Contacts of the strand formed by residues 157 - 168 (chain B) in PDB entry 1UDY
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 GLU 157 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153B LYS* 3.4 6.8 - - - +
154B LYS* 2.7 69.1 + - + +
155B GLY 3.1 1.0 + - - -
156B ASP* 1.3 83.6 - - - +
158B TYR* 1.3 64.8 + - - +
159B ILE* 4.2 0.9 - - + -
231B ARG* 3.3 40.3 + - - +
232B VAL 3.0 13.5 - - - +
233B PRO* 4.2 8.3 - - + +
234B LYS* 4.2 1.5 - - - +
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Residues in contact with TYR 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ALA* 5.0 5.6 - - + -
152B GLU* 3.5 6.5 - - - +
153B LYS* 3.2 48.6 + - + -
157B GLU* 1.3 77.2 - - - +
159B ILE* 1.3 65.2 + - - +
160B ILE* 3.5 5.5 + - + +
182B SER* 5.7 4.0 - - - -
195B THR* 5.7 0.4 - - + -
197B PHE* 3.5 36.6 - + + -
230B VAL 3.5 0.7 - - - +
231B ARG* 3.5 2.3 - - - -
232B VAL* 2.6 41.8 + - + +
233B PRO 5.0 0.2 - - - -
234B LYS* 4.0 17.0 - - + +
237B VAL* 3.1 27.2 - - + +
241B GLU* 2.8 42.4 + - + +
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Residues in contact with ILE 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ALA* 3.5 1.6 - - - -
152B GLU* 2.7 54.5 + - + +
154B LYS* 3.8 30.3 - - + -
157B GLU* 4.3 0.7 - - - +
158B TYR* 1.3 72.8 - - - +
160B ILE* 1.3 60.5 + - - +
161B ASN* 4.0 6.8 + - - +
229B ASP* 3.8 35.7 - - + +
230B VAL 3.3 2.0 - - - +
231B ARG* 3.4 37.2 - - + -
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Residues in contact with ILE 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B THR* 4.0 16.8 - - + -
150B LYS 3.4 16.6 - - - +
151B ALA* 4.4 8.5 - - + -
158B TYR* 4.2 11.0 - - + +
159B ILE* 1.3 74.8 - - - +
161B ASN* 1.3 65.7 + - - +
178B LEU* 4.0 23.8 - - + -
180B ALA* 4.9 0.4 - - + -
197B PHE* 4.1 19.7 - - + -
199B VAL* 4.5 5.4 - - + -
227B PHE* 4.1 17.4 - - + +
228B GLU 3.9 0.7 - - - -
229B ASP* 3.1 7.3 + - - -
230B VAL* 2.8 44.4 + - + +
232B VAL* 3.8 24.7 - - + -
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Residues in contact with ASN 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B THR* 3.5 3.8 - - - -
150B LYS* 2.8 40.9 + - + +
152B GLU* 4.5 9.4 - - - +
159B ILE* 4.0 7.5 + - - +
160B ILE* 1.3 77.2 - - - +
162B GLY* 1.3 58.4 + - - +
227B PHE 3.4 2.2 + - - -
228B GLU* 3.2 11.9 - - - +
229B ASP* 2.4 52.5 + - - +
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Residues in contact with GLY 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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149B THR* 3.7 13.7 - - - -
161B ASN* 1.3 75.6 - - - +
163B GLN* 1.3 57.5 + - - +
226B VAL* 3.6 4.2 - - - +
227B PHE* 2.6 45.5 + - - +
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Residues in contact with GLN 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B GLU* 3.4 14.4 + - - +
138B PRO* 3.7 23.9 - - + +
149B THR* 3.0 16.3 + - - +
162B GLY* 1.3 74.4 - - - +
164B LYS* 1.3 89.7 + - - +
165B MET* 3.1 25.3 - - - +
224B GLY* 4.3 4.7 - - - -
225B ILE 3.1 17.7 - - - +
226B VAL* 4.0 22.7 - - + +
227B PHE* 4.4 0.7 - - - +
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Residues in contact with LYS 164 (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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134B CYS* 3.6 16.2 - - + +
135B VAL 3.0 18.9 + - - +
136B THR 3.1 16.2 - - - +
137B GLU* 2.6 26.9 + - - +
138B PRO* 4.4 0.2 - - - -
147B ILE* 4.1 4.2 - - - +
149B THR* 3.6 8.2 + - - -
163B GLN* 1.3 103.4 - - - +
165B MET* 1.3 63.3 + - - +
167B ILE* 3.5 19.7 - - + -
178B LEU* 3.4 23.8 - - - -
179B LEU 2.9 20.2 + - - -
224B GLY* 3.6 0.2 - - - -
225B ILE* 2.9 20.5 + - + +
227B PHE* 4.0 19.7 - - + -
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Residues in contact with MET 165 (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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136B THR* 3.1 20.2 + - - -
137B GLU 4.0 2.7 - - - -
138B PRO* 4.0 29.4 - - + -
163B GLN* 3.1 28.9 - - - +
164B LYS* 1.3 78.2 - - - +
166B TRP* 1.3 112.6 + - + +
167B ILE* 3.2 10.0 + - - +
212B GLU* 4.5 16.4 - - - +
223B ARG 4.6 0.4 - - - -
224B GLY* 3.8 20.6 - - - -
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Residues in contact with TRP 166 (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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353A GLY* 4.3 10.8 - - - -
354A ASN* 3.5 33.1 + - - -
357A ASN* 3.5 29.2 - - + -
360A TYR* 5.4 1.8 - + - -
136B THR* 4.4 6.5 - - + -
137B GLU 5.4 0.7 - - - -
138B PRO* 6.1 0.4 - - - +
165B MET* 1.3 109.0 - - + +
167B ILE* 1.3 61.3 + - - +
212B GLU* 3.8 32.3 - - + -
214B ASN* 3.8 16.6 - - - -
222B THR* 3.8 19.0 + - - -
223B ARG 3.5 6.1 + - - -
1399B FAD 2.7 80.0 + + + +
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Residues in contact with ILE 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ALA* 4.0 7.4 - - + -
133B TYR 3.3 15.3 - - - +
134B CYS* 3.3 36.1 - - - -
136B THR 4.1 3.6 - - - +
164B LYS* 3.5 28.5 - - + -
165B MET* 3.3 17.5 - - - +
166B TRP* 1.3 70.6 - - - +
168B THR* 1.3 72.1 + - - +
170B GLY* 3.3 7.4 + - - -
222B THR* 3.2 2.0 - - - -
223B ARG 3.0 34.5 + - - +
225B ILE* 3.7 24.2 - - + -
1399B FAD 3.9 7.9 - - + -
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Residues in contact with THR 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B THR* 4.2 12.9 - - + +
97B ALA* 4.7 0.7 - - - -
100B ALA* 3.5 27.6 - - + +
132B ALA* 3.2 17.7 - - - +
166B TRP 3.2 1.4 + - - -
167B ILE* 1.3 66.3 - - - +
169B ASN* 1.3 76.3 + - - +
170B GLY 2.9 6.0 + - - -
220B SER* 3.8 15.4 + - - +
221B ASP 3.0 13.7 - - - +
222B THR* 4.2 1.9 - - - +
1399B FAD 2.7 48.9 + - - +
1400B CS8 4.1 6.8 - - - +
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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