Contacts of the helix formed by residues 177 - 192 (chain A) in PDB entry 5JAJ
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 SER 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A GLU* 4.4 3.8 + - - -
176A THR* 1.3 81.0 + - - +
178A PHE* 1.3 60.2 + - - +
179A GLU* 3.8 7.9 + - - +
180A GLY* 3.0 22.2 + - - -
181A ALA* 2.9 30.5 + - - +
500A LEU* 3.8 3.5 - - - +
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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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177A SER* 1.3 73.6 - - - +
179A GLU* 1.3 67.2 + - + +
181A ALA* 3.2 1.6 + - - +
182A VAL* 2.9 53.2 + - + +
500A LEU* 3.9 16.1 - - + +
503A ARG* 3.5 57.9 - - + +
504A ALA* 4.1 13.5 - - + -
507A ALA* 3.7 17.3 - - + -
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Residues in contact with GLU 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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177A SER* 3.8 7.4 + - - +
178A PHE* 1.3 84.1 - - - +
180A GLY* 1.3 57.7 + - - +
182A VAL* 3.4 5.6 + - - +
183A GLU* 3.0 28.9 + - + +
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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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175A GLU* 3.4 37.9 - - - +
177A SER* 3.0 14.9 + - - -
179A GLU* 1.3 76.9 - - - +
181A ALA* 1.3 60.2 + - - +
183A GLU* 3.3 8.6 + - - +
184A HIS* 3.0 23.6 + - - +
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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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172A THR* 4.2 16.9 - - + -
175A GLU* 3.8 6.6 - - + +
177A SER 2.9 17.7 + - - +
178A PHE 3.2 3.8 + - - +
180A GLY* 1.3 75.2 - - - +
182A VAL* 1.3 62.2 + - - +
184A HIS* 3.2 7.2 + - - +
185A ILE* 3.0 26.7 + - - +
500A LEU* 3.8 26.7 - - + -
504A ALA* 3.7 14.6 - - + -
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Residues in contact with VAL 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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178A PHE* 2.9 54.9 + - + +
179A GLU* 3.7 5.4 - - - +
181A ALA* 1.3 77.1 - - - +
183A GLU* 1.3 63.8 + - - +
185A ILE* 3.1 5.6 + - - +
186A LEU* 2.9 34.8 + - + +
504A ALA* 3.9 18.4 - - + +
507A ALA* 4.4 4.3 - - + -
508A VAL* 3.9 16.6 - - + -
511A MET* 5.7 2.9 - - + -
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Residues in contact with GLU 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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175A GLU* 6.2 0.2 - - - -
179A GLU* 3.0 16.3 + - + +
180A GLY* 3.5 11.0 - - - +
182A VAL* 1.3 77.4 - - - +
184A HIS* 1.3 56.0 + - - +
186A LEU* 3.3 6.9 + - - +
187A GLN* 2.9 29.7 + - + +
519A LYS* 2.9 32.8 + - - -
523A LEU* 3.4 30.2 - - - +
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Residues in contact with HIS 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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137A GLN* 2.9 30.8 + - - -
170A PRO 3.1 27.1 - - - -
171A GLY 3.0 19.0 + - - -
172A THR 3.5 16.2 - - - +
173A GLY* 3.5 24.7 - - - -
175A GLU* 4.7 3.1 - - + -
180A GLY 3.0 14.0 + - - +
181A ALA 3.5 7.6 - - - +
182A VAL 3.2 0.2 - - - -
183A GLU* 1.3 73.8 - - - +
185A ILE* 1.3 67.6 + - - +
187A GLN* 3.1 10.6 + - + +
188A ILE* 3.0 35.0 + - + +
461A ILE* 5.8 0.4 - - + -
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Residues in contact with ILE 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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170A PRO* 3.6 18.4 - - + -
171A GLY 3.6 23.6 - - - +
181A ALA* 3.0 14.7 + - + +
182A VAL 3.6 5.8 - - - +
184A HIS* 1.3 76.3 - - - +
186A LEU* 1.3 63.1 + - - +
