Contacts of the helix formed by residues 155 - 166 (chain L) in PDB entry 2B4X
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 155 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20L MET* 5.0 1.4 - - - +
154L PHE* 1.3 72.2 - - - +
156L GLU* 1.3 62.8 + - - +
157L THR 2.6 28.8 + - - -
158L TYR* 3.0 10.0 + - - +
159L GLN* 3.1 20.6 + - - +
352L PRO 5.4 1.2 + - - +
353L GLY* 3.4 22.0 + - - +
354L ILE 2.7 13.9 + - - +
356L ALA* 3.2 20.6 + - - +
841L NAG 1.4 66.5 + - - +
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Residues in contact with GLU 156 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153L THR* 6.1 0.5 - - - +
154L PHE 3.2 10.1 + - - +
155L ASN* 1.3 72.9 + - - +
157L THR* 1.3 64.1 + - - +
159L GLN* 4.0 22.1 + - - +
160L ASP* 3.1 41.9 + - - +
841L NAG 4.1 9.1 - - + +
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Residues in contact with THR 157 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L ASN* 4.5 8.5 - - + +
19L PRO* 5.3 0.7 - - + -
155L ASN* 2.6 15.4 + - - -
156L GLU* 1.3 72.3 - - - +
158L TYR* 1.3 58.6 + - - -
160L ASP* 3.5 2.9 + - - +
161L ILE* 3.0 57.5 + - + +
841L NAG 3.1 44.3 + - - +
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Residues in contact with TYR 158 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89L MET 4.5 2.4 + - - -
90L THR 5.3 0.4 - - - -
92L LEU* 3.9 12.6 - - + -
93L GLY* 3.8 30.5 - - - -
146L LEU* 4.0 15.1 - - + +
154L PHE* 5.1 5.6 - + - -
155L ASN* 3.0 11.9 + - + +
157L THR* 1.3 77.5 - - - +
159L GLN* 1.3 58.2 + - + +
161L ILE* 3.2 2.9 + - - -
162L SER* 2.6 59.6 + - - -
170L LEU* 5.2 2.5 - - + -
213L LEU* 3.4 21.2 - - + +
215L LEU* 3.5 20.3 - - - +
353L GLY 2.9 25.5 + - - +
354L ILE* 3.6 34.9 - - + +
841L NAG 4.6 3.1 + - - +
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Residues in contact with GLN 159 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146L LEU* 5.2 1.3 - - + -
154L PHE* 3.4 16.7 - - + +
155L ASN 3.1 11.0 + - - +
156L GLU* 4.2 19.4 + - - +
158L TYR* 1.3 84.2 - - + +
160L ASP* 1.3 63.3 + - - +
162L SER* 4.0 4.5 - - - -
163L GLU* 3.3 28.6 + - - +
168L ALA 4.4 1.0 - - - +
170L LEU* 2.9 56.3 + - + +
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Residues in contact with ASP 160 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156L GLU* 3.1 34.9 + - - +
157L THR* 4.0 4.0 - - - +
158L TYR 3.2 0.2 - - - -
159L GLN* 1.3 78.8 - - - +
161L ILE* 1.3 61.2 + - + +
163L GLU* 3.5 8.8 + - - +
164L LEU* 3.0 25.5 + - - +
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Residues in contact with ILE 161 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L PRO* 5.4 1.8 - - + -
17L MET* 3.8 20.2 - - + -
18L ASN 3.8 24.9 - - - +
19L PRO* 4.6 9.4 - - + -
92L LEU* 4.0 25.5 - - + +
120L HIS* 6.3 0.4 - - + -
157L THR* 3.0 36.6 + - + +
158L TYR* 4.0 2.5 - - - +
160L ASP* 1.3 77.1 - - + +
162L SER* 1.3 66.1 + - - +
163L GLU 3.1 1.6 - - - -
164L LEU* 2.9 21.0 + - + -
165L VAL* 3.2 22.9 + - + +
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Residues in contact with SER 162 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89L MET* 5.0 4.9 + - - +
92L LEU* 3.8 14.3 - - - +
146L LEU* 3.4 28.7 - - - +
158L TYR* 2.6 50.6 + - - -
159L GLN 4.0 3.4 - - - -
161L ILE* 1.3 74.9 - - - +
163L GLU* 1.3 59.4 + - - +
164L LEU 3.4 0.3 + - - -
166L TYR* 3.4 15.7 + - - +
168L ALA* 3.3 21.6 + - - +
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Residues in contact with GLU 163 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L ILE* 5.8 1.0 - - - +
159L GLN* 3.3 18.4 + - - +
160L ASP* 3.6 8.2 - - - +
161L ILE 3.1 0.6 - - - -
162L SER* 1.3 79.5 - - - +
164L LEU* 1.3 57.4 + - - +
167L GLY* 3.4 17.1 - - - -
168L ALA 3.2 21.5 + - - +
169L LYS* 3.6 35.8 - - + +
170L LEU 5.2 0.9 + - - -
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Residues in contact with LEU 164 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5L VAL 5.9 1.1 - - - +
7L ILE* 2.9 49.9 - - + +
15L ILE* 5.4 4.9 - - + -
16L PRO* 4.4 27.8 - - + -
17L MET* 4.9 7.2 - - + +
160L ASP 3.0 15.5 + - - +
161L ILE* 2.9 18.2 + - + +
163L GLU* 1.3 81.6 - - - +
165L VAL* 1.3 73.6 + - + +
166L TYR 3.5 0.2 - - - -
167L GLY* 4.4 1.7 + - - -
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Residues in contact with VAL 165 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L ILE* 4.3 5.4 - - + -
17L MET* 5.2 7.6 - - + -
120L HIS* 3.1 38.8 - - + +
121L PHE* 5.1 4.9 - - + +
124L ALA* 3.5 28.2 - - + +
127L ASN* 4.4 2.8 + - - +
161L ILE* 3.2 16.5 + - + +
164L LEU* 1.3 91.6 - - + +
166L TYR* 1.3 92.4 + - + +
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Residues in contact with TYR 166 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85L THR* 4.4 8.1 - - + -
88L ALA* 3.4 25.0 - - + +
89L MET* 3.6 32.5 - - + -
92L LEU* 4.2 17.5 - - + -
120L HIS* 3.0 37.6 + + - -
123L PHE* 4.1 11.3 - + - +
127L ASN* 4.2 17.9 - - - +
144L ASN* 3.4 31.5 + - - +
162L SER 3.4 15.9 + - - +
165L VAL* 1.3 103.7 - - + +
167L GLY* 1.3 66.4 + - - +
168L ALA* 3.2 6.2 + - + +
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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