Contacts of the helix formed by residues 155 - 168 (chain A) in PDB entry 3B3S
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 155 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ALA 3.5 1.5 + - - -
151A GLU* 3.1 34.8 + - + +
154A GLY* 1.3 79.7 - - - +
156A ARG* 1.3 59.2 + - - +
157A GLY 3.5 2.2 - - - -
158A SER* 3.8 7.0 - - - +
159A GLN* 3.0 30.7 + - + +
226A ALA* 3.8 23.6 - - + +
227A CYS 4.4 1.6 - - - +
228A SER* 3.4 45.5 - - - +
229A ASP* 4.1 0.7 - - - +
231A ALA* 3.9 14.4 - - + -
232A SER* 3.7 16.6 - - - +
235A ASN* 6.1 1.1 - - - +
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Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TYR* 3.7 26.9 + - - -
71A SER 3.5 23.0 + - - -
72A GLY* 5.1 2.4 - - - -
73A TYR* 3.8 23.8 - - - +
150A ALA* 3.0 11.3 + - + +
153A VAL* 3.3 33.6 - - - +
154A GLY* 3.7 8.1 - - - +
155A LEU* 1.3 77.4 - - - +
157A GLY* 1.3 63.8 + - - +
159A GLN* 3.5 10.5 + - - +
160A ASP* 3.1 27.9 + - - +
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Residues in contact with GLY 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A HIS* 3.6 22.2 - - - -
73A TYR* 3.7 4.1 + - - -
77A SER* 4.0 7.0 - - - -
148A TYR* 4.5 1.8 - - - -
149A ALA 3.0 23.1 + - - -
156A ARG* 1.3 78.4 - - - +
158A SER* 1.3 58.6 + - - +
160A ASP* 3.2 5.7 + - - +
161A LEU* 2.9 31.5 + - - +
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Residues in contact with SER 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A TYR* 3.6 28.5 - - - +
155A LEU* 3.4 5.4 + - - +
157A GLY* 1.3 73.8 - - - +
159A GLN* 1.3 60.6 + - - +
161A LEU* 4.3 0.9 - - - +
162A ALA* 2.8 34.0 + - - +
229A ASP* 2.6 42.8 + - - +
232A SER* 2.7 27.1 + - - -
233A TRP* 5.0 2.2 - - - -
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Residues in contact with GLN 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A GLY 5.1 6.0 + - - +
155A LEU* 3.0 21.9 + - + +
156A ARG* 3.7 10.9 - - - +
158A SER* 1.3 78.4 + - - +
160A ASP* 1.3 67.2 + - - +
162A ALA* 4.1 1.1 - - - -
163A ASN* 2.9 49.7 + - - +
232A SER* 3.3 12.5 + - - +
235A ASN* 5.9 3.8 - - - +
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Residues in contact with ASP 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A VAL* 6.0 0.7 - - + -
69A SER 5.1 0.2 - - - +
70A HIS* 2.8 38.8 + - + +
71A SER 4.8 2.4 + - - -
73A TYR* 4.6 0.9 + - - -
156A ARG* 3.1 14.4 + - - +
157A GLY 3.5 7.9 - - - +
159A GLN* 1.3 85.5 - - - +
161A LEU* 1.3 60.3 + - + +
163A ASN* 3.7 4.8 + - - +
164A GLN* 2.8 31.6 + - - +
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Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A VAL* 3.8 21.5 - - + -
70A HIS* 3.7 20.2 - - + -
77A SER* 3.9 10.3 - - - -
79A VAL* 3.8 28.0 - - + -
146A MET* 4.1 10.3 - - + -
148A TYR* 3.9 30.5 - - + -
157A GLY 2.9 18.8 + - - +
158A SER* 3.3 4.2 + - - +
160A ASP* 1.3 74.4 - - + +
162A ALA* 1.4 62.2 + - - +
164A GLN* 3.0 20.2 - - + +
165A TYR* 2.8 31.9 + - + -
233A TRP* 4.4 7.2 - - + -
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Residues in contact with ALA 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A SER 2.8 21.8 + - - +
159A GLN* 4.1 2.2 - - - +
161A LEU* 1.4 73.4 - - - +
163A ASN* 1.3 60.7 + - - +
165A TYR* 3.4 2.1 + - - +
166A LYS* 2.9 28.6 + - - +
232A SER* 3.6 26.2 - - - +
233A TRP* 3.7 34.6 - - + +
236A ALA* 4.0 7.3 - - + +
238A TYR* 4.1 4.5 - - - -
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Residues in contact with ASN 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A GLN* 2.9 46.8 + - - +
160A ASP* 3.9 5.0 + - - +
162A ALA* 1.3 80.9 - - - +
164A GLN* 1.3 55.6 + - - +
166A LYS* 3.7 8.8 - - - +
167A SER* 2.9 33.6 + - - -
232A SER 5.1 0.9 - - - +
236A ALA* 4.1 14.9 + - - +
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Residues in contact with GLN 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A VAL* 3.9 30.4 - - - +
160A ASP* 2.8 13.9 + - - +
161A LEU* 3.0 33.4 - - - +
163A ASN* 1.3 73.0 - - - +
165A TYR* 1.3 78.9 + - + +
167A SER* 3.2 7.0 + - - -
168A GLU* 2.8 54.1 + - - +
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Residues in contact with TYR 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A VAL* 4.3 10.0 - - + +
81A THR* 4.3 2.9 - - - +
91A TRP* 4.0 22.6 - + - -
93A VAL* 4.5 4.5 - - + -
144A ALA* 3.5 19.6 - - - +
146A MET* 3.5 22.2 - - + +
161A LEU* 2.8 24.2 + - + +
162A ALA 3.8 4.5 - - - +
164A GLN* 1.3 94.2 - - + +
166A LYS* 1.3 61.8 + - - +
168A GLU* 3.2 6.4 + - - -
169A GLY 3.1 4.2 + - - -
170A LYS* 2.9 61.2 + - + +
172A VAL* 3.6 23.6 - - + -
233A TRP* 3.9 16.8 - + + -
238A TYR* 3.6 5.6 - - - +
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Residues in contact with LYS 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ALA 2.9 18.6 + - - +
163A ASN* 3.7 9.4 - - - +
165A TYR* 1.3 75.5 - - - +
167A SER* 1.3 58.5 + - - +
169A GLY* 2.9 19.9 + - - -
170A LYS 4.9 0.2 - - - +
235A ASN 4.9 1.8 + - - -
236A ALA* 3.2 38.0 + - + +
237A GLY* 5.3 0.6 - - - -
238A TYR* 3.2 18.3 + - + +
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Residues in contact with SER 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ASN 2.9 17.5 + - - -
164A GLN* 3.4 11.4 - - - -
166A LYS* 1.3 77.9 - - - +
168A GLU* 1.3 61.2 + - - +
169A GLY* 3.1 1.3 + - - -
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Residues in contact with GLU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLN* 2.8 47.3 + - - +
165A TYR* 3.2 8.3 + - - +
167A SER* 1.3 74.3 - - - +
169A GLY* 1.3 62.4 + - - +
170A LYS* 2.6 45.9 + - + +
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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