Contacts of the strand formed by residues 153 - 164 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79B PHE* 4.0 7.4 - - - -
149B PRO* 3.4 0.7 - - - +
150B ALA 2.8 31.1 + - - -
151B ASP 3.2 2.4 + - - -
152B GLY* 1.3 79.7 - - - +
154B LEU* 1.3 64.9 + - - -
178B TYR 3.5 11.4 - - - -
179B ARG* 3.5 11.8 - - - +
189B MET* 3.3 13.8 - - - +
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Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B PHE* 3.7 31.1 - - + -
80B PHE* 4.0 7.4 - - + -
147B LEU* 3.9 25.4 - - + -
148B TYR 3.6 6.7 - - - +
149B PRO* 4.2 9.4 - - + -
150B ALA* 4.8 0.7 - - - -
153B GLY* 1.3 80.3 - - - +
155B GLU* 1.3 65.2 + - - +
177B THR* 3.6 4.0 - - - +
178B TYR* 2.9 49.6 + - + +
189B MET* 3.7 19.3 - - + -
190B PRO* 3.8 17.3 - - + -
193B TYR* 3.9 18.8 - - + +
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Residues in contact with GLU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ASN* 3.1 15.0 + - - -
234A CIT 2.9 36.8 + - - +
147B LEU* 3.2 5.2 - - - +
148B TYR* 2.8 65.4 + - + +
150B ALA* 3.8 14.6 - - + +
154B LEU* 1.3 74.1 - - - +
156B GLY* 1.3 57.6 + - - +
157B ARG* 2.9 27.1 + - - +
176B THR 3.2 5.2 - - - +
177B THR* 2.5 31.7 + - - +
178B TYR* 4.5 2.9 - - - -
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Residues in contact with GLY 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B NRQ 5.3 0.4 - - - -
145B GLU* 3.3 23.8 - - - -
146B MET 3.3 7.2 - - - -
147B LEU* 4.3 0.9 - - - -
155B GLU* 1.3 72.9 - - - +
157B ARG* 1.3 72.8 + - - -
174B LEU 3.8 0.4 - - - +
175B LYS* 3.6 0.5 - - - -
176B THR* 2.9 35.7 + - - -
178B TYR* 4.0 5.5 - - - -
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Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ASN* 3.5 13.1 - - - +
234A CIT 5.4 0.8 + - - -
144B THR 4.0 0.9 - - - +
145B GLU* 3.4 5.1 - - - +
146B MET* 2.9 50.4 + - + +
148B TYR* 3.4 33.4 + - + +
155B GLU* 2.9 29.9 + - - +
156B GLY* 1.3 89.5 + - - +
158B SER* 1.3 61.3 + - - +
173B ASN* 5.0 7.4 - - - +
174B LEU 3.4 13.0 - - - -
175B LYS* 3.6 29.8 - - - +
176B THR 3.7 7.3 - - - +
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Residues in contact with SER 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B NRQ 2.9 30.7 + - - -
143B SER* 3.8 8.1 + - - -
144B THR 3.2 20.4 + - - -
145B GLU* 4.2 1.6 - - - -
157B ARG* 1.3 74.0 - - - +
159B ASP* 1.3 66.7 + - - +
160B MET* 3.7 12.0 - - - +
173B ASN* 2.8 8.8 + - - +
174B LEU* 2.8 37.6 + - - +
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Residues in contact with ASP 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLU* 5.0 2.6 - - - +
143B SER* 4.0 8.5 - - - -
144B THR 4.7 3.1 + - - +
158B SER* 1.3 75.0 + - - +
160B MET* 1.3 65.0 + - - +
171B ILE* 4.0 17.1 - - + +
172B CYS 3.3 7.2 - - - +
173B ASN* 3.2 27.2 + - - +
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Residues in contact with MET 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B THR* 3.9 18.8 - - + -
63B NRQ 3.9 13.2 - - + -
140B TRP* 3.7 46.4 - - + -
141B GLU 4.6 4.9 - - - +
143B SER* 3.9 17.7 - - - +
158B SER* 3.7 13.0 - - - +
159B ASP* 1.3 79.4 - - - +
161B ALA* 1.3 60.4 + - - +
162B LEU 3.9 0.2 + - - -
170B LEU 3.8 0.7 - - - +
171B ILE* 3.3 7.9 - - - +
172B CYS* 2.8 40.7 + - - -
174B LEU* 3.8 31.6 - - + -
197B ARG* 5.9 1.1 - - - -
199B LEU* 4.9 7.2 - - + -
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Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B TRP* 3.5 4.5 - - - -
141B GLU* 3.0 54.0 + - + +
142B ALA 5.6 1.4 + - - -
160B MET* 1.3 72.5 - - - +
162B LEU* 1.3 62.2 + - - +
163B LYS 3.6 0.2 + - - -
169B HIS* 3.8 11.0 - - + -
171B ILE* 3.5 24.2 - - + -
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ASP* 3.5 37.9 - - + +
57B ILE* 4.9 1.1 - - + -
96B TYR* 4.3 14.1 - - + -
132B VAL* 4.3 16.8 - - + -
137B THR* 3.5 32.3 - - + -
139B GLY 3.5 15.9 - - - +
140B TRP* 3.5 24.0 - - + -
161B ALA* 1.3 71.1 - - - +
163B LYS* 1.3 63.0 + - - +
164B LEU* 3.7 6.5 - - + +
169B HIS* 3.1 7.4 - - - -
170B LEU* 2.8 51.1 + - + +
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Residues in contact with LYS 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B THR* 3.4 6.8 - - - -
138B LEU* 2.8 49.0 + - + +
139B GLY 2.9 18.3 + - - +
140B TRP 4.5 11.9 + - - -
141B GLU* 3.3 42.8 + - + +
161B ALA 3.6 0.8 + - - -
162B LEU* 1.3 72.8 - - - +
164B LEU* 1.3 62.8 + - - +
168B GLY 3.8 4.7 - - - +
169B HIS* 4.0 6.3 - - + +
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B PRO* 3.7 36.6 - - + -
136B LYS 3.5 6.1 - - - +
137B THR* 4.1 8.3 - - + -
138B LEU* 3.8 11.4 - - - +
162B LEU* 3.7 14.4 - - + +
163B LYS* 1.3 84.5 - - - +
165B VAL* 1.3 71.1 + - - +
167B GLY* 3.1 17.7 + - - -
168B GLY* 2.9 20.0 + - - +
169B HIS 3.6 26.0 - - - +
170B LEU* 3.8 12.8 - - + +
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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