Contacts of the strand formed by residues 143 - 152 (chain B) in PDB entry 4AEJ
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 ALA 143 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B ARG* 1.3 78.1 - - - +
144B SER* 1.3 63.1 + - - +
211B ARG* 3.5 2.5 - - - +
212B THR* 2.9 31.5 + - + +
215B ALA* 3.6 23.3 - - + +
218B LEU* 3.7 19.2 - - + +
242B VAL* 5.0 0.4 - - + -
243B CYS 3.1 13.5 - - - +
244B PHE* 3.8 15.0 - - + -
245B LEU 4.9 0.2 - - - +
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Residues in contact with SER 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLU* 4.1 8.7 + - - -
143B ALA* 1.3 76.6 - - - +
145B GLN* 1.3 62.9 + - - +
209B GLU* 4.8 3.3 + - - -
210B TYR 3.2 13.5 - - - -
211B ARG* 3.9 37.9 + - - -
218B LEU* 3.6 4.5 - - - +
241B PRO 4.0 0.2 - - - +
242B VAL* 3.8 0.3 - - - -
243B CYS* 2.9 42.7 + - - +
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Residues in contact with GLN 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B TYR* 2.6 32.9 + - - -
144B SER* 1.3 78.9 - - - +
146B GLN* 1.3 69.4 - - - +
209B GLU* 3.4 3.1 - - - +
210B TYR 3.1 30.7 + - - -
218B LEU* 3.9 7.6 - - + +
219B PRO* 3.4 7.1 - - - +
220B ILE* 2.7 48.8 + - + +
239B VAL* 3.6 7.9 - - - +
240B GLY 2.8 28.6 + - - +
241B PRO 3.5 10.3 - - - +
242B VAL* 4.0 10.3 - - + +
243B CYS* 6.2 0.2 - - - -
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Residues in contact with GLN 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B GLN* 1.3 80.9 - - - +
147B ILE* 1.3 64.0 + - - +
148B THR* 5.8 0.7 - - - +
192B LEU* 3.6 25.4 - - + +
207B VAL* 3.9 15.3 - - + +
208B PHE 3.1 12.1 - - - +
209B GLU* 3.7 21.2 + - + +
211B ARG* 5.7 0.2 - - - +
220B ILE* 5.2 0.2 - - - -
240B GLY* 2.9 31.7 + - - -
241B PRO 4.5 2.8 + - - -
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Residues in contact with ILE 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PHE* 3.8 24.2 - - + -
146B GLN* 1.3 75.8 - - - +
148B THR* 1.3 64.0 + - - +
149B TYR 4.2 0.2 - - - -
171B LEU* 3.8 32.5 - - + -
207B VAL* 3.6 2.3 - - - -
208B PHE* 2.8 53.5 + - + +
220B ILE* 4.2 21.5 - - + -
223B ILE* 4.6 7.9 - - + -
237B VAL* 3.7 28.9 - - + -
238B ASP 3.6 7.2 - - - +
239B VAL* 4.3 11.7 - - + -
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Residues in contact with THR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B GLN* 5.6 1.0 - - - +
147B ILE* 1.3 75.8 - - - +
149B TYR* 1.3 60.1 + - - +
150B HIS* 3.9 12.3 + - + +
205B LYS* 3.7 38.6 - - + +
206B THR 3.4 6.5 - - - +
207B VAL* 3.8 18.4 - - + +
237B VAL* 3.3 8.1 - - - +
238B ASP* 2.9 54.3 + - - +
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Residues in contact with TYR 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ILE 4.2 1.0 + - - -
148B THR* 1.3 70.3 - - - +
150B HIS* 1.3 61.6 + - - +
151B CYS* 3.8 21.5 - - + -
154B SER* 2.8 28.5 + - - -
155B ILE 4.4 1.5 + - - -
156B ALA* 3.5 27.8 - - + -
169B LEU* 3.6 15.9 - - + -
196B CYS* 4.0 0.2 - - - -
205B LYS* 3.1 6.0 - - - -
206B THR 2.9 36.4 + - - +
208B PHE* 3.9 16.3 - - + -
223B ILE* 3.9 14.4 - - + -
225B PRO* 3.4 33.2 - - + +
228B ILE* 3.6 4.0 - - - +
235B PHE* 3.4 34.5 - + + +
236B GLY 3.6 8.5 - - - -
237B VAL* 4.7 1.8 - - + +
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Residues in contact with HIS 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ARG* 4.4 20.9 + - + +
148B THR* 4.0 18.6 - - + +
149B TYR* 1.3 72.8 - - - +
151B CYS* 1.3 59.6 + - - +
203B TRP* 3.6 14.1 - - + -
204B SER 3.3 9.3 + - - +
205B LYS* 4.1 18.5 - - + +
235B PHE* 3.0 11.8 - - - +
236B GLY* 2.9 52.8 + - - +
237B VAL 4.1 0.4 - - - -
238B ASP* 2.8 39.1 + - - -
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Residues in contact with CYS 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B TYR* 3.8 9.4 - - + -
150B HIS* 1.3 73.9 - - - +
152B LYS* 1.3 59.4 + - - +
153B ASN 4.2 0.2 - - - -
154B SER* 3.4 21.1 - - - +
196B CYS* 2.0 54.7 - - - -
202B GLU 3.5 1.9 - - - +
203B TRP* 3.4 8.8 - - - -
204B SER* 2.8 47.1 + - - -
234B GLU 3.7 3.6 - - - -
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Residues in contact with LYS 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B CYS* 1.3 72.1 - - - +
153B ASN* 1.3 86.3 + - - +
154B SER 3.4 0.2 + - - -
201B GLY* 3.8 20.7 + - - -
202B GLU 3.7 13.7 - - - +
203B TRP* 3.7 38.9 - - + +
232B ASP* 3.6 7.7 - - - +
234B GLU* 2.9 55.5 + - + +
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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