Contacts of the strand formed by residues 153 - 164 (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 GLY 153 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79D PHE* 4.2 4.5 - - - -
149D PRO* 3.4 0.7 - - - +
150D ALA 2.7 33.1 + - - -
151D ASP 2.9 3.7 + - - -
152D GLY* 1.3 80.4 - - - +
154D LEU* 1.3 62.7 + - - -
177D THR* 6.3 0.7 - - - -
178D TYR 3.5 13.2 - - - -
179D ARG* 5.2 4.3 - - - -
189D MET* 3.3 14.1 - - - +
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Residues in contact with LEU 154 (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* 3.8 34.0 - - + -
80D PHE* 4.3 5.2 - - + -
147D LEU* 3.8 25.1 - - + -
148D TYR* 3.4 17.0 - - - +
149D PRO* 3.9 6.3 - - + -
153D GLY* 1.3 83.7 - - - +
155D GLU* 1.3 64.2 + - - +
177D THR* 3.7 2.9 - - - +
178D TYR* 2.8 50.7 + - + +
189D MET* 3.9 9.9 - - + -
190D PRO* 3.8 23.3 - - + -
191D GLY 5.3 0.4 - - - +
193D TYR* 4.1 12.1 - - + +
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Residues in contact with GLU 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ASN* 3.9 9.7 - - - +
147D LEU* 3.1 5.1 - - - +
148D TYR* 2.8 74.4 + - + +
150D ALA* 4.6 19.0 - - + +
153D GLY 4.3 0.2 - - - -
154D LEU* 1.3 79.5 - - - +
156D GLY* 1.3 59.6 + - - +
157D ARG* 4.0 13.5 + - - +
176D THR 3.3 10.8 - - - +
177D THR* 3.6 22.0 + - + +
178D TYR* 4.3 2.2 - - - -
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Residues in contact with GLY 156 (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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145D GLU* 3.3 24.5 - - - -
146D MET 3.2 7.0 - - - -
147D LEU* 4.4 0.9 - - - -
155D GLU* 1.3 73.4 - - - +
157D ARG* 1.3 72.4 + - - -
174D LEU 4.0 0.6 - - - +
175D LYS* 3.9 0.5 - - - -
176D THR* 2.9 32.1 + - - -
178D TYR* 3.7 7.9 - - - -
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Residues in contact with ARG 157 (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 18.6 + - - +
97C GLU* 2.9 42.6 + - - -
159C ASP* 3.8 28.1 - - + +
171C ILE* 4.0 11.1 - - + +
144D THR 3.9 1.0 - - - +
145D GLU* 3.4 2.2 - - - +
146D MET* 2.8 41.4 + - + +
148D TYR* 3.2 37.0 + - + +
155D GLU* 4.0 14.3 + - - +
156D GLY* 1.3 87.6 + - - +
158D SER* 1.3 65.3 + - - +
173D ASN* 5.1 1.1 - - - -
174D LEU 3.7 12.6 - - - -
175D LYS* 3.7 21.2 - - - +
176D THR 3.9 10.5 + - - -
177D THR* 5.8 0.2 + - - -
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Residues in contact with SER 158 (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* 4.0 5.0 + - - -
143D SER* 4.4 0.5 - - - -
144D THR 3.1 12.3 + - - -
145D GLU* 4.3 2.5 - - - -
157D ARG* 1.3 77.7 - - - +
159D ASP* 1.3 68.7 + - - +
160D MET* 4.6 1.4 - - - +
173D ASN* 3.2 7.3 + - - -
174D LEU* 2.8 51.0 + - - +
197D ARG* 3.0 39.7 + - - -
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Residues in contact with ASP 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C MET* 4.2 16.3 - - + +
157C ARG* 3.8 37.2 - - + +
158C SER* 3.6 21.7 + - - -
159C ASP* 3.1 18.0 + - - +
173C ASN* 3.7 5.5 + - - +
143D SER* 3.9 12.5 - - - -
144D THR 4.5 3.7 + - - +
158D SER* 1.3 73.5 + - - +
160D MET* 1.3 67.7 + - - +
171D ILE* 4.7 1.8 - - + +
172D CYS 3.4 11.3 - - - +
173D ASN* 2.7 25.3 + - - +
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Residues in contact with MET 160 (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* 4.2 3.8 - - - -
60D THR* 3.8 21.1 - - + -
63D NRQ 3.4 40.6 - - + +
140D TRP* 3.5 49.4 - - + -
141D GLU 4.9 2.2 - - - +
143D SER* 3.8 17.0 - - - +
158D SER* 4.3 3.6 - - - +
159D ASP* 1.3 80.0 - - - +
161D ALA* 1.3 59.3 + - - +
170D LEU 3.9 0.9 - - - +
171D ILE* 3.4 6.2 - - - +
172D CYS* 2.9 39.4 + - - +
174D LEU* 4.0 20.2 - - + +
197D ARG* 5.2 0.2 - - - -
199D LEU* 5.8 0.2 - - + -
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Residues in contact with ALA 161 (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* 3.8 20.9 - - + +
148C TYR* 5.2 3.6 - - + -
192C VAL* 5.5 1.3 - - + -
140D TRP* 3.4 5.4 - - - -
141D GLU* 2.9 41.2 + - + +
142D ALA 5.7 0.4 + - - -
160D MET* 1.3 74.2 - - - +
162D LEU* 1.3 61.7 + - - +
169D HIS* 3.7 20.9 - - + -
170D LEU 3.9 3.1 - - - -
171D ILE* 3.8 17.9 - - + -
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Residues in contact with LEU 162 (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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56D ASP* 3.5 37.5 - - + +
57D ILE* 5.0 1.3 - - + -
96D TYR* 4.4 7.6 - - + -
132D VAL* 4.5 5.8 - - + -
137D THR* 3.7 30.3 - - + -
139D GLY 3.5 16.4 - - - +
140D TRP* 3.4 33.0 - - + -
161D ALA* 1.3 72.6 - - - +
163D LYS* 1.3 63.2 - - - +
164D LEU* 3.8 3.8 + - + +
169D HIS* 3.1 6.1 - - - -
170D LEU* 2.9 55.5 + - + +
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Residues in contact with LYS 163 (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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228C LEU* 6.2 2.6 - - - +
137D THR* 3.4 6.1 - - - -
138D LEU* 2.6 53.3 + - + +
139D GLY 2.8 20.4 + - - +
140D TRP 4.0 15.3 + - - -
141D GLU* 3.3 35.9 + - + +
162D LEU* 1.3 71.9 - - - +
164D LEU* 1.3 56.5 + - - +
168D GLY 3.8 6.7 - - - +
169D HIS* 3.8 9.2 - - + +
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Residues in contact with LEU 164 (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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131D PRO* 3.8 36.1 - - + -
136D LYS 3.6 5.2 - - - +
137D THR* 4.4 8.1 - - + -
138D LEU* 3.7 12.1 - - - +
162D LEU* 3.8 13.2 - - + +
163D LYS* 1.3 77.2 - - - +
165D VAL* 1.3 73.3 + - - +
166D GLY 3.3 0.5 + - - -
167D GLY* 3.1 22.6 + - - +
168D GLY* 3.1 27.2 + - - +
169D HIS* 4.2 8.7 - - - +
170D LEU* 4.0 13.0 - - + +
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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