Contacts of the helix formed by residues 159 - 177 (chain B) in PDB entry 2BME
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 ASN 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LYS* 3.4 15.0 - - - +
150B LEU* 4.2 21.1 - - + +
151B GLU 2.9 29.1 + - - +
152B THR* 3.8 7.7 - - + +
157B GLY 3.1 2.4 + - - -
158B GLU* 1.3 78.3 + - - +
160B VAL* 1.3 58.7 + - - +
161B GLU 3.7 1.1 - - - -
162B GLU* 3.8 18.5 - - + +
163B ALA* 3.0 27.4 + - - +
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Residues in contact with VAL 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 3.6 49.1 - - + +
29B GLN* 4.2 8.3 - - + -
30B PHE* 4.0 19.3 - - + +
152B THR* 4.5 2.7 - - - -
153B SER 3.3 27.8 - - - +
157B GLY* 3.0 18.6 + - - +
158B GLU 3.8 3.6 - - - +
159B ASN* 1.3 73.2 - - - +
161B GLU* 1.3 69.3 + - - +
162B GLU 3.1 0.9 - - - -
163B ALA* 3.1 13.1 + - - +
164B PHE* 3.3 23.3 + - + -
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Residues in contact with GLU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PHE* 3.8 25.7 - - + +
33B LYS* 4.7 7.8 - - - -
50B LYS* 3.8 23.0 + - - -
52B ILE* 5.0 5.1 - - - +
157B GLY 4.5 1.8 + - - -
160B VAL* 1.3 78.9 - - - +
162B GLU* 1.3 58.8 + - - +
164B PHE* 3.1 4.3 + - - +
165B VAL* 2.9 49.1 + - + +
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Residues in contact with GLU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B LEU* 4.1 12.8 - - + -
159B ASN* 3.6 26.3 + - + +
160B VAL 3.1 0.6 - - - -
161B GLU* 1.3 80.9 - - - +
163B ALA* 1.3 55.8 + - - +
165B VAL* 4.4 7.0 - - - +
166B GLN* 2.8 40.1 + - + +
169B ARG* 2.9 35.0 + - - -
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Residues in contact with ALA 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 3.9 11.4 - - + +
119B ILE* 3.7 10.6 - - + +
121B CYS* 3.8 26.7 - - - -
150B LEU* 3.5 19.9 - - + +
152B THR* 4.6 2.9 - - + -
159B ASN 3.0 18.2 + - - +
160B VAL* 3.1 5.8 + - - +
162B GLU* 1.3 76.3 - - - +
164B PHE* 1.3 60.7 + - - +
166B GLN* 3.5 0.6 + - - +
167B CYS* 3.1 23.7 + - - +
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Residues in contact with PHE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 3.7 22.1 - + - -
14B LEU 6.0 0.2 - - - -
15B VAL* 4.4 12.1 - - + -
26B LEU* 4.4 7.9 - - + -
27B LEU* 4.4 12.6 - - + -
30B PHE* 3.5 58.8 - + + -
52B ILE* 4.5 2.5 - - - +
61B LEU* 4.3 3.5 - - + +
63B ILE* 3.6 31.9 - - + -
87B LEU* 3.5 33.2 - - + -
160B VAL* 3.3 28.5 - - + -
161B GLU 3.1 4.1 + - - +
163B ALA* 1.3 77.4 - - - +
165B VAL* 1.3 62.4 + - - +
167B CYS* 3.4 3.6 + - - +
168B ALA* 3.1 20.1 + - - +
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Residues in contact with VAL 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ILE* 3.9 26.0 - - + -
53B ASN 5.8 2.7 - - - +
54B VAL* 4.5 12.8 - - + -
161B GLU* 2.9 39.9 + - + +
162B GLU* 3.9 9.2 - - - +
164B PHE* 1.3 76.3 - - + +
166B GLN* 1.3 60.2 + - - +
168B ALA* 3.2 2.3 + - - +
169B ARG* 2.8 63.1 + - + +
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Residues in contact with GLN 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ILE* 4.2 13.0 - - + -
148B MET* 3.5 38.2 - - - +
150B LEU* 4.6 3.8 - - + +
162B GLU* 2.8 37.1 + - + +
163B ALA* 3.7 5.6 - - - +
165B VAL* 1.3 76.8 - - - +
167B CYS* 1.3 63.9 + - - +
169B ARG* 3.0 32.2 + - - +
170B LYS* 3.0 40.9 + - - +
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Residues in contact with CYS 167 (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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13B PHE* 3.5 26.5 - - + -
85B GLY* 3.6 25.4 - - - -
86B ALA 3.9 9.2 - - - -
87B LEU* 4.2 4.0 - - + -
117B VAL* 3.7 18.7 - - - +
119B ILE* 3.6 20.5 - - + +
163B ALA 3.1 9.4 + - - +
164B PHE 3.5 9.2 - - - +
165B VAL 3.2 0.2 - - - -
166B GLN* 1.3 78.8 - - - +
168B ALA* 1.3 64.0 + - - +
170B LYS* 3.2 2.3 + - - +
171B ILE* 3.0 26.8 + - - +
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Residues in contact with ALA 168 (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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11B PHE* 4.1 2.6 - - + -
