Contacts of the strand formed by residues 157 - 168 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A LYS* 3.3 7.8 - - - +
154A LYS* 2.8 42.3 + - + +
155A GLY 3.2 2.0 + - - -
156A ASP* 1.3 82.4 - - - +
158A TYR* 1.3 63.7 + - - +
159A ILE* 4.9 1.2 - - + +
231A ARG* 3.6 44.2 + - - +
232A VAL 3.3 23.7 - - - +
233A PRO* 4.0 7.8 - - + +
234A LYS* 3.6 2.8 - - - +
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Residues in contact with TYR 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ALA* 4.5 3.1 - - + -
152A GLU* 2.9 22.2 - - - +
153A LYS* 2.7 39.7 + - + -
157A GLU* 1.3 78.2 - - - +
159A ILE* 1.3 63.6 + - - +
160A ILE* 5.0 0.7 - - + -
182A SER* 5.4 2.9 - - - -
197A PHE* 3.5 23.3 - + + -
230A VAL 3.3 2.6 - - - +
231A ARG* 3.5 1.6 - - - -
232A VAL* 2.7 52.7 + - + +
233A PRO 4.8 0.2 - - - -
234A LYS* 4.0 18.8 - - + -
237A VAL* 3.4 30.9 - - + +
241A GLU* 2.6 45.2 + - + +
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Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LYS 3.9 1.2 - - - +
151A ALA* 3.4 1.9 - - - -
152A GLU* 2.4 60.7 + - + +
154A LYS* 4.1 21.3 - - + -
157A GLU* 4.9 3.1 - - - +
158A TYR* 1.3 74.1 - - - +
160A ILE* 1.3 60.5 + - - +
161A ASN* 3.8 22.6 + - - +
229A ASP* 4.1 18.4 - - + +
230A VAL 3.4 0.9 - - - -
231A ARG* 3.0 57.2 - - + +
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Residues in contact with ILE 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A THR* 3.9 9.4 - - - +
150A LYS 3.3 13.2 - - - +
151A ALA* 4.1 11.0 - - + -
158A TYR 4.8 0.4 - - - -
159A ILE* 1.3 75.4 - - - +
161A ASN* 1.3 70.2 + - - +
178A LEU* 3.4 36.3 - - + -
180A ALA* 4.8 1.1 - - + -
197A PHE* 3.9 19.7 - - + -
199A VAL* 4.5 7.0 - - + -
227A PHE* 3.7 17.7 - - + +
229A ASP 3.5 0.9 + - - -
230A VAL* 2.8 43.7 + - + +
232A VAL* 3.9 28.9 - - + -
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Residues in contact with ASN 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LYS 4.6 0.5 - - - +
149A THR* 3.3 5.1 - - - -
150A LYS* 2.9 36.7 + - + +
152A GLU* 5.0 6.1 + - - -
159A ILE* 3.8 17.0 + - - +
160A ILE* 1.3 74.2 - - - +
162A GLY* 1.3 58.7 + - - +
227A PHE 3.2 7.1 - - - +
228A GLU* 3.3 3.8 - - - +
229A ASP* 2.4 49.6 + - - +
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Residues in contact with GLY 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A THR* 3.6 17.0 - - - -
161A ASN* 1.3 75.1 - - - +
163A GLN* 1.3 57.6 + - - +
226A VAL* 3.7 3.2 - - - +
227A PHE* 2.7 41.7 + - - +
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Residues in contact with GLN 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLU* 3.3 28.1 - - - +
138A PRO* 3.5 30.6 - - + +
149A THR* 4.3 2.2 - - - +
162A GLY* 1.3 76.6 - - - +
164A LYS* 1.3 65.6 + - - +
165A MET* 6.2 0.2 - - - +
225A ILE 3.3 10.3 - - - +
226A VAL* 3.8 23.4 - - + +
227A PHE* 4.9 0.2 - - - -
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Residues in contact with LYS 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A CYS* 3.5 20.6 - - + +
135A VAL 2.7 31.9 + - - +
136A THR 3.3 7.9 - - - +
137A GLU* 3.3 11.9 + - + +
138A PRO* 4.4 1.1 - - - -
147A ILE* 4.0 4.0 - - - +
149A THR* 2.9 34.4 - - - +
163A GLN* 1.3 77.6 + - - +
165A MET* 1.3 62.3 + - - +
167A ILE* 4.0 18.4 - - + -
178A LEU* 3.7 11.2 - - + -
179A LEU 3.0 17.6 + - - -
224A GLY* 3.4 1.9 - - - -
225A ILE* 2.7 36.8 + - + +
227A PHE* 4.0 20.4 - - + -
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Residues in contact with MET 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A THR* 2.8 24.4 + - - +
137A GLU* 3.9 3.5 - - - +
138A PRO* 3.8 31.0 - - + -
164A LYS* 1.3 75.3 - - - +
166A TRP* 1.3 120.6 + - + +
167A ILE* 3.5 6.1 - - - +
212A GLU* 3.4 43.5 - - + +
224A GLY* 3.8 18.2 - - - +
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Residues in contact with TRP 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A THR* 4.5 7.2 - - + -
137A GLU 5.1 1.8 - - - -
138A PRO* 5.9 1.0 - - - +
165A MET* 1.3 125.6 - - + +
167A ILE* 1.3 60.4 + - - +
212A GLU* 3.9 12.6 - - + -
214A ASN* 3.9 21.3 - - - -
222A THR* 3.8 19.5 - - - -
223A ARG 3.9 3.0 + - - -
399A FAD 2.8 77.5 + + + +
353B GLY* 4.0 20.7 - - - -
354B ASN* 3.6 26.2 + - - +
357B ASN* 3.5 30.7 - - + -
360B TYR* 5.6 0.2 - + - -
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Residues in contact with ILE 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ALA* 3.9 5.2 - - + -
133A TYR 3.7 20.4 - - - +
134A CYS* 3.6 34.5 - - - -
135A VAL 4.3 0.2 - - - +
136A THR 4.2 4.3 - - - +
164A LYS* 4.0 24.2 - - + -
165A MET 3.6 16.2 - - - +
166A TRP* 1.3 75.3 - - - +
168A THR* 1.3 70.9 + - - +
170A GLY* 3.0 23.7 + - - -
222A THR* 3.3 3.3 - - - -
223A ARG 3.1 33.1 + - - +
225A ILE* 4.0 11.7 - - + -
399A FAD 4.0 8.1 - - + +
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Residues in contact with THR 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A THR* 4.0 13.4 - - + +
100A ALA* 3.7 26.9 - - + +
132A ALA* 3.3 15.9 - - - +
167A ILE* 1.3 68.3 - - - +
169A ASN* 1.3 77.8 + - - +
170A GLY 2.8 5.8 + - - -
220A SER* 3.7 22.0 - - - +
221A ASP 3.2 5.8 - - - -
222A THR* 4.3 1.8 - - - +
399A FAD 2.5 51.1 + - + +
400A CS8 4.2 7.2 - - - +
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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