Contacts of the strand formed by residues 174 - 183 (chain D) in PDB entry 3UAJ
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 TYR 174 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104D LYS* 5.2 4.5 + - - -
106D GLU* 3.1 40.4 + - - +
139D ASN* 3.4 2.3 - - - -
140D PHE* 2.8 57.4 + - + +
141D TYR* 3.7 24.9 - + - -
143D ARG* 3.6 53.8 - - + -
164D VAL* 4.2 8.7 - - + -
165D THR* 3.6 18.8 - - - -
166D GLU 5.1 0.2 - - - -
167D GLN* 3.5 35.4 - - + +
173D THR* 1.3 73.1 - - - +
175D SER* 1.3 66.4 + - - +
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Residues in contact with SER 175 (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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174C HIS* 3.8 18.4 + - - -
176C PHE* 3.3 21.7 - - - -
137D LEU 3.3 9.0 - - - -
138D ASN* 3.6 12.6 + - - -
139D ASN* 3.4 15.4 + - - -
140D PHE* 3.7 2.5 - - - -
164D VAL* 3.4 6.7 - - - +
165D THR* 3.1 40.3 + - - -
174D TYR* 1.3 78.0 + - - +
176D LEU* 1.3 58.4 + - - +
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Residues in contact with LEU 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C PHE* 3.5 4.8 - - - -
135D CYS 3.5 2.5 - - - +
136D LEU* 3.6 1.7 - - - -
137D LEU* 2.8 50.6 + - + +
140D PHE* 3.6 16.8 - - + -
143D ARG 5.2 2.9 - - - +
145D ALA* 4.5 17.5 - - + +
147D VAL* 3.8 18.8 - - + -
162D GLU* 3.5 42.4 - - + +
163D SER 3.5 8.5 - - - +
164D VAL* 3.8 20.9 - - + -
175D SER* 1.3 72.1 - - - +
177D SER* 1.3 71.2 + - - +
178D SER 4.1 8.1 - - - +
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Residues in contact with SER 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C PHE* 3.2 30.8 - - - +
189C SER* 3.1 26.9 + - - -
191C VAL* 5.6 1.6 - - - -
134D ALA* 6.1 4.0 - - - -
135D CYS 3.4 8.3 - - - -
136D LEU* 5.2 2.9 - - - -
161D GLN 3.5 5.4 - - - +
163D SER* 3.1 28.1 + - - -
176D LEU* 1.3 77.1 - - - +
178D SER* 1.3 61.6 + - - +
179D THR* 4.0 5.6 + - - -
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Residues in contact with SER 178 (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 ALA* 3.5 1.9 - - - -
135D CYS 2.9 34.5 + - - -
147D VAL* 3.8 21.4 - - - +
149D TRP* 2.9 35.8 + - - -
160D SER* 4.5 4.7 - - - -
161D GLN 3.4 8.1 + - - -
162D GLU* 3.9 21.0 + - - +
176D LEU* 4.1 4.1 - - - +
177D SER* 1.3 72.3 - - - +
179D THR* 1.3 60.1 + - - +
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Residues in contact with THR 179 (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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151C LEU* 4.3 18.1 - - + +
153C LYS* 6.2 0.4 - - + -
179C VAL* 6.0 2.8 - - - +
187C SER* 5.0 11.3 + - - +
189C SER* 5.2 6.1 + - - -
132D SER* 3.9 27.1 - - - -
133D VAL 3.4 8.3 - - - +
134D ALA* 4.6 6.5 - - - +
149D TRP* 4.5 1.1 - - - -
159D ASN 3.1 13.7 - - - +
160D SER* 3.5 2.0 - - - -
161D GLN* 3.1 30.9 + - - +
177D SER* 4.3 6.6 + - - -
178D SER* 1.3 75.4 + - - +
180D LEU* 1.3 59.5 + - - +
181D THR* 3.8 12.7 + - + +
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Residues in contact with LEU 180 (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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131D ALA 3.5 2.9 - - - +
132D SER* 3.4 2.6 - - - -
133D VAL* 3.0 39.0 + - + +
149D TRP* 3.7 49.1 - - + +
150D LYS 5.7 0.2 - - - -
151D VAL* 5.5 2.5 - - - +
156D GLN* 4.1 18.4 - - + +
158D GLY 4.1 11.4 - - - +
159D ASN* 3.5 8.7 - - + +
160D SER* 3.6 20.9 - - - +
179D THR* 1.3 69.4 - - - +
181D THR* 1.3 60.1 + - - +
182D LEU* 3.8 27.7 + - + +
193D TYR* 4.6 12.8 - - + -
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Residues in contact with THR 181 (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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153C LYS* 3.9 17.3 - - - -
181C GLN* 4.2 9.5 + - - +
130D THR* 6.5 0.9 - - - -
131D ALA 3.6 3.1 - - - -
132D SER* 3.4 24.7 - - - +
159D ASN* 3.1 43.3 + - - +
161D GLN* 5.4 6.6 + - - +
179D THR* 4.2 12.6 - - + +
180D LEU* 1.3 71.2 - - - +
182D LEU* 1.3 60.8 + - - +
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Residues in contact with LEU 182 (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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130D THR* 3.7 4.2 - - - -
131D ALA* 2.7 41.8 + - + +
133D VAL* 5.6 3.1 - - + -
151D VAL* 4.3 11.2 - - + -
156D GLN* 4.3 12.3 - - - +
159D ASN* 3.7 20.6 - - + +
180D LEU* 3.8 30.7 + - + +
181D THR* 1.3 75.4 - - - +
183D SER* 1.3 62.7 + - - +
186D ASP* 4.2 21.3 - - + +
187D TYR* 4.7 9.0 - - + +
193D TYR* 3.9 26.0 - - + +
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Residues in contact with SER 183 (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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129D GLY 3.7 9.0 - - - -
130D THR* 4.5 4.7 - - - +
131D ALA 4.6 0.9 - - - -
182D LEU* 1.3 76.5 - - - +
184D LYS* 1.4 58.9 + - - +
185D ALA* 4.0 6.0 + - - +
186D ASP* 2.7 35.6 + - - +
187D TYR* 2.9 28.9 + - - +
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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