Contacts of the strand formed by residues 145 - 152 (chain A) 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 LEU 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A LEU* 4.6 12.8 - - + -
130A PHE 3.6 10.3 - - - +
131A GLU* 4.5 2.5 - - - +
144A THR* 1.3 97.1 - - + +
146A VAL* 1.3 62.0 + - - +
161A TRP* 4.0 23.3 - - + -
195A ARG* 3.2 5.1 - - - +
196A LEU* 2.8 41.8 + - + +
198A VAL* 3.9 14.4 - - + -
203A TRP* 3.7 29.8 - - + -
210A PHE* 3.6 35.9 - - + -
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Residues in contact with VAL 146 (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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128A SER 3.5 1.0 - - - +
129A LEU* 3.4 8.0 - - - +
130A PHE* 2.8 54.5 + - + +
132A PRO* 3.4 32.5 - - + -
143A ALA* 5.0 1.8 - - + -
144A THR 3.9 1.1 - - - +
145A LEU* 1.3 81.9 - - - +
147A CYS* 1.3 69.4 + - - +
148A LEU* 5.3 2.0 - - + -
161A TRP* 4.6 0.2 - - - -
193A SER* 5.3 5.2 - - - -
194A SER 3.4 10.8 - - - +
195A ARG* 3.6 20.2 - - + +
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Residues in contact with CYS 147 (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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127A VAL* 3.7 20.9 - - - -
128A SER 3.4 5.6 - - - -
129A LEU* 4.3 2.5 - - + -
146A VAL* 1.3 77.3 - - - +
148A LEU* 1.3 64.8 + - - +
159A LEU* 4.2 7.0 - - - -
161A TRP* 3.6 15.4 - - + -
192A LEU 4.6 0.2 - - - -
193A SER* 3.3 4.7 - - - -
194A SER* 2.8 38.0 + - - +
212A CYS* 2.0 51.6 - - + -
214A VAL* 4.7 0.2 - - - -
239A ALA* 4.7 0.2 - - - -
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Residues in contact with LEU 148 (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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126A LYS 3.3 4.6 - - - +
127A VAL* 3.4 2.5 - - - -
128A SER* 3.0 31.7 + - - -
130A PHE* 4.0 28.5 - - + -
146A VAL* 5.3 2.0 - - + -
147A CYS* 1.3 75.5 - - - +
149A ALA* 1.3 65.9 + - - +
150A ARG* 4.6 14.4 - - + +
191A CYS* 3.5 28.7 - - - -
192A LEU 3.4 19.1 - - - +
193A SER* 3.9 10.5 - - - -
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Residues in contact with ALA 149 (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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125A PRO* 4.3 2.0 - - + -
126A LYS 3.1 7.9 - - - +
127A VAL* 4.1 17.5 - - + +
148A LEU* 1.3 75.4 - - - +
150A ARG* 1.3 62.8 + - - +
152A PHE* 3.9 19.7 - - + -
157A VAL* 6.0 0.2 - - + -
159A LEU* 5.5 2.0 - - + +
191A CYS* 3.3 2.3 - - - -
192A LEU* 2.8 42.6 + - + +
214A VAL* 4.3 18.4 - - + -
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Residues in contact with ARG 150 (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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126A LYS* 2.9 68.9 + - + +
148A LEU* 4.6 18.8 - - + +
149A ALA* 1.3 76.7 - - - +
151A GLY* 1.3 76.5 + - - +
152A PHE* 3.4 3.8 - - - -
181A GLU* 2.6 47.5 + - - +
189A SER* 4.8 0.2 + - - -
190A TYR 3.3 8.5 - - - +
191A CYS* 4.4 4.5 - - + -
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Residues in contact with GLY 151 (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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123A THR* 3.2 16.0 + - - -
124A PRO 3.2 11.2 - - - +
126A LYS* 5.4 0.2 - - - -
150A ARG* 1.3 94.5 - - - +
152A PHE* 1.3 58.9 + - - +
181A GLU* 3.5 1.6 + - - -
189A SER* 3.0 21.2 + - - -
190A TYR 3.0 7.3 + - - -
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Residues in contact with PHE 152 (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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123A THR* 3.3 7.2 - - - +
125A PRO* 3.5 38.4 - - + -
149A ALA* 3.7 25.8 - - + -
150A ARG 3.4 5.4 - - - -
151A GLY* 1.3 80.3 - - - +
153A PHE* 1.3 63.9 + - - +
154A PRO 3.2 19.3 - - - -
155A ASP* 3.7 13.7 - - - -
157A VAL* 3.6 35.7 - - + -
178A ALA* 3.8 12.6 - - + -
189A SER* 3.5 1.0 - - - -
190A TYR* 2.8 61.4 + - + +
191A CYS* 4.0 3.4 - - - -
192A LEU* 4.2 1.3 - - + -
216A PHE* 3.8 5.2 - + + -
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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