Contacts of the strand formed by residues 176 - 187 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B ILE* 3.3 43.4 - - + +
142B GLU* 3.6 9.5 - - - +
169B LYS* 3.8 23.6 - - + -
170B SER 3.6 9.2 - - - +
171B TYR* 3.5 29.3 - - + +
175B THR* 1.3 70.8 - - - +
177B VAL* 1.3 59.5 + - - +
178B PHE 3.4 21.8 - - - +
179B LYS* 4.0 25.6 - - + +
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Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LEU* 4.6 0.2 - - + -
140B PHE* 3.6 4.5 - - - +
141B ILE* 2.9 25.0 + - - -
142B GLU* 3.3 33.5 + - + +
143B LYS 5.1 2.7 - - - +
144B VAL* 3.7 28.5 - - + +
150B VAL* 4.5 3.1 - - + -
170B SER* 3.0 25.4 + - - +
171B TYR* 4.1 1.1 - - - -
172B VAL* 3.9 28.5 - - + -
175B THR* 3.4 17.5 - - + +
176B LEU* 1.3 74.7 - - - +
178B PHE* 1.3 63.4 + - + +
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Residues in contact with PHE 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LEU* 4.1 17.7 - - + -
115B PHE* 4.3 12.8 - - - -
118B ALA* 3.7 28.5 - - + -
138B ILE* 3.5 38.8 - - + -
139B GLN 3.5 10.8 - - - -
140B PHE* 3.8 37.5 - + + -
141B ILE* 3.7 3.4 - - - -
168B VAL* 4.5 4.7 - - + -
169B LYS* 3.6 0.3 - - - -
170B SER* 2.9 54.3 + - - -
176B LEU* 3.4 9.6 - - - +
177B VAL* 1.3 79.8 - - - +
179B LYS* 1.3 60.2 + - - +
180B GLY* 3.9 16.4 - - - -
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Residues in contact with LYS 179 (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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137B SER 4.1 0.6 - - - +
138B ILE* 3.4 2.6 - - - +
139B GLN* 2.8 59.4 + - + +
141B ILE* 3.6 11.9 - - + -
168B VAL 3.4 8.1 - - - +
169B LYS* 3.8 35.9 - - + +
176B LEU* 4.0 20.9 - - + +
178B PHE* 1.3 75.3 - - - +
180B GLY* 1.3 59.0 + - - +
181B ASN* 5.1 8.7 + - - +
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Residues in contact with GLY 180 (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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137B SER 3.4 7.4 - - - -
138B ILE* 3.9 12.8 - - - -
167B GLU* 3.5 2.5 - - - +
168B VAL* 2.6 44.8 + - - +
178B PHE* 3.9 8.8 - - - -
179B LYS* 1.3 76.6 - - - +
181B ASN* 1.3 64.3 + - - -
182B PHE* 3.7 7.9 - - - -
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Residues in contact with ASN 181 (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 SER* 3.2 8.5 + - - -
137B SER* 2.8 50.2 + - - +
166B VAL 3.4 4.3 - - - +
167B GLU* 3.3 29.4 - - - +
179B LYS* 5.1 7.3 - - - +
180B GLY* 1.3 79.6 - - - +
182B PHE* 1.3 60.8 + - - +
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Residues in contact with PHE 182 (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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115B PHE* 3.5 25.4 - + - -
118B ALA* 3.7 22.4 - - + -
119B ASN* 3.7 22.7 - - - -
122B CYS* 3.7 18.2 - - - -
133B THR* 4.0 17.7 - - + -
135B GLU 3.7 1.1 - - - -
136B SER* 3.4 21.5 - - - -
138B ILE* 4.3 1.8 - - + -
164B TYR 3.5 1.0 - - - +
165B TYR* 3.4 8.2 - - - +
166B VAL* 2.7 42.7 + - + +
168B VAL* 3.8 25.6 - - + -
180B GLY* 3.7 21.3 - - - -
181B ASN* 1.3 77.5 - - - +
183B LYS* 1.3 59.2 + - - +
184B MSE 3.8 9.2 - - - -
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Residues in contact with LYS 183 (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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133B THR* 3.8 0.9 - - - -
134B HIS* 2.8 37.8 + - + +
135B GLU* 2.9 58.9 + - + +
163B HIS* 3.6 35.5 - - + +
164B TYR 3.8 2.7 - - - -
165B TYR* 3.6 40.6 + - + -
182B PHE* 1.3 70.1 - - - +
184B MSE 1.3 56.2 + - - +
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Residues in contact with MSE 184 (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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119B ASN 4.7 0.2 - - - +
122B CYS* 3.8 20.9 - - + -
123B VAL* 3.8 20.6 - - + +
126B ILE* 3.7 27.6 - - + -
131B VAL* 3.7 26.5 - - + -
132B LEU* 3.6 2.2 - - - +
133B THR* 3.4 45.3 - - - +
163B HIS* 3.3 3.4 - - - -
164B TYR* 2.7 48.2 + - + +
166B VAL* 4.1 10.5 - - + -
182B PHE* 4.0 12.6 - - + -
183B LYS* 1.3 70.7 - - - +
185B PHE* 1.3 62.9 + - - +
186B TYR* 3.7 0.7 + - + +
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Residues in contact with PHE 185 (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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143A LYS* 6.1 1.8 - - - -
130B THR* 5.1 5.6 - - - -
131B VAL* 3.4 7.1 - - - +
132B LEU* 2.7 58.7 + - + +
134B HIS* 3.4 42.0 - + + +
162B LYS* 3.2 40.2 - - + -
163B HIS* 3.7 9.0 - + + -
183B LYS 3.8 1.0 + - - -
184B MSE 1.3 73.3 - - - +
186B TYR* 1.3 66.9 + - - +
187B ASP* 3.9 30.5 - - + -
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Residues in contact with TYR 186 (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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126B ILE* 4.5 4.7 - - + -
128B GLN* 3.7 32.8 - - + -
130B THR 3.4 6.5 - - - +
131B VAL* 5.0 0.4 - - + -
159B GLN* 3.2 17.7 + - + -
160B THR 2.7 29.4 + - - -
161B ALA* 3.1 24.0 + - - +
162B LYS* 3.1 24.8 + - - +
163B HIS 3.4 18.4 - - - -
164B TYR* 3.4 30.5 - + + -
184B MSE 4.7 0.2 - - - +
185B PHE* 1.3 83.2 - - - +
187B ASP* 1.3 63.6 + - - +
188B LYS* 4.2 28.4 - - + -
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Residues in contact with ASP 187 (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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128B GLN* 4.5 1.1 - - - +
129B PRO* 3.4 15.8 - - - +
130B THR* 3.0 33.8 + - - +
185B PHE* 3.9 21.3 - - + -
186B TYR* 1.3 75.6 - - - +
188B LYS* 1.3 65.4 + - - +
189B ARG* 3.0 49.6 + - - +
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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