Contacts of the helix formed by residues 157 - 172 (chain B) in PDB entry 1SBB
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 ALA 157 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B VAL 3.8 1.4 + - - -
156B THR* 1.3 71.6 - - - +
158B GLN* 1.3 52.4 + - - +
160B LEU* 3.0 14.7 + - - +
161B ASP* 2.7 36.8 + - - +
189B PHE* 3.9 7.8 - - + -
196B PHE* 3.7 33.7 - - + -
198B TYR* 4.2 15.9 - - + +
217B TYR* 5.1 0.4 - - - -
221B LYS* 2.9 19.7 + - + +
222B MET* 4.5 1.4 - - - +
223B VAL* 5.0 2.5 - - + -
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Residues in contact with GLN 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PHE 3.5 1.4 - - - +
86B GLY* 3.5 16.6 - - - -
87B ALA* 3.4 28.1 + - + +
114B MET* 4.4 0.6 - - - +
115B TYR 3.1 28.7 + - - +
117B GLY* 3.3 21.2 + - - +
156B THR* 3.2 8.0 - - - +
157B ALA* 1.3 78.5 - - - +
159B GLU* 1.3 56.9 + - - +
161B ASP* 3.7 1.3 - - - +
162B TYR* 2.9 31.3 + - + +
214B LEU* 5.4 0.2 - - - +
217B TYR* 3.2 59.1 + - + +
221B LYS 4.8 0.4 + - - -
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Residues in contact with GLU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PHE* 3.6 50.5 + - + +
119B THR* 5.9 0.3 - - - +
150B THR* 3.9 14.3 + - - -
152B LYS* 3.1 31.0 + - - -
155B VAL* 3.3 20.5 - - + +
156B THR* 3.2 21.8 + - - +
157B ALA 3.2 0.6 - - - -
158B GLN* 1.3 76.7 - - - +
160B LEU* 1.3 61.5 + - - +
162B TYR* 3.8 0.9 - - - +
163B LEU* 3.1 45.2 + - + +
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Residues in contact with LEU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ILE* 4.7 14.6 - - + -
148B VAL* 4.2 19.2 - - + +
150B THR* 5.0 5.4 - - - -
155B VAL* 4.0 20.9 - - + -
156B THR 3.7 9.4 - - - +
157B ALA* 3.0 7.0 + - - +
159B GLU* 1.3 72.6 - - - +
161B ASP* 1.3 56.4 + - - +
163B LEU* 3.1 9.5 + - + +
164B THR* 2.7 39.7 + - - -
189B PHE* 4.0 12.6 - - + -
223B VAL* 3.4 33.0 - - + -
228B VAL* 4.7 10.5 - - + -
230B ILE* 3.8 24.2 - - + -
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Residues in contact with ASP 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B TYR* 4.8 0.2 - - - -
157B ALA 2.7 20.6 + - - +
158B GLN* 3.7 5.4 - - - +
160B LEU* 1.3 72.0 - - - +
162B TYR* 1.3 63.8 + - - +
164B THR* 3.0 1.6 + - - -
165B ARG* 2.8 65.5 + - - +
187B ILE* 3.3 24.0 - - - +
189B PHE* 3.6 19.4 - - + -
198B TYR* 3.7 12.5 - - + -
217B TYR* 2.9 23.8 + - + +
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Residues in contact with TYR 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU 3.7 22.0 - - - -
28B TYR* 3.8 24.4 - + + -
29B ASP 2.6 30.5 + - - -
30B ASP* 3.2 8.7 + - - -
31B ASN 4.0 6.1 - - - -
32B HIS* 3.0 41.1 - + + -
85B PHE* 3.4 16.2 - + + -
87B ALA* 4.9 8.7 - - + +
158B GLN* 2.9 21.6 + - + +
159B GLU 3.8 2.0 - - - +
161B ASP* 1.3 75.2 - - - +
163B LEU* 1.3 89.9 + - + +
165B ARG* 4.0 0.7 - - - +
166B HIS* 2.9 47.1 + + + +
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Residues in contact with LEU 163 (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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32B HIS* 5.5 0.4 - - - +
85B PHE* 3.5 15.0 - - + -
146B PHE* 4.6 0.5 - - - -
148B VAL* 3.7 23.8 - - + +
149B GLN 3.8 23.1 - - - +
150B THR* 5.5 0.7 - - - -
159B GLU* 3.1 37.4 + - + +
160B LEU* 3.5 7.6 - - + +
162B TYR* 1.3 105.0 - - + +
164B THR* 1.3 60.5 + - - +
166B HIS* 3.8 10.4 - - + +
167B TYR* 3.7 17.3 + - - +
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Residues in contact with THR 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B VAL* 3.8 16.2 - - + +
146B PHE* 3.8 7.4 - - + -
148B VAL* 3.7 15.5 - - - +
160B LEU 2.7 20.9 + - - -
161B ASP 3.5 3.6 - - - -
163B LEU* 1.3 71.4 - - - +
165B ARG* 1.3 68.2 + - + +
166B HIS 3.1 1.5 + - - -
