Contacts of the helix formed by residues 159 - 177 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C LEU* 4.2 19.1 - - + +
151C GLU 3.0 24.4 + - - +
152C THR* 3.9 8.0 - - + +
157C GLY 3.1 2.0 + - - -
158C GLU* 1.3 87.4 + - - +
160C VAL* 1.3 57.9 + - - +
161C GLU 3.6 1.6 - - - -
162C GLU* 3.8 19.5 - - + +
163C ALA* 2.9 30.0 + - - +
1179C TRS 3.5 20.6 + - - -
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Residues in contact with VAL 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 3.5 50.3 - - + +
29C GLN* 4.1 10.8 - - + -
30C PHE* 4.0 18.6 - - + +
152C THR* 4.4 4.0 - - - -
153C SER 3.3 27.1 - - - +
157C GLY* 3.1 17.4 + - - +
158C GLU 3.6 4.9 - - - +
159C ASN* 1.3 73.4 - - - +
161C GLU* 1.3 69.4 + - - +
163C ALA* 3.1 12.6 + - - +
164C PHE* 3.2 22.9 - - + -
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Residues in contact with GLU 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C PHE* 3.7 32.7 - - + +
33C LYS* 4.6 16.6 + - - -
50C LYS* 3.7 14.7 + - - -
52C ILE* 5.1 3.1 - - - +
157C GLY 4.5 1.8 + - - -
160C VAL* 1.3 79.0 - - - +
162C GLU* 1.3 59.2 + - - +
164C PHE* 3.2 4.3 + - - +
165C VAL* 2.8 48.1 + - + +
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Residues in contact with GLU 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C LEU* 4.0 15.9 - - + -
159C ASN* 3.6 25.7 - - - +
160C VAL 3.1 0.4 - - - -
161C GLU* 1.3 80.2 - - - +
163C ALA* 1.3 56.5 + - - +
165C VAL* 4.3 5.6 - - - +
166C GLN* 2.7 37.6 + - + +
169C ARG* 2.8 36.6 + - - -
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Residues in contact with ALA 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LEU* 3.9 11.2 - - + +
119C ILE* 3.6 14.9 - - + +
121C CYS* 3.9 28.3 - - - -
150C LEU* 3.5 19.0 - - + +
152C THR* 4.7 3.1 - - + -
159C ASN 2.9 17.9 + - - +
160C VAL* 3.1 6.4 + - - +
162C GLU* 1.3 74.7 - - - +
164C PHE* 1.3 63.0 + - - +
166C GLN* 3.4 0.7 + - - +
167C CYS* 3.1 19.4 + - - +
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Residues in contact with PHE 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C PHE* 3.7 26.9 - + - -
15C VAL* 4.5 10.5 - - + -
26C LEU* 4.3 11.2 - - + -
27C LEU* 4.2 17.7 - - + -
30C PHE* 3.6 56.1 - + + -
52C ILE* 4.9 1.8 - - - -
61C LEU* 4.4 3.3 - - + +
63C ILE* 3.9 26.9 - - + -
87C LEU* 3.6 29.8 - - + -
160C VAL* 3.2 26.0 - - + -
161C GLU 3.2 5.6 + - - +
163C ALA* 1.3 78.1 - - - +
165C VAL* 1.3 64.5 + - - +
167C CYS* 3.3 4.3 + - - +
168C ALA* 3.1 22.9 + - - +
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Residues in contact with VAL 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ILE* 4.1 26.9 - - + -
53C ASN 5.9 1.8 - - - +
54C VAL* 4.7 11.4 - - + -
161C GLU* 2.8 40.5 + - + +
162C GLU* 3.9 9.4 - - - +
164C PHE* 1.3 74.5 - - + +
166C GLN* 1.3 57.0 + - - +
168C ALA* 3.2 3.5 + - - +
169C ARG* 2.8 64.5 + - + +
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Residues in contact with GLN 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C ILE* 4.0 13.5 - - + -
148C MET* 3.6 37.0 - - - +
150C LEU* 4.6 2.7 - - + -
162C GLU* 2.7 35.0 + - + +
163C ALA* 3.8 5.2 - - - +
165C VAL* 1.3 68.7 - - - +
167C CYS* 1.3 67.9 + - - +
169C ARG* 2.9 38.4 + - - +
170C LYS* 3.0 41.4 + - - +
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Residues in contact with CYS 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C PHE* 3.5 25.8 - - + -
85C GLY* 3.6 14.6 - - - -
86C ALA 3.8 7.2 - - - -
87C LEU* 4.4 3.6 - - + -
117C VAL* 3.6 30.1 - - - +
119C ILE* 3.7 18.3 - - + +
163C ALA 3.1 11.2 + - - +
164C PHE 3.5 9.2 - - - +
165C VAL 3.3 0.2 - - - -
166C GLN* 1.3 81.4 - - - +
168C ALA* 1.3 62.7 + - - +
170C LYS* 3.3 2.6 + - - +
171C ILE* 3.1 26.7 + - - +
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Residues in contact with ALA 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C PHE* 3.9 13.0 - - + -
