Contacts of the strand formed by residues 169 - 180 (chain C) 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 HIS 169 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141C GLU* 2.8 45.6 + - + +
161C ALA* 3.7 12.6 - - + -
162C LEU 3.5 1.8 - - - -
163C LYS* 3.4 26.7 - - + +
164C LEU* 3.7 10.5 - - - +
168C GLY* 1.3 81.8 - - - -
170C LEU* 1.3 59.8 - - - +
171C ILE* 3.9 22.7 + - + +
148D TYR* 4.2 22.5 - + + +
149D PRO* 5.0 8.2 + - + +
192D VAL* 3.7 15.0 - - + -
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Residues in contact with LEU 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C TYR* 3.7 27.8 - - + -
97C GLU* 4.3 7.0 - - + +
98C ASP* 3.7 50.5 - - + +
131C PRO* 4.8 11.4 - - + -
132C VAL* 3.8 17.5 - - + -
140C TRP* 4.8 0.7 - - - -
160C MET 3.9 0.7 - - - +
161C ALA* 3.7 0.7 - - - -
162C LEU* 2.9 48.5 + - + +
164C LEU* 3.7 19.5 - - + +
169C HIS* 1.3 72.5 - - - +
171C ILE* 1.3 63.9 + - - +
172C CYS 4.0 0.3 + - - -
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Residues in contact with ILE 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C TYR* 3.9 0.7 - - - -
97C GLU* 3.0 58.9 + - - +
159C ASP* 3.7 21.1 - - + +
160C MET 3.5 6.5 - - - +
161C ALA* 3.6 30.1 - - + -
169C HIS* 3.9 9.4 + - + +
170C LEU* 1.3 80.4 - - - +
172C CYS* 1.3 65.0 + - - +
146D MET* 4.3 2.5 - - + -
148D TYR* 3.1 44.9 - - + +
157D ARG* 4.0 11.2 - - + +
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Residues in contact with CYS 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C THR* 3.8 10.5 - - + -
95C THR 3.2 14.6 - - - +
96C TYR* 3.7 21.1 - - + -
97C GLU* 5.0 0.9 - - - -
140C TRP* 3.7 35.2 - - - -
159C ASP* 3.4 10.1 - - - +
160C MET* 2.9 35.3 + - - -
170C LEU 4.0 0.2 + - - -
171C ILE* 1.3 76.1 - - - +
173C ASN* 1.3 62.0 + - - +
174C LEU* 3.8 18.6 - - - +
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Residues in contact with ASN 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C VAL 3.6 1.7 - - - +
94C THR* 3.2 5.7 - - - -
95C THR* 2.9 43.1 + - - +
97C GLU* 6.4 1.1 - - + -
157C ARG* 5.4 1.2 - - - -
158C SER 3.5 5.9 + - - -
159C ASP* 2.9 33.2 + - - +
172C CYS* 1.3 75.2 - - - +
174C LEU* 1.3 65.5 + - - +
175C LYS* 3.8 28.6 + - - +
159D ASP* 3.7 5.3 + - - +
173D ASN* 3.0 23.7 + - - +
175D LYS* 6.2 0.2 - - - -
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Residues in contact with LEU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C THR* 4.4 13.0 - - + +
63C NRQ 4.4 9.2 - - + -
92C ARG* 4.1 25.8 - - - +
93C VAL 3.7 3.6 - - - -
94C THR* 3.8 15.3 - - + +
156C GLY 3.6 0.9 - - - +
157C ARG* 3.4 9.5 - - - -
158C SER* 2.8 45.4 + - - +
160C MET* 3.8 33.0 - - + -
172C CYS* 3.8 26.9 - - - +
173C ASN* 1.3 83.9 - - - +
175C LYS* 1.3 65.2 + - - +
176C THR* 4.0 2.5 - - - +
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Residues in contact with LYS 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A GLY* 6.6 0.2 - - - -
124A VAL* 5.6 0.2 - - - +
125A ASN* 4.2 21.9 - - - +
91C GLU 3.9 0.5 - - - +
92C ARG* 3.5 3.0 - - - +
93C VAL* 3.1 48.3 + - + +
95C THR* 5.3 6.6 + - - +
156C GLY 3.7 4.5 - - - -
157C ARG* 3.8 23.1 - - - +
173C ASN* 3.8 18.8 + - - +
174C LEU* 1.3 76.7 - - - +
176C THR* 1.3 59.9 + - - +
177C THR 4.2 0.2 + - - -
97D GLU* 3.0 36.0 - - - +
173D ASN* 6.2 1.6 - - - +
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Residues in contact with THR 176 (chain C).
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* 5.8 0.4 - - - -
90C TRP* 4.2 4.0 - - + -
91C GLU 3.1 18.6 - - - +
92C ARG* 2.9 33.3 + - + +
145C GLU* 4.2 3.9 + - - -
155C GLU* 3.1 10.8 - - - +
156C GLY 2.8 37.3 + - - -
157C ARG* 3.9 1.6 + - - +
174C LEU* 4.7 3.5 - - - +
175C LYS* 1.3 75.3 + - - +
177C THR* 1.3 65.7 + - - +
178C TYR* 3.3 43.6 + - + +
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Residues in contact with THR 177 (chain C).
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* 3.8 17.2 + - - +
90C TRP* 3.3 5.9 - - - +
91C GLU* 2.9 52.7 + - - +
151C ASP* 6.2 0.4 - - - +
154C LEU 3.5 6.7 - - - +
155C GLU* 3.7 22.0 + - + +
175C LYS 4.2 0.4 + - - -
176C THR* 1.3 75.5 - - - +
178C TYR* 1.3 65.6 + - - +
179C ARG* 3.6 38.4 + - + +
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Residues in contact with TYR 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C LYS* 2.8 45.5 + - + -
79C PHE* 3.6 20.3 - - + -
80C PHE* 3.5 17.3 - + + -
88C PHE* 5.3 0.2 - + - -
89C THR 3.8 3.8 - - - +
90C TRP* 3.5 22.2 - + + -
92C ARG* 3.3 15.7 + - - -
145C GLU* 2.8 22.1 + - - -
147C LEU* 3.6 22.2 - - + -
153C GLY* 3.5 6.8 - - - -
154C LEU* 2.6 46.1 + - + +
156C GLY 4.0 3.1 - - - -
176C THR* 3.3 26.4 - - + +
177C THR* 1.3 74.2 - - - +
179C ARG* 1.3 61.0 + - - +
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Residues in contact with ARG 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ASN* 3.5 35.8 + - - +
21A ASN* 4.0 13.5 - - - +
125A ASN* 5.6 0.6 - - - +
126A PHE 4.9 1.2 + - - -
79C PHE* 4.1 1.1 - - - -
88C PHE* 3.3 3.4 - - - +
89C THR* 2.8 50.1 + - - +
90C TRP* 6.1 0.6 - - - -
91C GLU* 2.4 47.1 + - - +
153C GLY* 5.0 3.1 - - - -
177C THR* 3.6 22.8 + - + +
178C TYR* 1.3 77.0 - - - +
180C SER* 1.3 65.0 + - - +
181C LYS* 5.0 0.2 - - - +
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Residues in contact with SER 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C PHE* 3.6 21.3 - - - -
83C SER* 2.9 22.9 + - - -
88C PHE* 3.8 8.5 - - - -
152C GLY 5.3 6.4 + - - -
179C ARG* 1.3 78.3 - - - +
181C LYS* 1.3 59.3 + - - +
182C LYS* 3.0 33.3 + - - +
187C LEU* 3.8 7.9 - - - +
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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