167B TYR* 3.2 6.1 + - - +
168B LEU* 3.2 25.5 + - + +
187B ILE* 3.8 14.1 - - + -
230B ILE* 3.8 14.4 - - - +
232B VAL* 3.7 30.5 - - + -
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Residues in contact with ARG 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B MET* 4.3 0.2 - - - -
28B TYR* 3.3 48.8 + - + -
161B ASP* 2.8 51.8 + - - +
164B THR* 1.3 73.1 - - - +
166B HIS* 1.3 63.9 + - - +
168B LEU* 3.1 11.3 + - - +
169B VAL* 2.8 28.3 + - - +
174B LEU* 4.1 7.4 - - + -
175B TYR* 2.9 24.2 + - - -
198B TYR* 4.2 7.3 - - - +
199B ASP 3.9 5.3 + - - -
200B MET* 3.4 35.3 + - + +
213B TYR* 2.7 31.7 + - - -
216B MET* 3.9 10.1 - - - +
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Residues in contact with HIS 166 (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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28B TYR* 3.2 26.3 + - - +
29B ASP* 3.8 2.8 - - - -
30B ASP* 3.4 44.3 + - - -
162B TYR* 2.9 35.8 + + + +
163B LEU* 3.8 12.8 - - + +
165B ARG* 1.3 78.5 - - - +
167B TYR* 1.3 66.0 + - + +
169B VAL* 3.2 8.5 + - - +
170B LYS* 3.2 40.3 + - + +
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Residues in contact with TYR 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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144B LEU* 4.0 25.0 - - + +
146B PHE* 3.5 65.7 - + + +
163B LEU 3.7 5.3 + - - +
164B THR 3.2 2.9 + - - +
166B HIS* 1.3 82.0 - - + +
168B LEU* 1.3 68.4 + - + +
169B VAL 3.3 0.2 + - - -
170B LYS* 3.3 3.8 + - - -
171B ASN* 2.9 61.3 + - + +
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Residues in contact with LEU 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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136B VAL* 4.3 15.0 - - + -
144B LEU* 4.2 16.4 - - + -
146B PHE* 3.9 23.8 - - + -
164B THR* 3.2 14.1 + - + +
165B ARG* 3.1 8.6 + - - +
167B TYR* 1.3 80.2 - - - +
169B VAL* 1.3 55.6 + - - +
172B LYS* 2.7 44.1 + - + +
173B LYS 3.2 1.6 + - - -
174B LEU* 3.5 27.5 + - + -
200B MET* 4.0 9.2 - - + -
232B VAL* 3.9 32.5 - - + -
234B LEU* 4.8 8.1 - - + -
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Residues in contact with VAL 169 (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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25B LYS* 4.0 30.1 - - + -
28B TYR* 4.4 12.8 - - + +
29B ASP* 4.2 11.7 - - - +
165B ARG 2.8 22.7 + - - +
166B HIS 3.2 8.5 + - - +
168B LEU* 1.3 72.0 - - - +
170B LYS* 1.3 64.4 + - + +
173B LYS* 3.1 31.4 + - - +
174B LEU* 3.9 9.0 - - + +
175B TYR* 3.7 42.1 - - + +
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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
----------------------------------------------------------
29B ASP* 5.7 4.0 - - - -
30B ASP* 2.8 36.2 + - - +
166B HIS* 3.2 37.7 - - + +
167B TYR* 3.3 5.3 + - - +
169B VAL* 1.3 81.0 - - + +
171B ASN* 1.3 68.5 + - - +
173B LYS* 3.1 24.0 + - - +
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Residues in contact with ASN 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 5.7 0.4 - - + -
167B TYR* 2.9 69.4 + - + +
170B LYS* 1.3 89.6 - - - +
172B LYS* 1.3 71.1 + - + +
173B LYS* 3.7 5.3 - - - +
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Residues in contact with LYS 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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136B VAL* 4.8 1.1 - - + +
138B GLU* 2.9 34.8 + - - +
143B LEU* 5.2 2.0 - - - +
144B LEU* 3.5 41.4 - - + +
168B LEU* 2.7 28.8 + - + +
171B ASN* 1.3 83.3 - - + +
173B LYS* 1.3 70.0 + - - +
174B LEU* 3.1 2.5 + - + +
181B PRO* 4.3 3.3 - - - +
182B TYR* 3.5 34.6 + - + +
234B LEU* 5.8 1.6 - - + -
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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