Contacts of the strand formed by residues 156 - 169 (chain E) in PDB entry 3SGB
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 GLY 156 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138E ARG* 3.3 12.6 + - - +
139E ARG* 3.3 6.8 - - - -
140E GLY 3.0 38.0 + - - -
142E THR 3.6 1.6 - - - -
143E THR* 1.3 78.0 - - - +
157E THR* 1.3 63.7 + - - -
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Residues in contact with THR 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E THR* 3.4 31.0 - - + -
138E ARG 3.1 5.4 - - - +
139E ARG* 3.5 24.7 + - + +
143E THR 3.6 1.6 + - - +
156E GLY* 1.3 70.8 - - - -
158E HIS* 1.3 72.4 + - - +
159E SER* 5.1 1.8 - - - +
200E TYR* 4.2 7.6 + - - +
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Residues in contact with HIS 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E THR* 3.4 1.7 - - - -
138E ARG* 2.7 66.2 + - - +
143E THR* 2.9 36.2 + - - -
156E GLY 3.9 0.4 - - - -
157E THR* 1.3 86.7 + - - +
159E SER* 1.3 63.2 + - - +
190E VAL* 3.8 14.1 - - + +
191E CYS* 3.6 15.3 - - - +
220E CYS* 3.9 17.2 - - + -
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Residues in contact with SER 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E VAL 3.3 9.6 - - - -
137E THR* 3.4 21.2 + - - +
157E THR* 5.1 2.1 - - - +
158E HIS* 1.3 77.9 - - - +
160E GLY* 1.3 61.3 + - - +
184E ASN 5.0 1.0 - - - +
190E VAL* 3.6 14.4 - - - +
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Residues in contact with GLY 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E ALA* 3.4 7.1 - - - +
136E VAL* 2.9 30.8 + - - -
159E SER* 1.3 79.3 - - - +
161E SER* 1.3 62.8 - - - -
184E ASN* 3.4 12.3 - - - -
190E VAL* 3.5 6.3 - - - +
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Residues in contact with SER 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E GLY* 4.5 8.5 - - - -
134E MET 3.1 14.8 - - - -
135E ALA* 4.5 2.5 - - - -
136E VAL* 4.1 3.3 - - - +
160E GLY* 1.3 76.7 - - - -
162E VAL* 1.3 68.4 + - - +
163E THR* 3.6 6.6 + - - +
183E THR* 3.3 6.9 - - - -
184E ASN* 2.8 44.5 + - - -
190E VAL* 4.4 0.6 - - - +
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Residues in contact with VAL 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E ALA* 4.1 9.4 - - + -
131E THR 3.3 27.4 - - - +
132E VAL* 3.8 2.1 - - - +
133E GLY* 2.8 27.4 + - - -
134E MET* 2.9 12.4 + - + +
136E VAL* 3.9 24.9 - - + -
161E SER* 1.3 72.4 + - - +
163E THR* 1.3 64.6 - - - +
164E ALA 3.7 20.4 - - - +
165E LEU* 3.9 12.8 - - + -
181E ILE* 3.8 25.4 - - + -
182E ARG 3.5 4.3 - - - -
183E THR* 4.2 4.9 - - + -
199E LEU* 5.1 0.4 - - + -
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Residues in contact with THR 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E VAL* 4.2 15.1 - - - +
161E SER* 3.8 17.9 - - - +
162E VAL* 1.3 77.6 - - - +
164E ALA* 1.3 64.9 + - - +
182E ARG* 2.8 38.0 + - - +
183E THR* 4.0 1.9 + - - -
184E ASN* 4.2 23.1 - - + +
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Residues in contact with ALA 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E VAL* 4.2 7.9 - - - -
162E VAL* 3.7 9.1 - - - +
163E THR* 1.3 82.5 + - - +
165E LEU* 1.3 67.2 + - - +
167E ALA* 5.5 3.6 - - + -
181E ILE* 3.7 1.2 - - - -
182E ARG* 2.8 49.5 + - + +
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Residues in contact with LEU 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E ALA* 3.8 36.1 - - + +
131E THR* 4.3 6.3 - - + +
132E VAL* 4.0 21.2 - - + +
162E VAL* 3.9 15.9 - - + -
164E ALA* 1.3 84.3 - - - +
166E ASN* 1.3 75.7 + - + +
167E ALA* 3.3 4.9 + - - -
180E MET 3.6 3.1 - - - -
181E ILE* 4.4 8.7 - - + -
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Residues in contact with ASN 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E LEU* 1.3 79.9 - - + +
167E ALA* 1.3 62.8 + - - +
168E THR* 4.0 2.8 + - - -
179E GLY* 3.1 33.5 + - - +
180E MET 3.1 6.5 + - - -
181E ILE* 5.9 0.2 - - - +
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Residues in contact with ALA 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E ALA* 5.5 3.4 - - + -
165E LEU 4.2 3.8 - - - +
166E ASN* 1.3 74.2 - - - +
168E THR* 1.3 62.4 + - - +
178E TYR 3.7 0.2 - - - -
179E GLY 3.2 7.0 + - - -
180E MET* 2.8 45.0 + - - +
182E ARG* 4.6 10.1 - - + +
227E PHE* 4.1 28.5 - - + -
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Residues in contact with THR 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E ASN 4.0 3.0 + - - -
167E ALA* 1.3 74.7 - - - +
169E VAL* 1.3 67.3 + - - +
170E ASN* 4.1 3.9 + - + +
176E VAL* 3.5 26.9 - - + -
177E VAL 3.3 4.3 - - - -
178E TYR* 3.6 24.2 - - + +
179E GLY 5.1 0.5 + - - -
227E PHE* 5.4 1.6 - - - -
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Residues in contact with VAL 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E ALA 4.4 0.7 - - - +
168E THR* 1.3 77.4 - - - +
170E ASN* 1.3 65.2 - - - +
171E TYR* 3.5 33.5 + - + +
175E ASP 3.9 0.2 - - - +
176E VAL* 3.5 2.7 - - - -
177E VAL* 2.8 44.9 + - + +
180E MET* 4.1 15.3 - - + -
227E PHE* 3.6 46.4 - - + -
14I PRO* 6.5 0.4 - - + -
15I ALA* 3.9 17.7 - - + -
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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