13C PHE* 3.7 13.6 - - + -
52C ILE* 3.8 22.9 - - + -
54C VAL* 4.6 7.0 - - + -
59C VAL* 4.6 3.6 - - + -
61C LEU* 4.5 5.8 - - + -
164C PHE 3.1 10.6 + - - +
165C VAL 3.2 7.4 + - - +
167C CYS* 1.3 80.2 - - - +
169C ARG* 1.3 62.5 + - - +
171C ILE* 3.3 3.0 + - - +
172C LEU* 2.9 30.2 + - - +
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Residues in contact with ARG 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C VAL* 3.8 23.2 - - + +
162C GLU* 2.8 31.5 + - - -
165C VAL* 2.8 43.1 + - + +
166C GLN* 2.9 33.2 + - - +
168C ALA* 1.3 72.6 - - - +
170C LYS* 1.3 61.3 + - + +
172C LEU* 3.3 9.0 + - - +
173C ASN* 2.9 40.0 + - - +
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Residues in contact with LYS 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C VAL* 3.7 31.2 - - + -
119C ILE* 4.1 8.3 - - + -
148C MET* 3.8 33.6 - - + +
166C GLN* 3.0 31.7 + - - +
167C CYS 3.3 0.2 + - - -
169C ARG* 1.3 77.7 - - + +
171C ILE* 1.3 60.4 + - - +
173C ASN* 3.4 10.6 + - - +
174C LYS* 3.0 31.8 + - + +
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Residues in contact with ILE 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A PHE* 5.1 0.9 - - + -
136A LEU* 4.7 10.3 - - + -
11C PHE* 3.6 33.4 - - + -
13C PHE* 3.5 32.3 - - + -
84C ALA* 3.6 33.9 - - + +
85C GLY* 4.0 3.1 - - - +
117C VAL* 3.7 20.0 - - + -
167C CYS* 3.1 16.3 + - - +
168C ALA 3.3 4.7 + - - +
170C LYS* 1.3 72.1 - - - +
172C LEU* 1.3 67.2 + - - +
174C LYS* 3.1 8.3 + - + +
175C ILE* 2.9 28.2 + - + +
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Residues in contact with LEU 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A GLN* 5.1 2.5 - - - +
9C PHE* 3.7 48.2 - - + -
11C PHE* 3.8 11.9 - - + -
54C VAL* 4.0 25.6 - - + -
57C LYS* 4.2 17.0 - - + -
59C VAL* 3.9 22.2 - - + -
168C ALA 2.9 22.3 + - - +
169C ARG* 3.6 4.0 - - - +
171C ILE* 1.3 77.0 - - - +
173C ASN* 1.3 61.7 + - - +
175C ILE* 3.2 7.3 + - + +
176C GLU* 2.9 35.1 + - - +
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Residues in contact with ASN 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C ARG* 2.9 28.0 + - - +
170C LYS* 3.7 10.5 - - - +
171C ILE 3.2 0.2 - - - -
172C LEU* 1.3 79.8 - - - +
174C LYS* 1.4 52.1 + - - +
176C GLU* 3.8 10.6 + - - +
177C SER* 2.8 37.8 + - - -
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Residues in contact with LYS 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A LEU* 3.9 33.0 - - + +
140A ARG* 3.2 18.5 + - - -
115C ASN* 3.1 30.6 + - - +
116C ILE 4.7 2.0 + - - -
117C VAL* 3.7 20.5 - - + +
170C LYS 3.0 19.5 + - - +
171C ILE* 3.1 9.6 + - + +
173C ASN* 1.4 73.5 - - + +
175C ILE* 1.3 65.0 + - - +
177C SER 3.2 9.9 - - - +
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Residues in contact with ILE 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A PHE* 5.1 0.4 - - + -
136A LEU* 4.4 18.6 - - + +
139A SER* 3.7 48.0 - - - +
140A ARG* 2.8 35.0 + - - +
143A GLN* 3.4 22.0 - - - +
9C PHE* 4.4 10.8 - - + -
11C PHE* 3.8 33.4 - - + -
171C ILE* 2.9 23.9 + - + +
172C LEU* 3.2 9.8 + - + +
174C LYS* 1.3 76.4 - - - +
176C GLU* 1.3 56.5 + - - +
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Residues in contact with GLU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ARG* 4.0 10.2 + - - +
143A GLN* 2.7 36.0 + - - +
57C LYS* 3.7 19.2 + - - -
172C LEU* 2.9 20.6 + - - +
173C ASN* 3.8 11.4 + - - +
175C ILE* 1.3 79.4 - - - +
177C SER* 1.3 67.5 + - - +
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Residues in contact with SER 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ARG* 2.5 23.0 + - - +
173C ASN 2.8 15.3 + - - -
174C LYS* 3.2 16.5 - - - +
176C GLU* 1.3 83.0 + - - +
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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
------------------------------------------------------------
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