Contacts of the strand formed by residues 153 - 164 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79H PHE* 4.2 8.5 - - - -
149H PRO* 3.4 0.7 - - - +
150H ALA 2.8 32.6 + - - -
151H ASP 3.1 2.1 - - - -
152H GLY* 1.3 80.8 - - - +
154H LEU* 1.3 61.9 + - - -
178H TYR 3.8 10.8 - - - -
179H ARG* 5.2 4.3 - - - -
189H MET* 3.4 14.7 - - - +
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Residues in contact with LEU 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79H PHE* 3.8 37.2 - - + -
80H PHE* 4.4 4.7 - - + -
147H LEU* 3.8 26.2 - - + -
148H TYR* 3.4 30.1 - - - +
149H PRO* 3.9 8.7 - - + -
150H ALA 4.5 0.4 - - - +
153H GLY* 1.3 74.7 - - - +
155H GLU* 1.3 65.2 + - - +
177H THR* 3.7 3.0 - - - +
178H TYR* 2.8 47.9 + - + +
189H MET* 4.5 1.1 - - + -
190H PRO* 4.4 18.4 - - + -
191H GLY 5.4 0.2 - - - +
193H TYR* 3.8 16.2 - - + +
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Residues in contact with GLU 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E ASN* 2.9 18.9 - - - +
147H LEU* 3.3 6.4 - - - +
148H TYR* 2.8 66.9 + - + +
150H ALA* 4.4 19.0 - - + +
154H LEU* 1.3 77.9 - - - +
156H GLY* 1.3 60.0 + - - +
157H ARG* 3.5 15.2 + - - +
176H THR 3.2 4.0 - - - +
177H THR* 2.9 31.1 + - + +
178H TYR* 4.6 2.7 - - - -
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Residues in contact with GLY 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145H GLU* 3.5 22.2 - - - -
146H MET 3.4 7.0 - - - -
147H LEU* 4.6 0.7 - - - -
155H GLU* 1.3 74.5 - - - +
157H ARG* 1.3 71.1 + - - -
174H LEU* 3.6 2.8 - - - +
176H THR* 2.8 34.2 + - - -
178H TYR* 4.1 6.1 - - - -
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Residues in contact with ARG 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E ASN* 4.4 6.5 + - - +
97G GLU* 2.6 44.3 + - - -
159G ASP* 3.5 28.8 - - + +
171G ILE* 3.7 18.4 - - + +
144H THR 4.0 0.5 - - - +
145H GLU* 3.4 2.6 - - - +
146H MET* 3.0 39.6 + - + +
148H TYR* 3.3 27.3 + - + -
155H GLU* 3.5 25.7 + - - +
156H GLY* 1.3 90.7 + - - -
158H SER* 1.3 64.0 + - - +
173H ASN* 4.7 2.7 - - - -
174H LEU 3.5 10.1 - - - -
175H LYS* 3.8 27.8 - - - +
176H THR 4.0 0.8 - - - +
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Residues in contact with SER 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159G ASP* 3.3 11.0 + - - -
143H SER* 4.0 0.9 + - - -
144H THR 3.1 19.3 + - - -
145H GLU* 4.1 5.4 - - - -
157H ARG* 1.3 76.0 - - - +
159H ASP* 1.3 69.0 + - - +
160H MET* 4.0 6.6 - - - +
173H ASN* 3.0 4.9 + - - -
174H LEU* 2.7 52.4 + - - +
197H ARG* 3.5 22.6 + - - -
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Residues in contact with ASP 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146G MET* 3.8 16.5 - - + +
157G ARG* 3.7 35.8 - - + +
158G SER* 3.3 21.2 + - - -
159G ASP* 3.0 18.0 - - - +
173G ASN* 3.7 8.7 + - - -
143H SER* 4.1 9.4 - - - -
144H THR 4.5 3.9 + - - +
158H SER* 1.3 78.3 + - - +
160H MET* 1.3 68.1 + - - +
171H ILE* 4.9 2.0 - - + +
172H CYS 3.5 6.5 - - - +
173H ASN* 2.6 26.1 + - - +
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Residues in contact with MET 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146G MET* 3.8 5.2 - - - -
60H THR* 3.7 20.0 - - + -
63H NRQ 3.2 43.5 - - + +
140H TRP* 3.5 46.7 - - + -
141H GLU 4.9 1.6 - - - +
143H SER* 3.9 13.7 - - - -
158H SER* 4.0 3.8 - - - +
159H ASP* 1.3 78.6 - - - +
161H ALA* 1.3 60.0 + - - +
170H LEU 3.8 1.0 - - - +
171H ILE* 3.5 6.9 - - - +
172H CYS* 2.9 40.4 + - - -
174H LEU* 3.8 20.9 - - + -
199H LEU* 6.0 0.4 - - + -
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Residues in contact with ALA 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146G MET* 3.8 23.2 - - + +
148G TYR* 5.4 2.2 - - + -
192G VAL* 5.3 2.2 - - + -
140H TRP* 3.4 7.5 - - - +
141H GLU* 2.8 45.3 + - + +
142H ALA 5.5 0.2 + - - -
160H MET* 1.3 74.4 - - - +
162H LEU* 1.3 60.1 + - - +
169H HIS* 3.7 21.8 - - + -
170H LEU 3.8 3.4 - - - -
171H ILE* 3.8 11.7 - - + -
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Residues in contact with LEU 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56H ASP* 3.7 20.4 - - + -
57H ILE* 5.5 1.8 - - + -
96H TYR* 4.5 6.1 - - + -
132H VAL* 4.7 5.2 - - + -
137H THR* 3.8 30.5 - - + +
139H GLY 3.4 14.1 - - - +
140H TRP* 3.4 44.6 - - + +
161H ALA* 1.3 72.2 - - - +
163H LYS* 1.3 65.9 + - - +
164H LEU* 3.5 2.7 + - + +
169H HIS* 3.3 5.1 - - - -
170H LEU* 2.8 69.0 + - + +
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Residues in contact with LYS 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228G LEU* 6.2 1.6 - - - +
137H THR* 3.4 8.5 - - - -
138H LEU* 2.8 52.7 + - + +
139H GLY* 2.8 18.1 + - - +
140H TRP 3.8 26.1 + - - +
141H GLU* 3.1 37.4 + - - +
161H ALA 4.1 0.4 + - - -
162H LEU* 1.3 71.2 - - - +
164H LEU* 1.3 59.2 + - - +
167H GLY 5.9 1.1 - - - +
168H GLY 3.9 5.6 - - - +
169H HIS* 4.0 6.5 - - + +
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Residues in contact with LEU 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H PRO* 3.6 38.6 - - + -
136H LYS 3.6 4.0 - - - +
138H LEU* 3.3 15.0 - - - +
162H LEU* 4.1 6.3 - - + +
163H LYS* 1.3 75.5 - - - +
165H VAL* 1.3 63.7 + - - +
166H GLY 3.2 0.7 + - - -
167H GLY* 3.1 21.9 + - - +
168H GLY* 3.1 20.6 + - - +
169H HIS 3.8 22.9 - - - +
170H LEU* 3.7 27.1 - - + +
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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