Contacts of the strand formed by residues 178 - 187 (chain A) in PDB entry 5MYO
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 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A LYS* 6.0 0.8 - - - -
110A GLU* 4.2 20.3 + - - +
111A ILE 4.8 0.7 + - - -
143A ASN* 3.0 4.4 + - - -
144A PHE* 2.8 58.6 + - + +
145A TYR* 3.9 18.1 - + - -
147A LYS* 3.7 53.5 - - + +
168A TRP* 5.6 1.6 - - + -
169A THR* 4.2 12.8 - - - +
170A ASP* 5.0 0.4 - - - -
171A GLN* 3.4 61.4 + - + +
177A THR* 1.3 75.4 - - - +
179A SER* 1.3 65.3 + - - +
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Residues in contact with SER 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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141A LEU 3.4 5.6 - - - -
142A ASN* 3.4 17.0 - - - -
143A ASN* 2.9 21.0 + - - -
144A PHE* 3.6 2.5 - - - -
168A TRP* 3.5 8.1 - - - -
169A THR* 3.1 37.9 + - - +
178A TYR* 1.3 72.7 + - - +
180A MET* 1.3 63.1 + - - +
170B HIS* 3.2 28.3 + - - -
172B PHE* 3.6 11.4 - - - -
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Residues in contact with MET 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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140A PHE* 3.6 2.4 - - - -
141A LEU* 2.8 47.1 + - + +
144A PHE* 3.9 10.3 - - + -
149A ILE* 3.7 22.9 - - - +
150A ASN* 4.6 3.6 - - - +
151A VAL* 3.6 26.2 - - + +
166A ASN* 3.5 28.3 - - + +
167A SER 3.4 8.3 - - - +
168A TRP* 3.5 48.2 - - + +
179A SER* 1.3 75.9 - - - +
181A SER* 1.3 64.3 + - - +
182A SER* 4.7 2.2 - - - -
172B PHE* 3.3 8.1 - - - -
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Residues in contact with SER 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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138A VAL* 4.3 3.5 - - - +
139A CYS 3.5 5.0 + - - -
140A PHE* 3.6 12.8 - - - -
166A ASN* 3.2 5.4 - - - +
167A SER 2.8 32.7 + - - -
180A MET* 1.3 77.6 - - - +
182A SER* 1.3 61.7 + - - +
302A GOL 2.9 16.1 + - - -
172B PHE* 3.4 21.7 - - - -
184B SER* 2.7 29.2 + - - -
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Residues in contact with SER 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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138A VAL* 3.5 2.6 - - - +
139A CYS* 2.8 40.5 + - - -
141A LEU* 4.6 4.3 - - - -
151A VAL* 3.4 19.0 - - - +
153A TRP* 2.9 33.5 + - - -
164A VAL* 3.4 5.4 - - - +
165A LEU 3.4 0.4 - - - -
166A ASN* 2.7 24.5 + - - -
180A MET* 4.7 0.4 - - - -
181A SER* 1.3 74.4 + - - +
183A THR* 1.3 59.0 + - - +
302A GOL 3.4 4.0 - - - -
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Residues in contact with THR 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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136A SER* 3.8 28.9 - - - +
137A VAL 3.4 6.5 - - - +
138A VAL* 4.0 15.8 - - + +
153A TRP* 4.6 0.2 - - - -
163A GLY 3.4 3.8 - - - +
164A VAL* 3.4 2.3 - - - -
165A LEU* 2.9 33.5 + - - +
182A SER* 1.3 75.3 + - - +
184A LEU* 1.3 61.4 + - - +
185A THR* 3.9 13.1 + - - +
302A GOL 2.6 42.2 + - - +
147B LEU* 4.4 7.6 - - + +
149B LYS* 6.3 0.2 - - - +
182B THR* 5.8 1.1 - - + -
184B SER* 5.3 0.2 + - - -
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Residues in contact with LEU 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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135A ALA 3.7 0.7 - - - +
136A SER* 3.5 1.2 - - - -
137A VAL* 2.8 44.6 + - + +
153A TRP* 3.7 43.6 - - + +
155A ILE* 4.0 29.4 - - + -
160A ARG* 4.9 9.0 - - + -
162A ASN 3.6 23.3 - - - +
163A GLY* 3.4 4.0 - - - +
164A VAL* 3.6 14.1 - - + +
183A THR* 1.3 72.5 - - - +
185A THR* 1.3 60.6 + - - +
186A LEU* 3.7 24.6 + - + +
197A TYR* 4.9 2.2 - - + -
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Residues in contact with THR 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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129A GLN* 5.7 0.4 - - - +
135A ALA 3.9 3.4 - - - +
136A SER* 3.9 19.0 + - - +
162A ASN 5.3 0.2 - - - +
163A GLY* 2.9 28.8 + - - +
165A LEU* 5.6 4.3 - - - +
183A THR* 4.0 11.1 + - - +
184A LEU* 1.3 70.8 - - - +
186A LEU* 1.3 76.2 + - - +
149B LYS* 4.4 19.7 + - - +
177B GLN* 4.7 12.7 + - - +
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Residues in contact with LEU 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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134A GLY* 4.4 1.4 - - - -
135A ALA* 2.8 36.4 + - + +
137A VAL* 4.4 4.9 - - + -
155A ILE* 4.0 18.8 - - + -
160A ARG* 6.2 0.2 - - - +
162A ASN 5.7 0.9 - - - +
184A LEU* 3.9 27.4 - - + +
185A THR* 1.3 88.0 - - - +
187A THR* 1.3 70.0 + - - +
190A GLU* 4.1 18.2 - - + +
191A TYR* 4.2 13.9 - - + -
197A TYR* 3.6 35.4 - - + +
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Residues in contact with THR 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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133A GLY 4.6 3.8 - - - -
134A GLY* 5.2 0.7 - - - -
135A ALA* 4.0 0.9 - - - -
186A LEU* 1.3 75.1 - - - +
188A LYS* 1.3 64.2 + - - +
189A ASP* 3.5 10.4 + - - +
190A GLU* 2.9 27.5 + - + +
191A TYR* 2.9 22.5 + - - +
193A ARG* 4.9 1.2 + - - -
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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