188A ILE* 3.2 6.8 + - + +
189A CYS* 3.0 22.5 + - - -
197A ILE* 3.8 28.0 - - + -
501A MET* 4.6 3.1 - - + -
504A ALA* 4.0 17.3 - - + -
505A ILE* 3.6 27.1 - - + +
508A VAL* 3.9 19.3 - - + -
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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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182A VAL* 2.9 34.3 + - + +
183A GLU* 3.6 9.9 - - - +
185A ILE* 1.3 76.1 - - - +
187A GLN* 1.3 58.0 + - - +
189A CYS* 3.3 5.3 + - - +
190A ALA* 2.8 29.1 + - - +
508A VAL* 3.9 18.8 - - + -
511A MET* 4.1 14.6 - - + -
516A TYR* 3.9 31.2 - - + -
519A LYS* 3.7 33.2 - - + -
520A ILE* 3.7 3.6 - - + +
523A LEU* 3.6 16.2 - - + +
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Residues in contact with GLN 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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137A GLN* 6.0 0.9 - - + +
183A GLU* 2.9 17.5 + - + +
184A HIS* 3.1 15.9 + - + +
186A LEU* 1.3 78.3 - - - +
188A ILE* 1.3 59.0 + - + +
190A ALA* 3.2 9.8 + - - +
191A ASN* 2.9 66.1 + - - +
523A LEU* 3.7 34.8 + - + +
527A ALA* 5.0 7.1 - - - +
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Residues in contact with ILE 188 (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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21A ILE* 4.1 11.4 - - + -
133A CYS* 4.8 6.1 - - - +
134A HIS* 4.4 7.2 - - - +
136A THR 3.8 5.4 - - - +
137A GLN* 2.9 50.0 - - + +
170A PRO* 4.6 16.8 - - + +
184A HIS* 3.0 33.1 + - + +
185A ILE* 3.6 9.4 - - + +
187A GLN* 1.3 76.3 - - + +
189A CYS* 1.3 64.6 + - - +
191A ASN* 3.2 8.9 + - - +
192A LEU* 3.1 42.3 + - + +
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Residues in contact with CYS 189 (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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21A ILE* 4.4 4.9 - - - -
185A ILE* 3.0 20.1 + - - -
186A LEU* 3.5 8.7 - - - +
188A ILE* 1.3 77.1 - - - +
190A ALA* 1.3 63.1 + - - +
192A LEU 3.3 0.9 + - - -
193A ASP 2.9 3.5 + - - -
194A THR* 2.9 39.4 + - - -
197A ILE* 3.6 35.7 - - - -
508A VAL* 4.5 1.8 - - - -
516A TYR* 3.3 32.1 - - - +
520A ILE* 3.7 7.4 - - + +
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Residues in contact with ALA 190 (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* 3.7 5.1 - - + +
186A LEU 2.8 19.8 + - - +
187A GLN* 3.2 10.1 + - - +
189A CYS* 1.3 73.1 - - - +
191A ASN* 1.3 63.2 + - - +
193A ASP 3.1 3.5 + - - -
520A ILE* 3.7 12.7 - - + +
523A LEU* 3.6 29.2 - - + -
524A GLN* 3.0 41.9 + - + +
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Residues in contact with ASN 191 (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 THR* 2.9 26.7 + - + +
137A GLN* 3.8 14.3 - - - +
138A LYS 4.8 0.6 - - - +
143A ASN* 3.5 25.8 + - - +
146A MET* 3.3 27.5 - - - +
150A LEU* 4.4 14.1 - - - +
187A GLN* 2.9 51.9 + - - +
188A ILE* 3.2 6.2 + - - +
190A ALA* 1.3 77.7 - - - +
192A LEU* 1.3 59.4 + - - +
193A ASP 3.3 0.6 + - - -
527A ALA* 5.1 6.9 - - - +
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Residues in contact with LEU 192 (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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19A ASN* 4.7 0.3 - - - +
20A SER 6.0 0.2 - - - +
21A ILE* 3.8 18.6 - - + -
130A ILE* 3.7 26.0 - - + -
133A CYS* 3.8 42.4 - - + +
136A THR* 3.6 28.7 - - + +
146A MET* 4.0 7.6 - - + -
163A ILE* 3.5 31.9 - - + +
165A GLY* 5.2 1.6 - - - -
188A ILE* 3.1 19.4 + - + +
191A ASN* 1.3 75.2 - - - +
193A ASP* 1.3 70.9 + - - +
194A THR* 3.2 15.4 + - - +
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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