13B PHE* 3.7 15.1 - - + -
52B ILE* 3.8 21.8 - - + -
54B VAL* 4.4 7.2 - - + -
59B VAL* 4.5 10.1 - - + -
61B LEU* 4.5 6.5 - - + -
164B PHE 3.1 10.8 + - - +
165B VAL 3.2 6.5 + - - +
167B CYS* 1.3 80.0 - - - +
169B ARG* 1.4 61.5 + - - +
171B ILE* 3.3 7.6 + - - +
172B LEU* 2.9 28.9 + - - +
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Residues in contact with ARG 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B VAL* 3.7 22.6 - - + +
162B GLU* 2.9 31.3 + - - -
165B VAL* 2.8 43.2 + - + +
166B GLN* 3.0 29.4 + - - +
168B ALA* 1.4 72.3 - - - +
170B LYS* 1.3 59.7 + - + +
172B LEU* 3.3 10.5 + - - +
173B ASN* 2.9 38.6 + - - +
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Residues in contact with LYS 170 (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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117B VAL* 3.6 31.2 - - + -
118B ILE 6.0 0.2 - - - +
119B ILE* 4.0 7.2 - - + -
148B MET* 3.7 34.6 - - + +
166B GLN* 3.0 34.4 + - - +
169B ARG* 1.3 77.4 - - + +
171B ILE* 1.3 62.9 + - - +
173B ASN* 3.4 9.3 + - - +
174B LYS* 3.1 27.6 + - - +
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Residues in contact with ILE 171 (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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11B PHE* 3.6 32.8 - - + -
13B PHE* 3.3 35.0 - - + -
84B ALA* 3.6 37.0 - - + +
85B GLY 4.1 0.2 - - - +
115B ASN 5.9 0.2 - - - +
117B VAL* 3.7 14.1 - - + -
167B CYS* 3.0 18.7 + - - +
168B ALA 3.6 5.8 - - - +
170B LYS* 1.3 76.8 - - - +
172B LEU* 1.3 62.1 + - - +
174B LYS* 3.1 8.9 + - + +
175B ILE* 3.0 30.0 + - + +
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Residues in contact with LEU 172 (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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9B PHE* 3.7 49.8 - - + -
11B PHE* 4.0 10.8 - - + -
54B VAL* 3.8 34.8 - - + -
57B LYS* 4.1 19.1 - - + +
59B VAL* 4.0 11.2 - - + -
168B ALA 2.9 20.7 + - - +
169B ARG* 3.6 4.5 - - - +
171B ILE* 1.3 75.8 - - - +
173B ASN* 1.3 61.4 + - - +
175B ILE* 3.3 9.0 + - + +
176B GLU* 3.0 30.4 + - - +
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Residues in contact with ASN 173 (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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169B ARG* 2.9 26.5 + - - +
170B LYS* 3.7 9.6 - - - +
171B ILE 3.2 0.2 - - - -
172B LEU* 1.3 75.8 - - - +
174B LYS* 1.4 59.9 + - + +
176B GLU* 3.8 9.2 + - - +
177B SER* 2.9 38.6 + - - +
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Residues in contact with LYS 174 (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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114B GLN 4.9 0.8 + - - -
115B ASN* 2.7 56.0 + - + +
116B ILE 3.9 4.6 + - - -
117B VAL* 3.7 20.7 - - + +
170B LYS* 3.1 17.3 + - - +
171B ILE* 3.1 10.3 + - + +
173B ASN* 1.4 73.0 - - - +
175B ILE* 1.3 69.3 + - + +
177B SER 3.3 18.3 + - - +
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Residues in contact with ILE 175 (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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9B PHE* 4.6 22.2 - - + -
11B PHE* 3.9 32.8 - - + -
171B ILE* 3.0 22.9 + - + +
172B LEU* 3.5 11.4 - - + +
173B ASN 3.3 0.2 - - - -
174B LYS* 1.3 79.2 - - + +
176B GLU* 1.3 63.9 + - + +
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Residues in contact with GLU 176 (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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57B LYS* 4.1 20.6 + - - -
172B LEU 3.0 16.3 + - - +
173B ASN* 3.8 10.4 + - - +
175B ILE* 1.3 82.5 - - + +
177B SER* 1.3 65.1 + - - +
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Residues in contact with SER 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ASN* 2.9 25.1 + - - +
174B LYS* 3.3 16.0 - - - +
175B ILE 3.6 0.6 - - - -
176B GLU* 1.3 87.6 - - - +
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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
------------------------------------------------------------
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