Contacts of the strand formed by residues 150 - 157 (chain A) in PDB entry 3BSQ
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 MET 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ILE* 4.1 20.6 - - + +
19A GLY 4.7 2.5 - - - -
20A ALA* 3.6 9.6 - - - +
21A PRO* 3.5 30.1 - - + -
22A CYS* 3.5 1.0 - - - -
133A SER* 3.2 9.5 - - - -
134A GLY 2.9 39.4 + - - +
138A THR* 4.2 19.3 - - + -
146A PRO* 3.4 24.5 - - + -
148A ASP* 2.9 39.3 - - + +
149A LEU* 1.3 76.0 - - - +
151A CYS* 1.3 62.1 + - - +
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Residues in contact with CYS 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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16A ILE* 4.0 3.7 - - - +
19A GLY* 3.1 2.6 - - - -
20A ALA* 2.7 47.7 + - + +
21A PRO 5.0 0.2 - - - +
22A CYS* 2.1 47.8 - - - -
23A ALA 5.0 0.9 - - - -
27A HIS* 3.5 17.3 - - - -
131A THR* 4.1 13.7 - - + -
132A VAL 3.7 2.9 - - - -
133A SER* 4.2 0.9 - - - -
150A MET* 1.3 74.3 - - - +
152A VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 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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16A ILE* 3.7 18.8 - - + +
17A ILE 4.2 1.6 - - - +
18A ASP 3.6 25.6 - - - +
19A GLY* 3.9 2.2 - - - -
131A THR* 3.4 2.0 - - - +
132A VAL* 3.1 57.4 + - + +
151A CYS* 1.3 76.2 - - - +
153A ASP* 1.3 73.1 + - - +
154A VAL* 4.9 1.3 - - + -
184A LYS* 3.6 28.0 - - + +
185A ASN* 4.2 16.4 - - - -
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Residues in contact with ASP 153 (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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129A THR* 4.2 16.6 - - + +
130A CYS 3.3 5.2 - - - +
131A THR* 2.6 30.2 + - - +
152A VAL* 1.3 78.4 - - - +
154A VAL* 1.3 69.4 + - - +
179A ILE* 3.4 18.8 - - + +
184A LYS* 3.7 13.6 - - - +
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Residues in contact with VAL 154 (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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129A THR* 3.6 2.2 - - - +
130A CYS* 2.6 41.3 + - + +
132A VAL* 4.9 7.9 - - + -
152A VAL* 4.9 3.8 - - + -
153A ASP* 1.3 78.9 - - - +
155A LYS* 1.3 59.4 + - - +
177A ALA* 3.2 35.0 - - + +
178A GLY* 3.5 24.2 - - - -
179A ILE* 4.1 6.4 - - + +
184A LYS 3.6 19.7 - - - +
185A ASN* 4.5 9.0 - - + -
195A LEU* 4.0 18.6 - - + -
221A TYR* 4.9 3.6 - - - +
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Residues in contact with LYS 155 (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 GLY* 3.3 25.6 + - - +
128A THR 3.5 1.1 - - - -
129A THR* 3.0 33.0 - - - +
154A VAL* 1.3 72.7 - - - +
156A LEU* 1.3 68.1 + - - +
157A ILE* 3.5 3.6 - - + +
177A ALA* 3.0 5.9 - - - -
178A GLY 2.8 45.3 + - - +
179A ILE* 4.2 16.1 - - + +
180A PRO* 5.6 4.3 - - + -
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Residues in contact with LEU 156 (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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124A GLU* 3.6 34.1 - - + +
125A PRO 3.7 10.1 - - - +
126A PRO* 4.0 3.0 - - + +
127A GLY* 2.7 35.7 + - - +
128A THR* 3.1 20.8 + - + +
130A CYS* 3.8 22.9 - - - -
154A VAL 4.1 0.2 + - - -
155A LYS* 1.3 75.0 - - - +
157A ILE* 1.3 61.4 + - - +
175A LEU* 3.6 45.1 - - + -
176A CYS 3.6 5.6 - - - +
177A ALA* 4.2 9.4 - - + -
195A LEU* 4.4 3.1 - - + -
197A CYS* 4.3 2.7 - - - -
202A GLN* 5.0 1.1 - - + +
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Residues in contact with ILE 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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126A PRO* 4.3 2.9 - - - +
155A LYS* 3.5 10.1 - - + +
156A LEU* 1.3 78.5 - - - +
158A SER* 1.3 69.0 + - - +
159A PRO* 3.6 2.8 - - - +
161A ASP* 3.6 28.3 - - + +
162A CYS* 4.1 8.1 - - - +
175A LEU* 5.2 4.3 - - - +
176A CYS* 3.0 29.0 + - + +
177A ALA 3.9 0.4 - - - -
178A GLY* 3.7 26.5 - - - +
179A ILE 6.1 0.7 - - - -
218A PRO* 3.7 29.2 - - + -
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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