Contacts of the strand formed by residues 169 - 180 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148C TYR* 4.3 21.2 - + + -
149C PRO* 4.9 10.4 + - + -
192C VAL* 3.7 16.5 - - + +
141D GLU* 2.8 34.0 + - + +
161D ALA* 3.7 22.9 - - + -
162D LEU 3.1 9.4 - - - +
163D LYS* 3.8 16.2 - - + +
164D LEU* 4.2 8.7 - - - +
168D GLY* 1.3 82.0 - - - -
170D LEU* 1.3 60.0 + - - +
171D ILE* 4.0 22.8 + - + +
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Residues in contact with LEU 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D TYR* 4.0 23.1 - - + -
97D GLU* 4.3 2.9 - - + +
98D ASP* 3.7 52.7 - - + +
131D PRO* 3.9 19.5 - - + -
132D VAL* 4.0 17.3 - - + -
140D TRP* 4.7 1.4 - - - -
160D MET 3.9 1.2 - - - +
162D LEU* 2.9 41.7 + - + +
164D LEU* 4.0 16.3 - - + +
169D HIS* 1.3 73.4 - - - +
171D ILE* 1.3 71.6 + - - +
172D CYS* 5.2 0.3 - - - -
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Residues in contact with ILE 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C MET* 4.5 2.9 - - + -
148C TYR* 3.1 47.3 - - + +
157C ARG* 3.8 29.2 - - + +
96D TYR* 3.8 1.2 - - - -
97D GLU* 3.1 46.0 + - + +
159D ASP* 4.7 2.2 - - - +
160D MET 3.4 7.6 - - - +
161D ALA* 3.8 24.2 - - + -
169D HIS* 4.0 10.3 + - + +
170D LEU* 1.3 82.4 - - - +
172D CYS* 1.3 73.8 + - - +
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Residues in contact with CYS 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D THR* 3.8 20.9 - - + -
95D THR 3.1 18.4 - - - +
96D TYR* 3.8 17.0 - - + -
97D GLU* 4.7 2.5 - - - +
140D TRP* 3.7 35.4 - - - -
159D ASP* 3.4 9.2 - - - +
160D MET* 2.9 36.1 + - - +
171D ILE* 1.3 77.1 - - - +
173D ASN* 1.3 59.7 + - - +
174D LEU* 3.9 9.6 - - - -
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Residues in contact with ASN 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C ASP* 2.8 28.9 + - - +
173C ASN* 3.0 17.7 + - - +
175C LYS* 6.2 1.6 - - - +
93D VAL 3.7 1.9 - - - +
94D THR* 3.3 3.8 - - - -
95D THR* 3.1 37.5 + - - +
157D ARG* 5.1 0.3 - - - -
158D SER 3.2 7.9 + - - -
159D ASP* 2.7 21.9 + - - +
172D CYS* 1.3 74.6 - - - +
174D LEU* 1.3 69.8 + - - +
175D LYS* 3.4 29.4 + - - +
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Residues in contact with LEU 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D THR* 4.5 13.0 - - + +
63D NRQ 4.6 7.2 - - + -
92D ARG* 3.8 27.6 - - - +
93D VAL 3.6 3.6 - - - -
94D THR* 3.6 28.0 - - + +
156D GLY 4.6 0.2 - - - -
157D ARG* 3.7 8.1 - - - -
158D SER* 2.8 45.0 + - - +
160D MET* 4.0 31.0 - - + -
172D CYS* 3.9 15.5 - - - +
173D ASN* 1.3 82.6 - - - +
175D LYS* 1.3 64.7 + - - +
176D THR* 4.2 4.7 - - - +
197D ARG* 4.8 1.8 - - - +
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Residues in contact with LYS 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLY 5.6 1.6 - - - +
101B VAL* 6.4 0.9 - - + -
125B ASN* 3.6 27.7 - - - +
97C GLU* 3.4 29.2 - - - +
173C ASN* 6.2 0.8 - - - +
91D GLU 3.9 0.3 - - - +
92D ARG* 3.2 3.9 - - - +
93D VAL* 2.9 54.1 + - + +
95D THR* 5.0 9.5 + - - -
156D GLY 3.9 4.0 - - - -
157D ARG* 3.7 20.2 - - - +
173D ASN* 3.4 19.8 + - - +
174D LEU* 1.3 76.3 - - - +
176D THR* 1.3 60.7 + - - +
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Residues in contact with THR 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D TRP* 4.2 4.3 - - + -
91D GLU 3.1 17.0 - - - +
92D ARG* 2.8 35.4 + - + +
145D GLU* 4.3 2.6 + - - -
155D GLU* 3.3 9.0 - - - +
156D GLY 2.9 34.2 + - - +
157D ARG* 3.9 3.1 + - - +
174D LEU* 4.6 4.3 - - - +
175D LYS* 1.3 76.9 + - - +
177D THR* 1.3 66.0 + - - +
178D TYR* 3.3 41.9 + - + +
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Residues in contact with THR 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ASN* 4.1 15.9 + - - +
89D THR 4.1 0.2 - - - +
90D TRP* 3.3 6.8 - - - +
91D GLU* 2.8 49.5 + - - +
153D GLY* 6.3 0.2 - - - -
154D LEU 3.7 6.3 - - - +
155D GLU* 3.6 22.0 + - + +
176D THR* 1.3 74.4 - - - +
178D TYR* 1.3 65.6 + - - +
179D ARG* 3.7 41.3 + - + +
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Residues in contact with TYR 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D LYS* 2.9 39.8 + - + -
79D PHE* 3.9 6.6 - - + -
80D PHE* 3.5 26.2 - + + -
88D PHE* 5.5 0.9 - + + -
89D THR 3.7 4.7 - - - +
90D TRP* 3.7 17.3 - + + -
92D ARG* 3.7 4.7 + - - -
145D GLU* 2.3 33.0 + - - -
147D LEU* 4.2 8.3 - - + -
153D GLY* 3.5 7.4 - - - -
154D LEU* 2.8 57.8 + - + +
156D GLY* 3.7 16.4 - - - -
176D THR* 3.3 26.6 - - + +
177D THR* 1.3 73.3 - - - +
179D ARG* 1.3 66.5 + - - +
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Residues in contact with ARG 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ASN* 3.5 34.8 + - - +
21B ASN* 3.7 11.5 - - - +
22B HIS* 6.2 0.4 - - - -
125B ASN* 6.0 0.6 - - - +
126B PHE 5.2 0.8 + - - -
79D PHE* 4.0 4.0 - - - -
88D PHE* 3.2 4.2 - - - +
89D THR* 2.9 46.1 + - - +
91D GLU* 2.0 46.4 + - - -
153D GLY* 5.2 3.8 - - - -
177D THR* 3.7 22.7 - - + +
178D TYR* 1.3 80.5 - - - +
180D SER* 1.3 63.7 + - - +
181D LYS* 3.9 0.3 + - - +
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Residues in contact with SER 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D PHE* 3.5 19.7 - - - -
83D SER* 2.8 25.9 + - - -
87D GLY 4.0 2.2 - - - -
88D PHE* 4.2 3.4 - - - -
152D GLY 5.3 2.3 + - - -
179D ARG* 1.3 76.5 - - - +
181D LYS* 1.3 61.0 + - - +
182D LYS* 3.2 28.0 + - - +
187D LEU* 3.6 20.5 - - - +
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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