Contacts of the strand formed by residues 154 - 168 (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 GLY 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A LEU* 3.8 13.1 - - - +
151A ARG* 2.9 29.8 + - - -
152A THR 3.1 2.1 - - - -
153A ASN* 1.3 80.7 - - - +
155A GLN* 1.3 62.1 + - - +
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Residues in contact with GLN 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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149A LEU* 3.6 7.8 - - - +
150A THR* 3.2 30.9 + - - +
154A GLY* 1.3 76.3 - - - +
156A LEU* 1.3 72.0 + - - +
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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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43A HIS* 4.2 40.2 - - + +
77A LEU* 4.9 4.9 - - + -
147A TRP 3.4 16.2 - - - +
148A GLY* 3.7 19.3 - - - -
149A LEU* 3.7 12.7 - - + +
150A THR* 4.9 0.7 - - - +
155A GLN* 1.3 88.3 + - - +
157A ALA* 1.3 67.3 + - - +
158A GLN* 3.8 3.1 + - - +
200A GLN 4.3 3.6 - - - +
201A GLY* 4.4 4.3 - - - -
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Residues in contact with ALA 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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77A LEU* 3.7 19.6 - - - +
147A TRP* 2.9 21.9 + - - +
148A GLY 3.5 5.4 + - - +
150A THR* 3.9 15.0 - - + -
155A GLN 3.8 0.4 + - - -
156A LEU* 1.3 75.6 - - - +
158A GLN* 1.3 63.2 + - - +
159A THR 3.5 19.3 - - - +
161A GLN* 3.8 23.1 - - + +
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Residues in contact with GLN 158 (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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75A HIS 3.6 0.7 - - - +
76A ASN* 3.3 23.7 + - - +
77A LEU* 2.7 30.1 + - - +
78A ASN* 3.3 30.3 + - - +
79A GLN* 4.8 7.1 - - - +
147A TRP* 3.7 3.3 - - - -
156A LEU 3.8 3.1 + - - +
157A ALA* 1.3 75.2 - - - +
159A THR* 1.3 63.8 + - + +
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Residues in contact with THR 159 (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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21A GLU* 3.5 31.0 + - - +
75A HIS* 3.3 14.4 - - + +
76A ASN* 3.6 31.0 - - + +
147A TRP* 3.6 4.0 - - - -
157A ALA* 3.5 10.6 - - - +
158A GLN* 1.3 80.3 - - + +
160A LEU* 1.4 65.5 + - - +
161A GLN* 3.0 28.4 + - - -
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Residues in contact with LEU 160 (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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21A GLU* 3.5 7.4 - - - +
22A ALA* 2.8 39.9 + - + +
23A GLN 5.5 1.8 - - - +
24A ARG 6.2 0.7 - - - +
27A TRP* 4.2 22.0 - - + +
30A GLN* 4.0 30.1 - - + +
74A GLU 5.1 4.9 - - - +
75A HIS* 3.2 25.4 + - - +
145A THR* 4.3 2.0 - - - -
146A GLY* 3.5 36.6 - - - +
147A TRP* 3.4 25.4 - - + +
159A THR* 1.4 73.0 - - - +
161A GLN* 1.3 62.8 + - - +
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Residues in contact with GLN 161 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A VAL* 3.9 22.3 - - + +
19A GLY* 3.9 6.5 - - - +
20A THR* 3.2 24.4 + - - +
21A GLU* 3.9 8.4 + - - +
22A ALA* 4.6 1.3 - - - -
145A THR* 3.3 7.4 - - - +
146A GLY 3.1 34.4 + - - +
150A THR* 4.7 11.5 - - + +
157A ALA* 3.8 20.9 - - + +
159A THR* 3.0 35.9 + - - +
160A LEU* 1.3 80.5 + - - +
