Contacts of the strand formed by residues 153 - 163 (chain B) in PDB entry 2Q4E
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 LEU 153 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144B LEU* 5.2 1.1 - - + -
150B PHE* 3.5 31.1 - - + -
151B GLY 3.7 3.2 + - - -
152B GLN* 1.3 87.7 + - - +
154B LYS* 1.3 76.2 + - - +
155B THR 3.4 25.1 - - - +
156B VAL* 4.1 7.6 - - + -
199B ALA* 3.2 37.5 - - + +
200B ASN* 3.5 30.7 - - - +
235B ARG* 3.2 23.9 - - + +
253B ALA* 4.3 4.9 - - + -
254B ILE 4.1 0.2 - - - +
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Residues in contact with LYS 154 (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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240A TYR* 4.3 8.1 - - + +
242A SER* 5.8 1.3 - - - +
244A LEU* 3.9 28.3 - - + +
245A ALA* 4.2 22.4 - - + -
152B GLN* 3.8 18.8 - - - +
153B LEU* 1.3 87.0 - - - +
155B THR* 1.3 56.3 + - - +
233B ASP 5.0 4.2 + - - -
234B GLY* 3.3 24.5 - - - +
235B ARG* 3.3 4.7 - - - +
236B THR* 2.6 40.2 + - - +
254B ILE 3.1 13.8 + - - +
255B GLY* 4.4 1.3 - - - -
256B THR* 3.9 23.7 - - - +
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Residues in contact with THR 155 (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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240A TYR* 3.3 36.3 - - + -
153B LEU* 3.4 5.1 - - - +
154B LYS* 1.3 80.4 - - + +
156B VAL* 1.3 65.2 + - - +
157B GLN* 3.6 15.1 + - + +
236B THR 3.1 10.5 + - - -
237B ALA* 4.6 1.7 - - - -
252B THR* 4.4 2.6 + - + +
253B ALA* 3.0 1.6 - - - -
254B ILE* 2.7 69.9 + - + +
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Residues in contact with VAL 156 (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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144B LEU* 5.6 0.7 - - + -
153B LEU* 4.1 4.3 - - + -
155B THR* 1.3 76.7 + - - +
157B GLN* 1.3 73.8 + - - +
158B SER* 3.5 3.6 + - - -
195B ALA 4.2 3.8 - - - +
196B THR* 3.7 25.9 - - + +
199B ALA* 3.5 22.0 - - + -
200B ASN* 3.9 13.7 - - - +
236B THR 4.0 2.6 + - - -
237B ALA* 3.6 20.6 - - + +
251B ILE* 3.8 16.4 - - + -
252B THR 3.1 7.6 - - - -
253B ALA* 3.3 23.6 - - + +
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Residues in contact with GLN 157 (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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157A GLN* 4.5 26.9 - - - +
158A SER 5.9 0.4 - - - +
159A CYS* 5.3 11.1 - - - +
250A GLU* 5.9 4.4 + - - +
252A THR* 4.6 7.6 + - - +
155B THR* 3.6 9.7 + - + +
156B VAL* 1.3 85.4 - - - +
158B SER* 1.3 66.9 + - - +
159B CYS* 4.7 5.9 + - - +
238B THR* 3.1 37.1 - - - +
250B GLU* 4.7 11.2 + - - +
251B ILE* 3.8 0.2 - - - -
252B THR* 3.0 54.8 + - + +
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Residues in contact with SER 158 (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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156B VAL 3.5 5.8 + - - -
157B GLN* 1.3 82.2 + - - +
159B CYS* 1.3 60.2 + - - +
192B ALA* 3.5 25.3 - - - +
195B ALA* 3.9 8.3 - - - +
196B THR* 4.7 0.2 - - - -
238B THR 2.6 10.1 + - - +
239B ILE* 2.8 28.8 - - - -
240B TYR 3.0 1.2 + - - -
250B GLU 2.8 21.6 + - - -
251B ILE* 4.1 1.6 - - - -
265B PHE* 3.4 21.0 - - - -
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Residues in contact with CYS 159 (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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157A GLN* 5.4 4.0 - - - +
252A THR* 5.4 4.5 - - - -
254A ILE* 4.2 22.4 - - + -
157B GLN* 4.7 6.2 + - - +
158B SER* 1.3 78.3 + - - +
160B PHE* 1.3 64.9 + - - +
192B ALA* 4.3 4.5 - - - -
240B TYR* 3.0 30.3 - - + +
248B THR* 4.0 22.0 - - - -
249B MSE 3.6 14.0 - - - -
250B GLU* 3.6 22.3 + - - +
265B PHE* 4.2 4.0 - - - -
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Residues in contact with PHE 160 (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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284A PHE* 5.2 7.2 - + - -
159B CYS* 1.3 77.3 - - - +
161B SER* 1.3 85.2 + - - +
162B PHE* 4.1 20.6 - + - -
187B ASP* 3.9 16.2 - - - -
188B ALA* 3.3 39.3 - - + +
191B TYR* 3.7 11.9 - + - -
192B ALA* 5.4 2.0 - - + -
240B TYR 2.7 9.2 + - - -
241B CYS* 3.1 24.4 - - - -
242B SER 3.2 2.3 + - - -
247B LEU* 4.0 15.0 - - + -
248B THR 3.4 9.0 - - - -
249B MSE 4.1 13.7 - - + -
266B ILE* 3.5 34.3 - - + -
267B ILE* 6.0 1.3 - - + -
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Residues in contact with SER 161 (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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254A ILE* 3.9 12.4 - - - +
160B PHE* 1.3 81.3 - - - +
162B PHE* 1.3 71.9 + - - +
188B ALA* 5.4 0.4 - - - -
240B TYR* 4.7 6.7 - - - -
242B SER* 3.3 26.9 - - - -
245B ALA* 3.3 9.8 + - - -
246B ASN 2.8 19.7 + - - -
247B LEU* 3.0 6.8 - - - +
248B THR* 3.0 32.2 + - - -
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Residues in contact with PHE 162 (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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283A TRP* 3.5 39.0 - + + -
284A PHE* 5.9 1.1 - + - -
160B PHE* 4.1 21.5 - + - -
161B SER* 1.3 78.3 - - - +
163B ALA* 1.3 65.5 + - - +
164B GLY* 4.1 16.4 - - - -
168B PHE* 4.2 14.1 - + - -
174B ARG* 5.7 0.2 - - - -
187B ASP* 4.0 10.1 - - - -
188B ALA* 5.7 2.5 - - + -
242B SER 3.3 4.0 + - - -
243B PHE* 3.2 63.0 - + - +
245B ALA 2.7 22.3 + - - +
247B LEU* 3.3 18.2 - - + +
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Residues in contact with ALA 163 (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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256A THR 4.1 19.3 - - - +
283A TRP* 4.7 10.8 - - - -
162B PHE* 1.3 78.1 - - - +
164B GLY* 1.3 62.6 + - - +
165B ASP 3.8 1.4 + - - -
243B PHE 4.3 1.1 - - - -
244B LEU* 4.9 1.8 - - - +
245B ALA 3.6 5.1 + - - +
246B ASN* 4.2 12.8 - - - +
247B LEU* 3.9 4.6 - - - +
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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
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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