Contacts of the helix formed by residues 157 - 172 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D VAL 3.8 1.6 + - - -
156D THR* 1.3 70.8 - - - +
158D GLN* 1.3 51.6 + - - +
160D LEU* 3.1 10.1 + - - +
161D ASP* 2.7 37.4 + - - +
189D PHE* 3.6 11.1 - - + -
196D PHE* 3.7 34.1 - - + -
198D TYR* 4.2 17.5 - - + +
217D TYR* 5.1 0.7 - - + -
221D LYS* 2.9 16.6 + - + +
222D MET* 4.6 0.6 - - - +
223D VAL* 4.8 3.1 - - + +
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Residues in contact with GLN 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D PHE 3.6 0.7 - - - +
86D GLY* 3.5 16.1 - - - -
87D ALA* 3.3 29.9 + - + +
114D MET* 3.8 1.5 - - - +
115D TYR 2.9 28.8 + - - +
117D GLY* 3.3 19.8 + - - +
156D THR* 3.2 9.3 - - - +
157D ALA* 1.3 77.2 - - - +
159D GLU* 1.3 57.1 + - - +
161D ASP* 3.2 1.6 + - - +
162D TYR* 2.9 30.7 + - + +
214D LEU* 5.4 0.2 - - - +
217D TYR* 3.3 57.1 + - + +
221D LYS 4.8 0.4 + - - -
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Residues in contact with GLU 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D PHE* 3.5 50.2 + - + +
129D TYR* 5.8 0.3 + - - -
150D THR* 4.0 12.6 + - - -
152D LYS* 3.4 28.5 + - - +
155D VAL* 3.2 23.9 - - + +
156D THR* 3.3 20.1 + - - +
158D GLN* 1.3 78.7 - - - +
160D LEU* 1.3 57.1 + - - +
162D TYR* 3.7 0.3 + - - +
163D LEU* 2.8 47.6 + - + +
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Residues in contact with LEU 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D ILE* 4.6 12.8 - - + -
148D VAL* 4.1 20.4 - - + +
150D THR* 5.0 3.6 - - - -
155D VAL* 3.9 20.6 - - + -
156D THR 3.5 10.5 + - - +
157D ALA* 3.1 7.0 + - - +
159D GLU* 1.3 76.1 - - - +
161D ASP* 1.3 55.6 + - - +
163D LEU* 3.2 8.6 + - + +
164D THR* 2.7 40.8 + - - -
189D PHE* 3.8 18.8 - - + -
223D VAL* 3.5 31.9 - - + -
228D VAL* 4.7 9.0 - - + -
230D ILE* 3.9 21.3 - - + -
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Residues in contact with ASP 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D TYR* 4.6 0.2 - - - -
157D ALA 2.7 19.8 + - - +
158D GLN* 3.5 3.8 - - - +
160D LEU* 1.3 72.5 - - - +
162D TYR* 1.3 57.4 + - - +
164D THR* 3.8 0.3 - - - -
165D ARG* 2.8 75.8 + - - +
187D ILE* 3.5 24.3 - - - +
189D PHE* 3.9 11.4 - - + -
198D TYR* 3.7 6.1 - - - -
216D MET* 3.6 6.8 - - - +
217D TYR* 2.6 30.5 + - + +
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Residues in contact with TYR 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LEU 3.6 22.7 - - - -
28D TYR* 3.7 23.8 - + + -
29D ASP 2.7 29.1 + - - -
30D ASP* 3.2 9.4 + - - -
31D ASN 3.8 6.5 - - - -
32D HIS* 3.0 40.0 - + + -
85D PHE* 3.6 17.0 - + + -
87D ALA* 4.6 11.2 - - + +
158D GLN* 2.9 18.1 + - + +
159D GLU 3.9 2.5 - - - +
161D ASP* 1.3 76.9 - - - +
163D LEU* 1.3 75.6 + - + +
165D ARG* 4.2 0.2 - - - +
166D HIS* 2.9 48.7 + + + +
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Residues in contact with LEU 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D PHE* 3.3 31.6 - - + -
148D VAL* 3.4 35.0 - - + +
149D GLN 3.6 15.5 - - - +
150D THR* 5.3 0.4 - - - -
159D GLU* 2.8 42.1 + - + +
160D LEU* 3.5 8.3 - - + +
162D TYR* 1.3 89.4 - - + +
164D THR* 1.3 63.6 + - - +
166D HIS* 3.7 6.2 - - - +
167D TYR* 3.6 16.1 + - - +
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Residues in contact with THR 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D VAL* 3.7 30.0 - - + +
146D PHE* 3.8 11.8 - - + -
148D VAL* 3.9 5.1 - - - +
160D LEU 2.7 27.6 + - - -
161D ASP 3.8 3.1 - - - -
163D LEU* 1.3 71.1 - - - +
165D ARG* 1.3 67.2 + - + +
167D TYR* 3.1 15.1 + - - +
168D LEU* 3.3 14.4 + - + +
