Contacts of the strand formed by residues 140 - 150 (chain A) in PDB entry 1BMA
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 SER 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A LEU* 3.7 21.2 - - - +
137A ALA* 2.8 35.1 + - - +
138A ASN 3.4 0.4 + - - -
139A ASN* 1.3 75.1 - - - +
141A PRO* 1.3 71.3 - - - +
142A CYS* 3.4 3.3 + - - -
166A PRO* 3.1 7.8 - - - +
167A THR* 2.9 32.8 + - - -
209A CYS* 5.6 0.9 - - - -
210A LEU 5.7 2.7 - - - -
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Residues in contact with PRO 141 (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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139A ASN 3.7 4.2 - - - +
140A SER* 1.3 84.6 - - - +
142A CYS* 1.3 63.2 + - - +
143A TYR* 5.5 3.8 - - + -
164A TYR* 3.7 31.0 - - + +
209A CYS* 3.5 0.9 - - - +
210A LEU* 3.2 49.3 + - + +
215A TYR* 4.9 1.9 - - - +
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Residues in contact with CYS 142 (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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136A LEU* 4.1 1.8 - - - -
140A SER 3.4 4.4 + - - -
141A PRO* 1.3 75.8 - - - +
143A TYR* 1.3 63.7 + - - +
164A TYR* 3.7 8.5 - - - -
165A LEU 2.8 39.7 + - - +
166A PRO* 4.4 0.2 - - - +
167A THR* 3.4 28.0 - - - -
207A LEU* 3.6 13.5 - - + -
208A HIS 3.1 6.5 - - - +
209A CYS* 2.0 47.3 - - - -
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Residues in contact with TYR 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TRP* 3.9 26.0 - + + -
141A PRO* 5.5 2.2 - - + -
142A CYS* 1.3 75.1 - - - +
144A ILE* 1.4 60.5 + - - +
145A THR* 5.0 0.2 - - + -
162A GLN* 3.7 31.2 - - + -
163A ALA 3.4 15.7 - - - -
164A TYR* 3.7 39.8 - + + +
207A LEU* 3.6 5.4 - - - -
208A HIS* 2.8 41.1 + - + +
215A TYR* 3.4 32.8 - + - -
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Residues in contact with ILE 144 (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 VAL* 4.2 11.8 - - + +
142A CYS 4.3 0.2 - - - -
143A TYR* 1.4 71.8 - - - +
145A THR* 1.3 71.3 + - - +
162A GLN* 3.2 6.1 - - - +
163A ALA* 3.0 48.8 + - + +
165A LEU* 3.8 23.7 - - + +
197A SER 4.7 2.5 - - - +
198A GLY* 3.5 30.3 - - - +
202A ASP* 4.5 7.9 - - + +
206A PRO 3.9 12.8 - - - +
207A LEU* 4.2 6.3 - - + +
221A THR* 3.9 17.0 - - + +
238A PHE* 3.9 20.9 - - + -
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Residues in contact with THR 145 (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 VAL* 4.1 4.7 - - - -
27A TRP* 3.5 39.7 - - + +
30A GLN* 2.7 28.5 + - - +
143A TYR* 4.0 0.6 + - + -
144A ILE* 1.3 89.2 - - - +
146A GLY* 1.3 58.5 + - - +
160A LEU* 4.3 6.1 - - + -
161A GLN 3.3 5.8 - - - +
162A GLN* 3.7 11.4 - - + -
202A ASP* 4.4 5.9 - - - +
205A GLY* 4.9 4.0 - - - -
206A PRO* 3.4 14.4 + - - +
208A HIS* 2.9 27.0 + - + +
221A THR* 5.5 0.2 + - - -
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Residues in contact with GLY 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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16A VAL* 3.8 4.6 + - - +
30A GLN* 4.3 5.2 - - - -
145A THR* 1.3 75.8 - - - +
147A TRP* 1.3 62.6 + - - -
148A GLY 3.9 0.2 + - - -
160A LEU* 3.5 16.2 - - - +
161A GLN* 3.1 36.8 + - - +
202A ASP* 3.3 19.0 - - - +
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Residues in contact with TRP 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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30A GLN* 3.6 37.2 - - + -
31A ILE 3.7 14.6 - - - -
32A SER* 3.9 9.2 - - - -
43A HIS* 3.8 25.7 + + - +
46A GLY* 5.5 0.2 - - - -
74A GLU* 3.5 49.4 - - + -
75A HIS 3.2 19.7 + - - -
77A LEU* 3.6 38.3 - - + +
146A GLY* 1.3 72.3 - - - -
148A GLY* 1.3 61.3 + - - +
156A LEU* 3.4 12.4 - - - +
157A ALA* 2.9 28.3 + - - -
158A GLN 3.7 4.2 + - - -
159A THR 3.6 18.8 - - - -
160A LEU* 3.4 19.6 - - + +
201A GLY 4.6 3.2 + - - -
202A ASP* 3.5 0.2 + - - -
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Residues in contact with GLY 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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16A VAL 3.4 8.4 + - - +
146A GLY 3.5 0.8 - - - -
147A TRP* 1.3 82.3 - - - +
149A LEU* 1.3 67.3 + - - +
150A THR* 3.4 5.4 + - - +
156A LEU* 3.7 8.3 - - - -
157A ALA* 3.5 8.7 + - - +
200A GLN 3.2 13.9 - - - -
201A GLY 3.6 11.8 + - - -
202A ASP* 2.9 18.7 + - - -
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Residues in contact with LEU 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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16A VAL 3.0 18.7 + - - +
148A GLY* 1.3 69.2 - - - -
150A THR* 1.3 62.0 + - - +
151A ARG 3.3 20.6 - - - +
153A ASN* 3.8 11.7 - - - +
154A GLY 3.8 20.4 - - - +
155A GLN* 3.3 24.5 - - - +
156A LEU* 3.7 14.4 - - + +
199A CYS* 3.2 24.6 - - - +
200A GLN* 2.9 42.8 + - + +
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Residues in contact with THR 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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16A VAL 3.4 14.5 - - - +
17A VAL* 3.5 22.0 - - - +
18A GLY 4.3 2.3 + - - -
148A GLY 3.8 9.4 - - - +
149A LEU* 1.3 76.5 - - - +
151A ARG* 1.3 69.5 + - - +
155A GLN* 3.2 18.7 + - - +
156A LEU 4.9 0.6 + - - +
157A ALA* 3.9 23.3 - - + -
161A GLN* 4.7 10.1 - - + +
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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