Contacts of the strand formed by residues 179 - 185 (chain A) in PDB entry 5J3S
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 PHE 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A GLU 3.4 4.5 + - - -
153A VAL* 2.9 57.2 + - + +
154A ILE 4.6 1.8 - - - -
155A PRO* 4.6 16.2 - - + -
158A TYR* 4.8 7.6 - + + -
172A THR* 3.8 28.7 - - + -
173A GLY 4.4 1.8 - - - -
174A HIS* 3.8 24.7 - - + +
175A GLU* 3.6 45.1 - - - -
176A GLU 4.1 2.9 - - - -
177A GLY 4.2 5.8 - - - -
178A TYR* 1.3 82.7 - - - +
180A THR* 1.3 82.9 - - - +
181A ALA* 5.4 0.9 - - + -
207A ASN* 5.7 2.2 - - - +
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Residues in contact with THR 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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150A LEU 3.3 8.3 - - - -
151A GLN* 3.7 28.0 - - + +
172A THR* 3.9 0.3 - - - -
173A GLY* 3.3 14.0 + - - -
179A PHE* 1.3 92.7 - - - +
181A ALA* 1.3 65.4 + - - +
207A ASN* 4.2 15.8 + - - +
209A LEU* 3.9 21.1 - - - +
224A THR* 4.0 9.4 + - - -
225A SER* 3.8 24.0 - - - +
226A HIS* 3.9 11.2 - - + +
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Residues in contact with ALA 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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148A ILE 3.8 0.3 - - - +
149A PHE* 3.6 2.9 - - - -
150A LEU* 2.8 46.1 + - + +
153A VAL* 4.3 17.9 - - + -
158A TYR* 5.6 1.6 - - + -
170A ILE* 4.4 15.7 - - + -
171A ILE 3.4 11.2 - - - +
172A THR* 4.9 5.6 - - + -
179A PHE* 5.2 0.7 - - + -
180A THR* 1.3 79.7 - - - +
182A ILE* 1.3 64.5 + - - +
183A MET* 4.3 0.7 - - + -
209A LEU* 4.0 1.3 - - - +
224A THR* 4.4 1.2 - - - +
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Residues in contact with ILE 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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147A VAL* 4.2 1.8 - - + -
148A ILE 3.3 8.5 - - - +
149A PHE* 3.7 28.9 - - + -
169A GLU 3.5 2.9 - - - +
170A ILE* 3.2 4.2 - - - -
171A ILE* 2.9 34.2 + - + +
181A ALA* 1.3 78.5 - - - +
183A MET* 1.3 65.0 + - - +
184A LEU* 3.6 27.1 - - + -
209A LEU* 3.6 35.0 - - + +
211A VAL* 3.9 23.8 - - + -
222A LEU* 4.0 7.9 - - + +
224A THR* 3.6 15.7 - - + -
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Residues in contact with MET 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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140A LEU* 4.7 1.6 - - + -
147A VAL* 3.4 6.1 - - - -
148A ILE* 2.9 54.6 + - + -
150A LEU* 3.7 30.3 - - + -
161A LEU* 4.2 15.5 - - + -
165A SER* 3.6 32.8 - - - +
168A TYR* 3.7 25.6 - - + -
169A GLU 4.1 3.1 - - - -
170A ILE* 3.8 35.2 - - + +
181A ALA 5.4 0.2 - - - -
182A ILE* 1.3 75.9 - - - +
184A LEU* 1.3 63.2 + - - +
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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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146A ASP 3.9 1.6 - - - -
147A VAL* 4.0 4.3 - - + -
168A TYR* 3.2 5.4 - - - -
169A GLU* 2.9 36.0 + - + +
171A ILE* 3.9 10.8 - - + -
182A ILE* 3.6 19.7 - - + -
183A MET* 1.3 74.8 - - - +
185A LYS* 1.3 60.0 + - - +
186A LYS* 2.9 11.4 + - - -
189A VAL* 4.2 18.2 - - + +
191A LEU* 3.8 23.3 - - + -
211A VAL* 3.7 25.6 - - + -
213A VAL* 3.7 12.3 - - + -
222A LEU* 3.5 31.0 - - + -
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Residues in contact with LYS 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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145A PRO 3.9 8.3 - - - +
146A ASP* 2.8 35.0 + - + +
167A ASN* 3.8 4.5 - - - +
168A TYR* 3.4 13.8 - - + -
184A LEU* 1.3 67.1 - - - +
186A LYS* 1.3 60.3 + - - +
187A SER* 3.1 11.0 - - - +
188A ARG* 3.0 8.4 + - + +
189A VAL* 2.7 37.7 + - + +
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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