Contacts of the strand formed by residues 176 - 187 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A ILE* 3.3 44.4 - - + +
142A GLU* 3.7 8.8 - - - +
169A LYS* 3.8 20.4 - - + -
170A SER 3.6 8.7 - - - +
171A TYR* 3.5 33.6 - - + +
175A THR* 1.3 69.9 - - - +
177A VAL* 1.3 60.0 + - - +
178A PHE 3.4 22.0 - - - +
179A LYS* 4.4 15.3 - - + -
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Residues in contact with VAL 177 (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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114A LEU* 4.6 0.4 - - + +
140A PHE* 3.5 5.2 - - - +
141A ILE* 2.9 25.3 + - - -
142A GLU* 3.3 34.2 + - + +
143A LYS 5.1 2.9 - - - +
144A VAL* 3.7 29.8 - - + +
150A VAL* 4.5 3.1 - - + -
170A SER* 3.0 26.1 + - - +
171A TYR* 4.1 1.1 - - - -
172A VAL* 3.9 28.0 - - + -
175A THR* 3.5 16.4 - - + +
176A LEU* 1.3 72.1 - - - +
178A PHE* 1.3 61.6 + - + +
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Residues in contact with PHE 178 (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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114A LEU* 4.1 18.8 - - + -
115A PHE* 4.3 12.8 - - - -
118A ALA* 3.7 28.7 - - + -
138A ILE* 3.5 38.8 - - + -
139A GLN 3.3 15.3 - - - -
140A PHE* 3.8 32.8 - + + -
141A ILE* 3.7 3.6 - - - -
168A VAL* 4.5 4.3 - - + -
170A SER* 2.9 53.1 + - - -
176A LEU* 3.4 9.9 - - - +
177A VAL* 1.3 80.1 - - - +
179A LYS* 1.3 70.1 + - - +
180A GLY* 3.9 7.0 - - - -
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Residues in contact with LYS 179 (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 SER 4.7 0.2 - - - -
138A ILE* 3.4 2.9 - - - +
139A GLN* 2.7 66.8 + - + +
141A ILE* 3.6 14.4 - - + -
167A GLU* 6.5 0.9 - - + -
168A VAL 3.4 9.4 - - - +
169A LYS* 4.3 23.8 - - + +
176A LEU* 4.4 15.3 - - + -
178A PHE* 1.3 77.9 - - - +
180A GLY* 1.3 59.1 + - - +
181A ASN* 4.7 14.8 - - - +
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Residues in contact with GLY 180 (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 SER 3.4 8.1 - - - -
138A ILE* 3.9 12.6 - - - -
167A GLU* 3.4 4.2 - - - +
168A VAL 2.7 39.0 + - - +
178A PHE* 3.9 7.4 - - - -
179A LYS* 1.3 77.2 - - - +
181A ASN* 1.3 66.2 + - - -
182A PHE* 4.0 7.8 - - - -
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Residues in contact with ASN 181 (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 SER* 3.2 8.3 + - - -
137A SER* 2.8 49.1 + - - +
139A GLN* 5.3 2.6 + - - -
166A VAL 3.4 3.8 - - - +
167A GLU* 3.3 28.5 - - - +
179A LYS* 4.7 17.6 - - - +
180A GLY* 1.3 78.8 - - - +
182A PHE* 1.3 60.3 + - - +
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Residues in contact with PHE 182 (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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115A PHE* 3.5 24.5 - + - -
118A ALA* 3.7 23.8 - - + -
119A ASN* 3.7 22.2 - - - -
122A CYS* 3.7 13.9 - - - -
133A THR* 4.0 17.9 - - + -
135A GLU 3.7 0.9 - - - -
136A SER* 3.4 21.1 - - - -
138A ILE* 4.3 1.6 - - + -
164A TYR 3.5 1.4 - - - +
165A TYR* 3.4 8.9 - - - +
166A VAL* 2.7 42.2 + - + +
168A VAL* 3.8 29.4 - - + -
180A GLY* 4.0 17.3 - - - -
181A ASN* 1.3 77.3 - - - +
183A LYS* 1.3 59.2 + - - +
184A MSE 3.8 14.4 - - - -
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Residues in contact with LYS 183 (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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133A THR* 3.8 0.9 - - - -
134A HIS* 2.8 37.0 + - + +
135A GLU* 2.9 59.4 + - + +
163A HIS* 3.6 36.5 - - + +
164A TYR 3.8 3.4 - - - -
165A TYR* 3.6 38.8 + - + -
182A PHE* 1.3 69.7 - - - +
184A MSE 1.3 56.4 + - - +
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Residues in contact with MSE 184 (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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119A ASN 4.6 0.4 - - - +
122A CYS* 3.7 25.8 - - + -
123A VAL* 3.9 21.8 - - + +
126A ILE* 3.7 26.9 - - + -
131A VAL* 3.9 20.2 - - + -
132A LEU 3.5 2.2 - - - +
133A THR* 3.4 44.6 - - - +
163A HIS* 3.3 4.4 - - - -
164A TYR* 2.7 47.4 + - + +
166A VAL* 4.0 11.2 - - + -
182A PHE* 3.9 14.1 - - + -
183A LYS* 1.3 71.5 - - - +
185A PHE* 1.3 63.0 + - - +
186A TYR* 6.2 0.2 - - + -
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Residues in contact with PHE 185 (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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130A THR* 5.1 5.6 - - - -
131A VAL* 3.4 7.3 - - - +
132A LEU* 2.7 59.6 + - + +
134A HIS* 3.4 42.0 - + + +
162A LYS* 3.2 47.1 - - + -
163A HIS* 3.7 9.4 - + + -
183A LYS 3.8 1.0 + - - -
184A MSE 1.3 71.5 - - - +
186A TYR* 1.3 68.7 + - - +
187A ASP* 3.9 29.6 - - + -
143B LYS* 5.8 4.9 - - + -
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Residues in contact with TYR 186 (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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126A ILE* 4.5 4.5 - - + -
128A GLN* 3.7 35.7 - - + -
130A THR 3.4 6.5 - - - +
131A VAL* 5.0 0.2 - - + -
159A GLN* 3.2 17.8 + - + -
160A THR 2.7 30.5 + - - -
161A ALA* 3.1 23.3 + - - +
162A LYS* 3.1 26.3 + - - +
163A HIS 3.4 17.7 - - - -
164A TYR* 3.4 30.5 - + + -
184A MSE 6.2 0.2 - - + -
185A PHE* 1.3 85.2 - - - +
187A ASP* 1.3 63.4 + - - +
188A LYS* 4.2 25.4 - - + -
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Residues in contact with ASP 187 (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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128A GLN* 4.5 3.3 - - - +
129A PRO* 3.3 16.8 - - - +
130A THR* 3.0 33.4 + - - +
185A PHE* 3.9 20.3 - - + -
186A TYR* 1.3 77.4 - - - +
188A LYS* 1.4 68.4 + - - +
189A ARG* 3.4 15.4 + - - +
190A GLY 3.3 17.1 + - - -
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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