Contacts of the strand formed by residues 169 - 180 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148E TYR* 4.3 23.1 - - + +
149E PRO* 4.9 9.6 + - + -
192E VAL* 3.6 22.7 - - + -
141F GLU* 2.9 39.6 + - + +
161F ALA* 3.9 9.9 - - + -
162F LEU 3.3 14.1 - - - -
163F LYS* 3.7 11.3 - - + +
164F LEU* 4.0 8.0 - - - +
167F GLY 4.5 7.9 + - - -
168F GLY* 1.3 80.9 - - - -
170F LEU* 1.3 60.0 + - - +
171F ILE* 4.1 20.3 + - + +
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Residues in contact with LEU 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F TYR* 3.8 27.3 - - + -
97F GLU* 4.5 2.9 - - + +
98F ASP* 3.9 40.2 - - + +
131F PRO* 4.2 16.4 - - + -
132F VAL* 4.1 21.1 - - + -
140F TRP* 4.6 1.0 - - - -
160F MET 3.9 0.3 - - - +
161F ALA* 3.6 0.2 - - - -
162F LEU* 2.7 49.9 + - + +
164F LEU* 3.9 23.3 - - + +
169F HIS* 1.3 73.6 - - - +
171F ILE* 1.3 73.3 + - - +
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Residues in contact with ILE 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E MET* 4.4 3.8 - - + -
148E TYR* 3.5 46.2 - - + +
157E ARG* 3.9 17.7 - - + -
96F TYR* 3.7 3.0 - - - -
97F GLU* 3.0 54.6 + - + +
159F ASP* 5.1 2.5 - - + +
160F MET 3.2 11.0 - - - +
161F ALA* 3.6 30.1 - - + -
169F HIS* 4.2 8.9 + - + +
170F LEU* 1.3 82.1 - - - +
172F CYS* 1.3 73.0 + - - +
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Residues in contact with CYS 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F THR* 3.7 23.3 - - + -
95F THR 3.3 13.2 - - - +
96F TYR* 3.7 16.6 - - + -
97F GLU* 5.6 1.1 - - - -
140F TRP* 3.7 35.9 - - - -
159F ASP* 3.4 5.0 - - - +
160F MET* 2.8 39.9 + - - -
171F ILE* 1.3 81.2 - - - +
173F ASN* 1.3 59.7 + - - +
174F LEU* 3.9 11.4 - - - +
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Residues in contact with ASN 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159E ASP* 3.6 22.8 + - - -
173E ASN* 4.4 14.6 - - - +
93F VAL 3.7 0.9 - - - +
94F THR* 3.3 3.3 - - - +
95F THR* 2.8 44.5 + - - +
157F ARG* 4.8 1.4 - - - +
158F SER 3.5 8.2 + - - -
159F ASP* 4.1 9.7 + - - +
172F CYS* 1.3 73.5 - - - +
174F LEU* 1.3 66.6 + - - +
175F LYS* 2.7 39.3 + - - +
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Residues in contact with LEU 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F THR* 4.6 11.7 - - + +
63F NRQ 4.9 4.9 - - + -
92F ARG* 3.5 33.9 - - - +
93F VAL 3.5 3.4 - - - -
94F THR* 3.4 17.0 - - + +
156F GLY 3.5 1.2 - - - +
157F ARG* 3.4 10.7 - - - -
158F SER* 2.9 43.8 + - - +
160F MET* 3.8 37.7 - - + -
172F CYS* 3.9 23.3 - - - +
173F ASN* 1.3 78.4 + - - +
175F LYS* 1.3 61.7 + - - +
176F THR* 4.1 3.7 + - - +
197F ARG* 5.2 0.7 - - - +
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Residues in contact with LYS 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E GLU* 3.2 30.5 + - - +
173E ASN* 5.9 3.2 - - - +
91F GLU 3.9 0.3 - - - +
92F ARG* 3.2 3.1 - - - +
93F VAL* 2.9 52.3 + - + +
95F THR* 5.6 2.7 + - - +
156F GLY 3.6 4.5 - - - -
157F ARG* 3.7 20.9 - - - +
173F ASN* 2.7 38.0 + - - +
174F LEU* 1.3 71.9 - - - +
176F THR* 1.3 61.3 + - - +
101G VAL* 6.0 1.6 - - + -
125G ASN* 3.8 28.1 - - - +
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Residues in contact with THR 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F TRP* 4.4 5.8 - - + -
91F GLU 3.0 18.6 - - - +
92F ARG* 3.4 35.8 + - + +
145F GLU* 4.2 4.2 + - - -
155F GLU* 3.3 7.8 - - - +
156F GLY* 2.8 39.4 + - - -
157F ARG* 3.8 2.1 + - - +
174F LEU* 4.3 4.3 - - - +
175F LYS* 1.3 77.4 + - - +
177F THR* 1.3 62.3 + - - +
178F TYR* 3.7 36.4 + - + +
125G ASN* 5.7 0.2 - - - -
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Residues in contact with THR 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F THR 4.7 0.2 - - - -
90F TRP* 3.4 4.2 - - - +
91F GLU* 2.9 41.3 + - - +
154F LEU 3.7 6.7 - - - +
155F GLU* 3.9 17.4 + - + +
176F THR* 1.3 74.6 + - - +
178F TYR* 1.3 65.2 + - - +
179F ARG* 3.4 45.4 + - + +
125G ASN* 4.1 19.4 + - - -
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Residues in contact with TYR 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F LYS* 3.1 41.7 + - + -
79F PHE* 3.9 9.8 - - + -
80F PHE* 3.5 26.2 - + + -
88F PHE* 5.3 0.9 - + + -
89F THR 3.6 4.9 - - - +
90F TRP* 3.6 25.1 - + + -
92F ARG* 3.8 6.9 + - - -
145F GLU* 2.5 30.5 + - - -
147F LEU* 3.8 14.1 - - + -
153F GLY* 3.5 6.2 - - - -
154F LEU* 2.8 53.0 + - + +
156F GLY 4.2 4.7 - - - -
176F THR* 3.7 24.6 - - + +
177F THR* 1.3 74.3 - - - +
179F ARG* 1.3 63.5 + - - +
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Residues in contact with ARG 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F PHE* 4.2 2.7 - - - -
88F PHE* 3.5 4.4 - - - +
89F THR* 3.0 40.5 + - - +
91F GLU* 2.3 45.2 + - - -
153F GLY* 5.1 2.7 - - - -
177F THR* 3.4 26.0 - - + +
178F TYR* 1.3 78.3 - - - +
180F SER* 1.3 65.0 + - - +
181F LYS* 5.1 0.5 - - - +
20G ASN* 4.0 23.8 + - - +
21G ASN* 3.6 20.2 - - - +
125G ASN* 6.2 0.2 - - - +
126G PHE 4.5 6.5 + - - -
128G SER* 4.9 13.3 - - - +
133G MET* 6.1 0.6 - - - +
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Residues in contact with SER 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F PHE* 3.7 20.1 - - - -
83F SER* 2.6 29.3 + - - -
87F GLY 4.4 1.3 - - - -
88F PHE* 4.4 0.9 - - - -
152F GLY 5.2 2.4 + - - -
153F GLY* 5.3 1.4 - - - -
179F ARG* 1.3 77.0 - - - +
181F LYS* 1.3 64.6 + - - +
182F LYS* 3.5 14.9 + - - +
187F LEU* 3.7 23.9 - - - +
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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