Contacts of the strand formed by residues 143 - 150 (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 SER 143 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C MET* 5.7 0.2 - - - -
194C TYR* 4.6 5.6 - - - -
63D NRQ 2.5 30.5 + - - -
141D GLU 4.4 1.1 - - - -
142D ALA* 1.3 77.1 - - - +
144D THR* 1.3 67.8 + - - +
159D ASP 3.9 11.0 - - - -
160D MET* 3.8 20.9 - - - -
195D VAL 3.7 0.3 - - - +
196D ASP* 3.4 2.1 - - - +
197D ARG* 2.6 52.6 + - - +
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Residues in contact with THR 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C THR* 3.7 27.2 - - - +
194C TYR* 4.6 7.3 - - - -
220C ARG* 3.7 12.3 + - - -
143D SER* 1.3 78.1 + - - +
145D GLU* 1.3 64.0 + - - +
146D MET 4.1 0.5 + - - -
157D ARG 3.9 2.3 - - - +
158D SER* 3.1 15.2 + - - -
159D ASP 4.5 3.8 + - - +
194D TYR* 4.2 15.5 - - + -
195D VAL 3.3 4.5 - - - +
196D ASP* 2.7 25.5 + - - +
197D ARG* 3.4 3.8 - - - -
220D ARG* 3.7 14.6 - - - +
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Residues in contact with GLU 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LYS* 2.8 23.6 + - - -
70D ILE* 5.6 0.2 - - - +
92D ARG* 5.8 0.4 - - - -
144D THR* 1.3 74.9 - - - +
146D MET* 1.3 62.9 + - - +
147D LEU* 3.8 22.2 - - + +
156D GLY* 3.3 12.7 - - - -
157D ARG 3.4 18.2 - - - +
158D SER* 3.9 2.0 - - - -
176D THR* 4.3 3.1 + - - -
178D TYR* 2.3 30.1 + - - -
194D TYR* 3.1 7.6 - - - +
195D VAL* 2.8 40.6 + - + +
197D ARG* 3.4 30.4 + - - +
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Residues in contact with MET 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C GLU* 5.0 0.2 - - - -
142C ALA 4.4 6.7 - - - +
143C SER* 5.7 0.2 - - - -
159C ASP* 4.4 20.4 - - + +
160C MET 4.4 1.6 - - - -
161C ALA* 3.9 38.1 - - + +
171C ILE* 4.3 5.2 - - + -
144D THR 4.1 0.8 + - - -
145D GLU* 1.3 73.0 - - - +
147D LEU* 1.3 63.8 + - - +
148D TYR* 4.1 24.8 - - + -
155D GLU 3.6 1.0 - - - +
156D GLY* 3.2 3.3 - - - -
157D ARG* 2.8 54.6 + - + +
192D VAL* 4.2 13.5 - - + -
193D TYR 3.6 5.4 - - - +
194D TYR* 3.5 31.2 - - + -
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Residues in contact with LEU 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LYS* 5.3 0.9 - - - +
70D ILE* 6.1 0.4 - - + -
80D PHE* 4.1 16.2 - - + -
145D GLU* 3.8 32.1 - - + +
146D MET* 1.3 78.4 - - - +
148D TYR* 1.3 62.8 + - - +
154D LEU* 3.8 25.8 - - + -
155D GLU 3.1 7.4 - - - +
156D GLY* 4.4 0.2 - - - -
178D TYR* 4.2 14.6 - - + -
191D GLY 3.9 1.7 - - - +
192D VAL* 3.3 6.6 - - - +
193D TYR* 3.0 62.3 + - + +
195D VAL* 3.9 25.8 - - + +
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Residues in contact with TYR 148 (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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161C ALA* 5.5 0.7 - - + -
169C HIS* 4.2 24.5 - + + +
171C ILE* 3.1 38.3 - - + +
146D MET* 4.1 17.5 - - + -
147D LEU* 1.3 79.4 - - - +
149D PRO* 1.3 80.0 - - + +
150D ALA* 5.0 5.2 - - + -
154D LEU* 3.4 7.0 - - - -
155D GLU* 2.8 71.5 + - + +
157D ARG* 3.2 40.7 + - + -
191D GLY 4.6 0.7 - - - -
192D VAL* 3.7 16.2 - - + +
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Residues in contact with PRO 149 (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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168C GLY* 5.3 6.9 - - - -
169C HIS* 5.0 9.2 + - + +
148D TYR* 1.3 90.4 - - + +
150D ALA* 1.3 63.0 + - - +
153D GLY 3.4 6.5 - - - +
154D LEU* 3.9 3.1 - - + -
189D MET* 3.9 22.2 - - + -
190D PRO 3.3 22.9 - - - +
191D GLY* 4.2 8.7 - - - +
192D VAL* 4.1 12.6 - - + -
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Residues in contact with ALA 150 (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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148D TYR* 3.8 8.6 + - + +
149D PRO* 1.3 73.9 - - - +
151D ASP* 1.3 66.4 + - - +
152D GLY 3.3 2.2 - - - +
153D GLY* 2.7 35.8 + - - +
155D GLU* 4.6 27.6 - - + +
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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
------------------------------------------------------------
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