Contacts of the strand formed by residues 157 - 168 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153D LYS* 3.4 6.6 - - - +
154D LYS* 2.8 59.5 + - + +
155D GLY 3.3 3.0 + - - -
156D ASP* 1.3 81.8 + - - +
158D TYR* 1.3 67.9 + - - +
159D ILE* 4.8 3.6 - - + -
231D ARG* 2.6 58.2 + - - +
232D VAL 3.2 18.6 + - - +
233D PRO* 4.3 1.3 - - + -
234D LYS* 3.9 8.4 - - - +
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Residues in contact with TYR 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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151D ALA 4.5 1.6 - - - -
152D GLU* 3.0 22.4 - - - +
153D LYS* 3.6 34.2 + - + +
157D GLU* 1.3 79.6 - - - +
159D ILE* 1.3 62.3 + - - +
160D ILE* 3.7 6.9 + - + +
182D SER* 4.9 5.6 - - - -
195D THR* 5.6 0.4 - - + -
197D PHE* 3.4 39.0 - + + -
230D VAL 3.2 5.4 - - - +
231D ARG* 3.5 1.4 - - - -
232D VAL* 2.8 39.2 + - + +
234D LYS* 4.4 17.5 - - + -
237D VAL* 3.6 24.3 - - + +
241D GLU* 2.7 39.7 + - + +
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Residues in contact with ILE 159 (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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150D LYS 3.7 0.9 - - - +
151D ALA* 3.3 3.1 - - - -
152D GLU* 2.8 54.1 + - + +
154D LYS* 3.9 38.4 - - + -
157D GLU* 4.8 2.2 - - + -
158D TYR* 1.3 75.1 - - - +
160D ILE* 1.3 61.5 + - - +
161D ASN* 3.8 7.1 + - - +
229D ASP* 3.5 40.2 - - + +
230D VAL 3.7 1.8 - - - -
231D ARG* 3.7 28.0 - - + +
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Residues in contact with ILE 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D THR* 4.0 18.6 - - + -
150D LYS 3.3 4.5 - - - +
151D ALA* 3.2 31.9 - - + -
158D TYR* 4.3 8.1 - - + +
159D ILE* 1.3 73.7 - - - +
161D ASN* 1.3 63.9 + - - +
178D LEU* 4.4 8.7 - - + -
180D ALA* 4.5 1.3 - - + -
197D PHE* 3.7 24.5 - - + -
199D VAL* 5.3 4.3 - - + -
227D PHE* 3.3 28.6 - - + +
229D ASP 3.4 3.1 + - - -
230D VAL* 2.8 48.8 + - + +
232D VAL* 4.3 14.8 - - + -
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Residues in contact with ASN 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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148D LYS 4.3 0.7 - - - +
149D THR* 3.4 3.0 - - - -
150D LYS* 2.6 48.4 + - + +
152D GLU* 4.8 4.7 - - - +
159D ILE* 3.8 8.0 + - - +
160D ILE* 1.3 78.6 - - - +
162D GLY* 1.3 54.9 + - - +
227D PHE 3.2 5.7 + - - -
228D GLU* 3.8 5.9 - - - +
229D ASP* 3.2 45.1 + - - +
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Residues in contact with GLY 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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149D THR* 3.4 19.9 - - - +
161D ASN* 1.3 75.0 - - - +
163D GLN* 1.3 61.7 + - - +
226D VAL* 3.8 3.9 - - - +
227D PHE* 2.8 39.5 + - - +
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Residues in contact with GLN 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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137D GLU* 3.4 29.2 + - - +
138D PRO* 3.6 24.9 - - + +
149D THR* 3.5 2.4 + - - +
162D GLY* 1.3 74.5 - - - +
164D LYS* 1.3 84.8 + - - +
165D MET* 3.4 20.3 - - - +
224D GLY* 4.3 0.9 - - - -
225D ILE 3.3 14.3 + - - -
226D VAL* 2.8 38.2 - - + +
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Residues in contact with LYS 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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134D CYS* 3.9 10.7 + - + +
135D VAL 3.1 20.3 + - - +
136D THR 3.2 15.9 - - - +
137D GLU* 3.0 21.1 + - + +
147D ILE* 4.3 2.2 - - - +
149D THR* 3.2 16.2 + - - +
163D GLN* 1.3 99.0 - - - +
165D MET* 1.3 62.4 + - - +
167D ILE* 4.1 16.4 - - + -
178D LEU* 3.3 34.3 - - + -
179D LEU 2.9 24.2 + - - -
224D GLY* 3.4 0.6 - - - -
225D ILE* 2.9 25.6 + - + +
227D PHE* 4.0 13.2 - - + -
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Residues in contact with MET 165 (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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354C ASN* 5.8 0.7 - - - +
136D THR* 2.9 23.8 + - - +
137D GLU 4.0 2.7 - - - -
138D PRO* 3.8 31.2 - - + -
163D GLN* 3.4 21.3 - - - +
164D LYS* 1.3 75.2 - - - +
166D TRP* 1.3 117.4 + - + +
167D ILE* 3.5 5.7 - - - +
212D GLU* 4.5 15.5 - - - +
223D ARG 4.6 0.4 - - - -
224D GLY* 3.9 20.2 - - - -
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Residues in contact with TRP 166 (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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353C GLY* 4.4 7.8 - - - -
354C ASN* 3.1 41.5 - - - +
357C ASN* 3.3 31.6 - - + -
360C TYR* 5.2 0.4 - + - -
136D THR* 4.3 7.9 - - + -
137D GLU 5.3 1.1 - - - -
138D PRO* 5.8 1.0 - - - +
165D MET* 1.3 110.0 - - + +
167D ILE* 1.3 60.6 + - - +
212D GLU* 3.8 27.4 - - + -
214D ASN* 3.7 20.4 - - - -
222D THR* 3.7 19.1 - - - -
223D ARG 3.6 4.1 + - - -
3399D FAD 2.8 75.7 + + + +
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Residues in contact with ILE 167 (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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132D ALA* 3.8 11.0 - - + -
133D TYR 3.6 26.9 - - - +
134D CYS* 3.9 22.7 - - - -
135D VAL 4.5 0.2 - - - +
136D THR 4.2 4.5 - - - +
164D LYS* 4.1 22.7 - - + -
165D MET 3.5 17.3 - - - +
166D TRP* 1.3 76.2 - - - +
168D THR* 1.3 65.0 + - - +
170D GLY* 3.0 31.3 + - - -
222D THR* 3.3 4.0 - - - -
223D ARG 2.9 34.4 + - - +
225D ILE* 4.3 6.3 - - + -
3399D FAD 4.1 8.5 - - + +
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Residues in contact with THR 168 (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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96D THR* 4.1 13.8 - - + +
100D ALA* 3.4 30.4 - - + +
131D CYS 4.5 0.2 - - - +
132D ALA* 3.3 16.5 - - - +
133D TYR 4.6 0.2 + - - -
167D ILE* 1.3 66.5 - - - +
169D ASN* 1.3 76.9 + - - +
170D GLY 2.9 4.9 + - - -
220D SER* 3.8 22.0 - - - +
221D ASP 3.2 4.9 - - - +
222D THR* 4.5 2.0 - - - +
3399D FAD 2.6 51.2 + - - +
3400D CS8 4.0 7.3 - - - +
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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