
139K CYS* 4.4 6.5 - - - -
141K ASP 3.8 18.6 - - - -
142K LEU* 3.2 22.3 + - + +
143K THR 3.2 1.0 - - - -
144K THR* 1.3 85.3 - - + +
146K GLU* 1.3 65.1 + - - +
147K HIS* 3.2 3.8 - - - -
148K LEU* 3.0 34.2 + - + +
157K PHE* 4.0 24.9 - + - -
168K ILE* 3.8 40.2 - - + -
171K TRP* 3.4 29.7 - + + -
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Residues in contact with GLU 146 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142K LEU 4.0 2.4 + - - +
143K THR* 3.2 25.9 + - + +
144K THR 3.4 0.4 - - - -
145K PHE* 1.3 75.8 - - - +
147K HIS* 1.3 62.0 + - - +
148K LEU 3.1 1.6 + - - -
149K ARG* 3.3 24.1 + - - +
150K GLU* 4.7 2.4 + - - +
171K TRP* 4.3 17.0 + - - -
175K HIS* 5.7 2.3 - - - +
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Residues in contact with HIS 147 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K ILE* 4.6 0.8 - - + +
115K ILE* 4.2 11.6 - - + +
135K HIS* 3.5 52.0 + + + +
144K THR* 3.0 30.0 + - + -
145K PHE* 4.2 0.2 - - - -
146K GLU* 1.3 76.2 - - - +
148K LEU* 1.3 90.4 + - + +
149K ARG 3.3 0.4 - - - -
150K GLU* 3.2 33.1 - - + +
151K MET* 4.3 11.1 - - + +
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Residues in contact with LEU 148 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84K THR* 5.3 0.2 - - + -
86K VAL* 4.1 20.4 - - + -
113K ILE* 3.7 33.0 - - + -
115K ILE* 4.0 17.9 - - + -
145K PHE* 3.0 36.5 + - + +
147K HIS* 1.3 98.4 - - + +
149K ARG* 1.3 63.3 + - - +
150K GLU 3.1 2.5 - - - -
151K MET* 3.1 24.1 + - + +
155K LEU* 5.6 0.4 - - + -
157K PHE* 4.6 3.6 - - + -
171K TRP* 4.3 2.5 - - + -
176K LEU* 3.2 36.0 - - + +
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Residues in contact with ARG 149 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145K PHE 4.6 0.2 + - - -
146K GLU* 3.3 21.2 + - - +
147K HIS 3.3 1.0 - - - -
148K LEU* 1.3 77.7 - - - +
150K GLU* 1.3 63.1 + - - +
151K MET 3.0 8.4 + - - +
153K HIS* 3.5 27.4 - - - -
171K TRP* 5.2 2.9 - - + -
175K HIS* 3.4 29.4 + - + +
176K LEU* 3.7 25.3 + - - +
177K LEU 5.4 0.6 + - - -
178K GLU* 4.2 11.9 + - - +
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Residues in contact with GLU 150 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146K GLU 5.1 1.5 - - - +
147K HIS* 3.2 26.5 - - + +
148K LEU 3.1 0.2 - - - -
149K ARG* 1.3 80.0 - - - +
151K MET* 1.3 65.7 + - + +
152K ALA 4.2 0.2 + - - -
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Residues in contact with MET 151 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84K THR* 3.6 18.4 - - + +
111K GLN* 5.2 13.7 - - + -
113K ILE* 3.4 36.1 - - + -
133K THR* 5.7 4.3 - - + +
135K HIS* 5.2 6.3 - - + -
147K HIS* 4.3 17.7 - - + +
148K LEU* 3.4 25.1 - - + +
149K ARG 3.0 7.3 + - - +
150K GLU* 1.3 87.0 - - + +
152K ALA* 1.3 64.8 + - - +
153K HIS* 3.5 18.7 + - - -
155K LEU* 4.8 4.0 - - + +
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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