187D ILE* 3.9 15.8 - - + +
230D ILE* 4.0 5.4 - - - +
232D VAL* 3.7 30.7 - - + -
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Residues in contact with ARG 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D MET* 4.0 0.8 - - - -
28D TYR* 3.4 48.7 + - + -
161D ASP* 2.8 55.1 + - - +
164D THR* 1.3 72.3 - - - +
166D HIS* 1.3 63.0 + - - +
168D LEU* 3.0 7.0 + - - +
169D VAL* 2.8 27.5 + - - +
174D LEU* 4.1 12.3 - - + -
175D TYR* 2.9 29.3 + - - -
187D ILE* 5.4 0.2 - - + -
198D TYR* 4.4 4.2 - - - +
199D ASP 3.8 6.9 + - - -
200D MET* 3.5 32.2 + - + +
213D TYR* 2.6 32.5 + - - -
216D MET* 3.9 7.7 - - - +
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Residues in contact with HIS 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D TYR* 3.1 25.1 + - - +
29D ASP* 3.7 4.1 - - - -
30D ASP* 3.4 42.7 + - - -
162D TYR* 2.9 36.3 + + + +
163D LEU* 3.7 9.0 - - - +
164D THR 3.2 0.2 - - - -
165D ARG* 1.3 77.0 - - - +
167D TYR* 1.3 64.3 + - - +
169D VAL* 3.3 1.7 + - - +
170D LYS* 3.1 57.4 + - + +
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Residues in contact with TYR 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D LEU* 4.3 19.1 - - + +
145D SER 5.3 0.2 + - - -
146D PHE* 3.6 60.6 - + + +
147D ASP 5.6 1.6 - - - -
163D LEU 3.6 6.1 + - - +
164D THR 3.1 10.8 + - - +
166D HIS* 1.3 82.4 - - - +
168D LEU* 1.3 62.3 + - + +
170D LYS* 3.3 1.9 + - - -
171D ASN* 2.9 68.1 + - + +
172D LYS* 5.6 0.2 - - + -
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Residues in contact with LEU 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D VAL* 4.5 10.8 - - + -
144D LEU* 4.0 27.1 - - + -
146D PHE* 4.3 11.7 - - + -
164D THR* 3.3 13.7 + - + +
165D ARG* 3.0 7.9 + - - +
167D TYR* 1.3 80.2 - - - +
169D VAL* 1.3 56.0 + - - +
172D LYS* 2.7 41.6 + - + +
173D LYS 3.0 7.3 + - - -
174D LEU* 3.2 21.6 + - + -
200D MET* 3.9 28.0 - - + -
232D VAL* 3.9 25.1 - - + -
234D LEU* 4.7 5.6 - - + -
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Residues in contact with VAL 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LYS* 4.2 12.8 - - + +
28D TYR* 4.1 17.3 - - + +
29D ASP* 4.0 20.4 - - - +
165D ARG 2.8 23.2 + - - +
166D HIS 3.7 6.7 - - - +
167D TYR 3.3 0.2 - - - -
168D LEU* 1.3 71.6 - - - +
170D LYS* 1.3 65.2 + - + +
173D LYS* 3.3 25.6 + - - +
174D LEU* 3.8 11.0 - - + +
175D TYR* 3.7 46.8 - - + +
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Residues in contact with LYS 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ASP* 6.1 1.8 - - - +
30D ASP* 2.9 34.2 + - - +
166D HIS* 3.1 42.3 + - + +
167D TYR* 4.0 3.4 - - - +
169D VAL* 1.3 82.5 - - + +
171D ASN* 1.3 66.7 + - - +
173D LYS* 2.8 23.1 + - - +
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Residues in contact with ASN 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D TYR* 2.9 70.1 + - + +
170D LYS* 1.3 88.4 - - - +
172D LYS* 1.3 71.4 + - + +
173D LYS* 3.6 6.9 - - - +
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Residues in contact with LYS 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D VAL* 6.1 0.2 - - + -
138D GLU* 2.7 31.5 + - - +
143D LEU* 5.6 1.4 - - - +
144D LEU* 3.2 42.8 - - + +
168D LEU* 2.7 32.7 + - + +
171D ASN* 1.3 85.0 - - + +
173D LYS* 1.3 71.2 + - - +
174D LEU 3.1 2.3 + - - +
181D PRO* 4.5 2.3 - - - +
182D TYR* 3.4 33.1 + - + +
234D LEU* 6.2 0.2 - - + -
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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
------------------------------------------------------------
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