Contacts of the strand formed by residues 176 - 187 (chain D) in PDB entry 4A12
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 176 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141D ILE* 3.3 44.3 - - + +
142D GLU* 3.7 9.4 - - - +
169D LYS* 3.8 20.2 - - + -
170D SER 3.6 8.7 - - - +
171D TYR* 3.5 34.0 - - + +
175D THR* 1.3 70.6 - - - +
177D VAL* 1.3 58.5 + - - +
178D PHE 3.4 21.5 - - - +
179D LYS* 4.4 15.7 - - + -
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Residues in contact with VAL 177 (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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114D LEU* 6.2 0.2 - - - +
140D PHE* 3.6 4.5 - - - -
141D ILE* 2.9 25.3 + - - -
142D GLU* 3.3 34.0 + - + +
143D LYS 5.1 2.7 - - - +
144D VAL* 3.7 28.6 - - + +
150D VAL* 4.5 2.9 - - + -
170D SER* 3.0 26.3 + - - +
171D TYR* 4.1 1.6 - - - -
172D VAL* 3.9 28.3 - - + -
175D THR* 3.2 17.0 + - + +
176D LEU* 1.3 72.7 - - - +
178D PHE* 1.3 61.6 + - + +
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Residues in contact with PHE 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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114D LEU* 4.1 19.3 - - + -
115D PHE* 4.3 13.2 - - - -
118D ALA* 3.7 28.7 - - + -
138D ILE* 3.5 39.0 - - + -
139D GLN 3.3 15.7 - - - -
140D PHE* 3.8 32.8 - + + -
141D ILE* 3.7 4.4 - - - +
168D VAL* 4.5 5.2 - - + -
169D LYS* 3.6 0.2 - - - -
170D SER* 2.9 53.3 + - - -
176D LEU* 3.4 10.1 - - - +
177D VAL* 1.3 80.5 - - - +
179D LYS* 1.3 60.5 + - - +
180D GLY* 3.9 15.9 - - - -
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Residues in contact with LYS 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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137D SER 4.2 0.2 - - - +
138D ILE* 3.4 2.1 - - - +
139D GLN* 2.7 64.9 + - + +
141D ILE* 3.5 14.8 - - + +
167D GLU* 6.5 1.1 - - + -
168D VAL 3.4 9.9 - - - +
169D LYS* 4.3 22.0 - - + -
176D LEU* 4.4 14.6 - - + -
178D PHE* 1.3 78.6 - - - +
180D GLY* 1.3 61.4 + - - +
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Residues in contact with GLY 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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137D SER 3.4 8.5 - - - -
138D ILE* 3.9 12.6 - - - -
166D VAL 3.7 0.7 - - - +
167D GLU* 3.5 5.4 - - - +
168D VAL* 2.7 41.4 + - - +
178D PHE* 3.9 7.7 - - - -
179D LYS* 1.3 77.6 - - - +
181D ASN* 1.3 60.3 + - - -
182D PHE* 3.9 7.1 - - - -
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Residues in contact with ASN 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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136D SER* 3.0 20.3 + - - -
137D SER* 2.8 34.2 + - - +
157D VAL* 5.2 4.9 - - - +
165D TYR* 4.9 11.1 - - - +
166D VAL 3.5 4.3 + - - +
167D GLU* 3.6 29.1 + - - +
180D GLY* 1.3 73.4 - - - -
182D PHE* 1.3 70.0 + - - +
183D LYS* 5.9 0.3 - - - +
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Residues in contact with PHE 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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115D PHE* 3.5 25.1 - + - -
118D ALA* 3.7 22.7 - - + -
119D ASN* 3.7 23.1 - - - -
122D CYS* 3.7 17.9 - - - -
133D THR* 4.0 17.5 - - + -
135D GLU 3.7 1.6 - - - -
136D SER* 3.4 20.6 - - - -
138D ILE* 4.3 2.0 - - + -
164D TYR 3.5 1.2 - - - +
165D TYR* 3.4 7.0 - - - +
166D VAL* 2.7 41.2 + - + +
168D VAL* 3.8 30.1 - - + -
180D GLY* 3.9 17.0 - - - -
181D ASN* 1.3 81.5 + - - +
183D LYS* 1.3 58.4 + - - +
184D MSE 3.8 9.0 - - - -
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Residues in contact with LYS 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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133D THR* 3.8 1.0 - - - -
134D HIS* 2.8 37.5 + - + +
135D GLU* 2.9 58.2 + - + +
163D HIS* 3.5 36.9 - - + +
164D TYR 3.8 2.5 - - - -
165D TYR* 3.6 40.2 + - + -
181D ASN* 5.9 0.2 - - - +
182D PHE* 1.3 71.3 - - - +
184D MSE 1.3 56.8 + - - +
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Residues in contact with MSE 184 (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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119D ASN 4.7 0.7 - - - +
122D CYS* 3.8 19.7 - - + -
123D VAL* 3.8 21.5 - - + +
126D ILE* 3.7 26.7 - - + -
131D VAL* 3.7 26.0 - - + -
132D LEU 3.6 2.2 - - - +
133D THR* 3.4 44.6 - - - +
163D HIS* 3.3 3.8 - - - -
164D TYR* 2.7 48.1 + - + +
166D VAL* 4.1 11.0 - - + -
182D PHE* 4.0 13.5 - - + -
183D LYS* 1.3 71.4 - - - +
185D PHE* 1.3 61.9 + - - +
186D TYR* 3.7 0.3 + - - +
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Residues in contact with PHE 185 (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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143C LYS* 6.0 2.7 - - - -
130D THR* 5.1 5.4 - - - -
131D VAL* 3.4 6.8 - - - +
132D LEU* 2.7 59.0 + - + +
134D HIS* 3.4 42.0 - + + +
162D LYS* 3.2 50.9 - - + -
163D HIS* 3.7 8.5 - + + -
183D LYS 3.8 1.2 + - - -
184D MSE 1.3 73.0 - - - +
186D TYR* 1.3 68.8 + - - +
187D ASP* 3.9 28.7 - - + -
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Residues in contact with TYR 186 (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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126D ILE* 4.5 4.3 - - + -
128D GLN* 3.7 31.6 - - + -
130D THR 3.4 7.0 - - - +
131D VAL* 5.0 0.4 - - + -
159D GLN* 3.2 16.6 + - + -
160D THR 2.7 30.0 + - - -
161D ALA* 3.1 23.7 + - - +
162D LYS* 3.1 27.6 + - - +
163D HIS 3.4 18.4 - - - -
164D TYR* 3.4 31.2 - + + -
184D MSE 6.2 0.2 - - + -
185D PHE* 1.3 84.5 - - - +
187D ASP* 1.3 63.6 + - - +
188D LYS* 4.2 28.0 - - + -
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Residues in contact with ASP 187 (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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128D GLN* 4.5 1.1 - - - -
129D PRO* 3.3 16.8 - - - +
130D THR* 3.0 35.7 + - - +
185D PHE* 3.9 20.3 - - + -
186D TYR* 1.3 77.0 - - - +
188D LYS* 1.4 64.6 + - - +
189D ARG* 3.2 34.6 + - - +
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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