162A GLN* 1.3 62.3 + - - +
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Residues in contact with GLN 162 (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* 4.3 2.0 - - - -
19A GLY* 3.1 3.3 - - - -
20A THR* 2.8 49.9 + - - +
21A GLU 4.9 1.3 - - - -
22A ALA* 3.5 18.0 - - + +
23A GLN 4.8 1.0 + - - -
26A SER* 4.8 3.1 + - - -
27A TRP* 2.8 32.7 + - - +
143A TYR* 3.7 28.8 - - + -
144A ILE 3.2 6.5 - - - +
145A THR* 3.7 16.4 - - + -
161A GLN* 1.3 77.3 - - - +
163A ALA* 1.3 60.9 + - - +
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Residues in contact with ALA 163 (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* 3.6 21.5 - - + -
17A VAL 4.5 1.1 - - - +
18A GLY 4.1 8.5 - - - +
19A GLY* 4.1 7.9 - - - -
143A TYR* 3.4 8.7 - - - -
144A ILE* 3.0 39.6 + - + +
162A GLN* 1.3 76.0 - - - +
164A TYR* 1.3 63.3 + - - +
165A LEU* 3.4 2.4 + - + -
196A ARG* 4.4 16.4 - - + +
197A SER 5.2 0.4 - - - +
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Residues in contact with TYR 164 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A ASN* 5.1 5.6 + - - -
141A PRO* 3.7 39.9 - - + +
142A CYS 3.7 11.9 - - - -
143A TYR* 3.7 34.1 - + + +
163A ALA* 1.3 70.4 - - - +
165A LEU* 1.3 63.7 + - - +
166A PRO* 3.7 28.1 - - + +
196A ARG* 3.6 47.6 + - - +
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Residues in contact with LEU 165 (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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142A CYS* 2.8 32.6 + - - +
144A ILE* 3.8 34.1 - - + +
163A ALA* 3.4 7.6 + - + +
164A TYR* 1.3 81.1 - - - +
166A PRO* 1.3 67.3 - - - +
190A ALA* 3.5 38.2 - - + +
191A GLY* 4.1 6.7 - - - +
196A ARG* 3.8 36.8 - - + +
197A SER* 4.1 1.8 - - - +
198A GLY 4.6 1.3 - - - +
207A LEU* 4.5 2.0 - - + -
236A THR* 4.1 10.5 - - - +
238A PHE* 4.0 12.6 - - + -
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Residues in contact with PRO 166 (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* 4.0 31.4 - - - +
140A SER 3.1 14.8 - - - +
142A CYS 4.2 2.9 - - - +
164A TYR* 3.7 33.4 - - + +
165A LEU* 1.3 88.9 - - - +
167A THR* 1.3 64.7 + - - +
168A VAL* 4.3 1.4 - - - +
190A ALA* 4.3 0.2 - - - -
191A GLY* 3.1 27.4 + - - +
196A ARG* 5.3 4.5 - - - +
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Residues in contact with THR 167 (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* 4.0 20.7 + - + +
137A ALA 2.9 26.7 + - - -
138A ASN* 3.8 1.7 + - - +
139A ASN* 2.9 26.2 + - - +
140A SER* 2.9 13.1 + - - +
142A CYS* 3.4 29.8 - - + -
166A PRO* 1.3 77.8 - - - +
168A VAL* 1.3 62.6 + - - +
169A ASP* 5.6 0.4 - - - -
188A VAL* 4.3 17.0 - - + -
189A CYS 3.5 9.0 - - - +
190A ALA* 4.1 3.6 - - + +
207A LEU* 4.8 0.2 - - + -
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Residues in contact with VAL 168 (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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138A ASN* 3.4 5.8 - - - +
166A PRO 4.3 0.9 - - - +
167A THR* 1.3 78.4 - - - +
169A ASP* 1.3 63.4 + - - +
172A ILE* 3.7 32.8 - - + -
173A CYS* 4.0 10.5 - - + +
178A TYR* 4.1 14.6 - - + -
188A VAL* 5.7 0.2 - - - +
189A CYS* 2.9 34.6 + - + +
191A GLY 3.5 29.4 - - - +
235A PRO* 4.2 14.1 - - + -
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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