Contacts of the strand formed by residues 153 - 164 (chain G) in PDB entry 3BXB
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79G PHE* 3.8 8.7 - - - -
149G PRO* 3.5 4.9 - - - +
150G ALA 2.7 42.1 + - - -
151G ASP 3.1 2.0 + - - -
152G GLY* 1.3 80.8 - - - +
154G LEU* 1.3 58.0 + - - -
177G THR* 6.2 0.7 - - - -
178G TYR 3.4 13.0 - - - -
179G ARG* 5.0 6.1 - - - -
180G SER 5.3 0.2 - - - -
189G MET* 3.6 6.1 - - - +
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Residues in contact with LEU 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G PHE* 3.8 38.4 - - + -
80G PHE* 3.9 10.5 - - + -
147G LEU* 3.6 26.2 - - + -
148G TYR 3.5 11.2 - - - +
149G PRO* 4.6 6.7 - - + -
150G ALA* 4.7 1.1 - - - -
153G GLY* 1.3 80.6 - - - +
155G GLU* 1.3 67.7 + - - +
177G THR* 3.5 5.7 - - - +
178G TYR* 2.8 44.8 + - + +
189G MET* 4.1 9.2 - - + -
190G PRO* 4.2 17.5 - - + -
193G TYR* 3.8 18.8 - - + +
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Residues in contact with GLU 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F ASN* 4.2 6.1 + - - +
147G LEU* 3.3 7.6 - - - +
148G TYR* 2.7 73.9 + - + +
150G ALA* 3.6 22.2 - - + +
151G ASP* 4.5 4.7 - - - +
153G GLY 4.4 0.2 + - - -
154G LEU* 1.3 79.1 - - - +
156G GLY* 1.3 58.1 + - - +
157G ARG* 2.8 19.3 + - - +
176G THR 3.2 11.2 - - - +
177G THR* 4.0 16.8 - - + +
178G TYR* 4.2 3.1 - - - -
97H GLU* 4.9 0.2 - - - +
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Residues in contact with GLY 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145G GLU* 4.1 17.3 - - - -
146G MET 3.4 7.9 - - - -
147G LEU* 4.4 1.3 - - - -
148G TYR* 4.6 0.4 - - - -
155G GLU* 1.3 74.4 - - - +
157G ARG* 1.3 86.0 + - - -
174G LEU 3.6 2.5 - - - +
176G THR* 2.8 29.2 + - - -
178G TYR* 3.9 6.9 - - - -
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Residues in contact with ARG 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F ASN* 4.0 12.1 + - - +
144G THR 4.1 0.2 - - - +
145G GLU* 3.3 3.4 - - - +
146G MET* 2.9 40.5 + - + +
148G TYR* 3.0 26.6 + - + -
155G GLU* 2.8 25.3 + - - -
156G GLY* 1.3 99.8 + - - +
158G SER* 1.3 65.1 + - - +
173G ASN* 5.4 1.1 - - - -
174G LEU 3.6 4.7 - - - -
175G LYS* 3.7 34.6 - - - +
176G THR 3.7 10.3 + - - +
97H GLU* 2.8 38.5 + - - -
159H ASP* 3.7 28.1 - - + +
171H ILE* 4.0 17.4 - - + +
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Residues in contact with SER 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143G SER* 4.2 3.1 - - - -
144G THR 2.8 22.5 + - - -
145G GLU* 4.1 3.1 - - - -
157G ARG* 1.3 77.9 - - - +
159G ASP* 1.3 68.1 + - - +
160G MET* 4.2 3.5 - - - +
173G ASN* 3.7 3.6 + - - -
174G LEU* 2.8 46.7 + - - +
197G ARG* 3.6 25.0 + - - -
159H ASP* 3.3 14.3 + - - -
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Residues in contact with ASP 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143G SER* 3.9 9.0 - - - -
144G THR 4.5 3.1 + - - +
158G SER* 1.3 77.3 + - - +
160G MET* 1.3 65.7 + - - +
171G ILE* 4.8 1.9 - - + +
172G CYS 3.3 9.1 - - - +
173G ASN* 3.1 14.7 + - - +
146H MET* 3.8 17.5 - - + +
157H ARG* 3.5 31.0 - - + +
158H SER* 3.3 22.7 + - - -
159H ASP* 3.0 18.1 + - - +
173H ASN* 3.1 24.2 + - - +
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Residues in contact with MET 160 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G THR* 3.8 19.1 - - + -
63G NRQ 3.2 43.1 - - + +
140G TRP* 3.4 52.7 - - + -
141G GLU 4.6 2.5 - - - +
143G SER* 3.8 14.8 - - - +
158G SER* 4.2 4.0 - - - +
159G ASP* 1.3 78.9 - - - +
161G ALA* 1.3 60.6 + - - +
170G LEU 3.9 0.5 - - - +
171G ILE* 3.5 6.6 - - - +
172G CYS* 3.0 38.4 + - - +
174G LEU* 4.0 18.4 - - + +
199G LEU* 5.8 0.9 - - + -
146H MET* 4.0 4.9 - - - -
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Residues in contact with ALA 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140G TRP* 3.4 7.1 - - - -
141G GLU* 2.9 42.3 + - + +
142G ALA 5.5 0.4 + - - -
160G MET* 1.3 75.0 - - - +
162G LEU* 1.3 61.1 + - - +
163G LYS 3.7 0.6 + - - -
169G HIS* 3.7 20.0 - - + -
170G LEU 3.7 3.1 - - - -
171G ILE* 3.6 20.4 - - + -
146H MET* 4.1 15.7 - - + +
148H TYR* 5.5 3.1 - - + -
192H VAL* 5.5 1.6 - - + -
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Residues in contact with LEU 162 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G ASP* 3.5 36.6 - - + +
57G ILE* 4.9 1.8 - - + -
96G TYR* 4.3 7.6 - - + -
132G VAL* 4.6 5.2 - - + -
137G THR* 3.6 30.7 - - + +
139G GLY 3.5 16.4 - - - +
140G TRP* 3.5 33.5 - - + -
161G ALA* 1.3 72.4 - - - +
163G LYS* 1.3 65.9 + - - +
164G LEU* 3.6 2.1 - - + +
169G HIS* 3.3 3.9 - - - -
170G LEU* 2.8 62.1 + - + +
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Residues in contact with LYS 163 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137G THR* 3.6 2.9 - - - -
138G LEU* 3.1 47.7 + - + +
139G GLY* 2.9 13.5 + - - +
140G TRP 3.6 24.3 + - - -
141G GLU* 3.4 33.2 - - + +
161G ALA 3.7 1.6 + - - -
162G LEU* 1.3 76.2 - - - +
164G LEU* 1.3 65.7 + - - +
168G GLY 3.8 5.4 - - - -
169G HIS* 4.0 10.7 - - + +
228H LEU* 5.8 5.9 - - - +
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Residues in contact with LEU 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131G PRO* 3.5 40.8 - - + -
136G LYS 3.7 7.0 - - - +
137G THR* 4.0 8.3 - - + -
138G LEU* 3.7 14.0 - - - +
162G LEU* 3.6 10.5 - - + +
163G LYS* 1.3 83.5 - - - +
165G VAL* 1.3 67.3 + - - +
166G GLY 3.4 0.2 + - - -
167G GLY* 3.1 24.0 + - - +
168G GLY* 2.8 21.7 + - - +
169G HIS 3.7 21.3 - - - +
170G LEU* 4.0 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