Contacts of the strand formed by residues 153 - 164 (chain A) in PDB entry 3BX9
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 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A PHE* 4.0 7.4 - - - -
149A PRO* 3.4 5.9 - - - +
150A ALA 2.9 29.2 + - - -
151A ASP 3.2 2.6 + - - -
152A GLY* 1.3 78.7 + - - +
154A LEU* 1.3 63.8 + - - -
177A THR* 6.1 0.7 - - - -
178A TYR 3.3 13.7 - - - -
179A ARG* 3.4 10.7 - - - +
189A MET* 3.5 7.3 - - - +
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Residues in contact with LEU 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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79A PHE* 3.5 41.2 - - + -
80A PHE* 4.0 7.0 - - + -
147A LEU* 4.0 19.5 - - + -
148A TYR 3.5 7.6 - - - +
149A PRO* 3.8 24.5 - - + -
150A ALA 5.2 0.4 - - - -
153A GLY* 1.3 76.4 - - - +
155A GLU* 1.3 64.5 + - - +
177A THR* 3.6 3.7 - - - +
178A TYR* 2.8 47.4 + - + +
189A MET* 4.1 6.1 - - + -
190A PRO* 3.7 23.3 - - + -
191A GLY 5.5 0.2 - - - +
193A TYR* 4.1 12.1 - - + +
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Residues in contact with GLU 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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147A LEU* 3.2 6.8 - - - +
148A TYR* 2.8 64.9 + - + +
150A ALA* 4.0 15.2 - - + +
153A GLY 4.4 0.2 + - - -
154A LEU* 1.3 73.9 - - - +
156A GLY* 1.3 58.0 + - - +
157A ARG* 2.8 26.6 + - - +
176A THR 3.3 6.1 - - - +
177A THR* 2.6 32.1 + - - +
178A TYR* 4.5 2.7 - - - -
125B ASN* 3.0 16.0 + - - -
235B CIT 3.0 35.2 + - + +
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Residues in contact with GLY 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A NRQ 5.4 0.4 - - - -
145A GLU* 3.4 22.7 - - - -
146A MET 3.3 7.6 - - - -
147A LEU* 4.4 0.9 - - - -
155A GLU* 1.3 74.2 - - - +
157A ARG* 1.3 81.8 + - - -
174A LEU 4.3 0.4 - - - -
175A LYS* 3.5 0.3 - - - -
176A THR* 2.9 27.3 + - - -
178A TYR* 4.1 5.3 - - - -
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Residues in contact with ARG 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A NRQ 4.5 0.7 - - - -
144A THR 3.9 0.9 - - - +
145A GLU* 3.4 4.6 - - - +
146A MET* 2.9 50.9 + - + +
148A TYR* 3.4 32.9 + - + +
155A GLU* 2.8 31.1 + - - -
156A GLY* 1.3 91.8 + - - +
158A SER* 1.3 60.5 + - - +
173A ASN* 5.2 6.7 - - - +
174A LEU 3.3 4.7 - - - -
175A LYS* 3.5 42.5 - - - +
176A THR 3.8 0.6 - - - +
125B ASN* 3.7 12.3 - - - +
235B CIT 5.3 0.8 + - - -
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Residues in contact with SER 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A NRQ 3.1 27.1 + - - -
143A SER* 3.9 8.5 + - - -
144A THR 3.2 19.6 + - - -
145A GLU* 4.0 2.9 - - - -
157A ARG* 1.3 74.9 - - - +
159A ASP* 1.3 68.4 + - - +
160A MET* 3.7 10.7 - - - +
173A ASN* 2.3 30.3 + - - -
174A LEU* 2.9 21.0 + - - -
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Residues in contact with ASP 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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97A GLU* 4.9 2.3 - - - +
143A SER* 3.9 8.0 - - - -
144A THR 4.8 2.4 + - - +
158A SER* 1.3 82.3 + - - +
160A MET* 1.3 62.3 + - - +
171A ILE* 3.7 22.0 - - + +
172A CYS 3.3 3.6 - - - +
173A ASN* 3.6 26.9 + - - +
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Residues in contact with MET 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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60A THR* 3.8 29.8 - - + -
63A NRQ 3.9 16.2 - - + -
140A TRP* 3.6 47.1 - - + -
141A GLU 4.6 2.9 - - - +
143A SER* 3.9 21.5 - - - +
158A SER* 3.7 11.7 - - - +
159A ASP* 1.3 78.8 - - - +
161A ALA* 1.3 59.8 + - - +
170A LEU 4.0 0.3 - - - +
171A ILE* 3.3 8.5 - - - +
172A CYS* 2.9 37.7 + - - -
174A LEU* 3.9 15.7 - - + -
197A ARG* 5.5 1.8 - - - -
199A LEU* 4.5 9.0 - - + -
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Residues in contact with ALA 161 (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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140A TRP* 3.5 6.0 - - - -
141A GLU* 2.9 56.1 + - + +
142A ALA 5.7 0.8 + - - -
160A MET* 1.3 74.0 - - - +
162A LEU* 1.3 61.2 + - - +
169A HIS* 3.9 8.5 - - + -
171A ILE* 3.7 24.0 - - + -
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Residues in contact with LEU 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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56A ASP* 3.6 33.4 - - + +
57A ILE* 4.8 2.0 - - + -
96A TYR* 4.4 14.1 - - + -
132A VAL* 4.4 9.2 - - + -
137A THR* 3.4 33.0 - - + -
139A GLY 3.3 21.5 - - - +
140A TRP* 3.6 29.9 - - + -
161A ALA* 1.3 71.1 - - - +
163A LYS* 1.3 64.7 + - - +
164A LEU* 3.7 5.3 - - + +
169A HIS* 3.1 6.0 - - - -
170A LEU* 2.8 49.8 + - + +
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Residues in contact with LYS 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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137A THR* 3.4 7.1 - - - -
138A LEU* 2.8 60.7 + - + +
139A GLY* 2.9 23.2 + - - +
140A TRP 4.1 12.9 + - - -
141A GLU* 3.2 35.6 + - + +
161A ALA 3.7 0.2 + - - -
162A LEU* 1.3 74.0 - - - +
164A LEU* 1.3 59.5 + - - +
167A GLY 6.4 0.2 - - - -
168A GLY 3.8 6.1 - - - +
169A HIS* 3.7 6.3 - - + +
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Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PRO* 3.7 37.5 - - + -
136A LYS* 3.4 5.4 - - + +
137A THR* 4.2 9.0 - - + -
138A LEU* 3.7 12.4 - - - +
162A LEU* 3.7 14.1 - - + +
163A LYS* 1.3 83.6 - - - +
165A VAL* 1.3 70.1 - - - +
166A GLY 3.3 0.3 + - - -
167A GLY* 2.9 18.2 + - - -
168A GLY* 3.0 20.5 + - - +
169A HIS 3.9 22.4 - - - +
170A LEU* 4.0 13.5 - - + +
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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