Contacts of the helix formed by residues 166 - 183 (chain A) in PDB entry 5A5J
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 PRO 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A LEU* 5.8 1.6 - - + -
164A CYS* 3.5 14.8 - - - +
165A ASP* 1.3 91.6 - - - +
167A THR* 1.3 54.6 + - - +
168A PHE 3.2 1.2 + - - -
169A ILE* 3.3 7.9 + - + +
170A LEU* 2.8 54.7 + - + +
307A ARG* 4.7 2.7 - - + -
310A LEU* 4.9 1.3 - - + -
483A TYR* 3.6 41.7 - - + +
485A LEU* 3.6 17.3 - - + -
487A PHE* 4.5 9.6 - - + -
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Residues in contact with THR 167 (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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165A ASP* 3.2 27.7 + - - -
166A PRO* 1.3 77.6 - - - +
168A PHE* 1.3 67.0 + - - +
170A LEU* 4.2 0.4 - - - +
171A GLY* 3.0 21.5 + - - -
300A GLU* 6.0 0.2 - - - +
303A SER* 4.3 2.3 + - - +
307A ARG* 3.3 40.4 + - - +
482A PHE* 5.7 0.9 - - - -
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Residues in contact with PHE 168 (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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165A ASP* 4.1 6.5 + - - +
166A PRO 3.2 0.8 + - - -
167A THR* 1.3 81.8 - - - +
169A ILE* 1.3 73.2 + - + +
171A GLY* 3.8 0.9 - - - -
172A CYS* 3.1 49.9 + - - -
189A TYR* 4.5 17.9 - + + -
194A PHE* 6.0 0.7 - + - -
195A LEU* 4.1 28.3 - - + -
198A MET* 4.2 16.3 - - + +
202A ASN* 5.5 10.1 - - - -
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Residues in contact with ILE 169 (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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152A LEU* 3.5 29.9 - - + +
155A GLU* 4.0 30.7 - - + +
156A LEU* 3.5 29.6 - - + -
159A THR* 4.4 11.2 - - + -
164A CYS* 5.0 6.7 - - - -
165A ASP 5.0 4.0 + - - +
166A PRO* 3.3 6.8 + - + +
168A PHE* 1.3 84.3 - - + +
170A LEU* 1.3 64.5 + - + +
172A CYS* 3.3 22.1 + - - +
173A ALA* 3.4 8.5 + - - +
189A TYR* 4.6 12.3 - - + -
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Residues in contact with LEU 170 (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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152A LEU* 4.4 22.7 - - + -
156A LEU* 5.4 4.0 - - + -
166A PRO* 2.8 45.4 + - + +
167A THR* 4.2 1.8 - - - +
169A ILE* 1.3 76.4 - - + +
171A GLY* 1.3 56.3 + - - +
173A ALA* 3.7 2.3 + - - +
174A PRO* 2.8 27.4 - - - +
303A SER* 3.6 10.0 - - - +
306A LEU* 3.6 31.7 - - + +
307A ARG* 3.6 31.4 - - + +
310A LEU* 4.2 11.9 - - + -
448A PHE* 6.1 0.2 - - + -
452A ILE* 4.4 17.3 - - + -
487A PHE* 6.1 0.4 - - + -
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Residues in contact with GLY 171 (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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167A THR 3.0 16.5 + - - -
168A PHE 3.8 0.7 - - - -
170A LEU* 1.3 73.8 - - - +
172A CYS* 1.3 62.0 + - - +
174A PRO* 3.4 8.2 - - - +
175A CYS* 3.4 15.1 - - - +
198A MET* 3.5 10.1 - - - +
299A THR* 3.5 9.3 - - - +
300A GLU* 5.6 2.0 - - - -
303A SER* 3.1 23.2 + - - -
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Residues in contact with CYS 172 (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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168A PHE* 3.1 48.3 + - - -
169A ILE* 3.3 10.3 + - - +
171A GLY* 1.3 76.9 - - - +
173A ALA* 1.3 60.9 + - - +
175A CYS* 3.4 0.5 + - - +
176A ASN* 2.9 31.1 + - - +
189A TYR* 4.1 21.3 - - + -
194A PHE* 3.4 14.0 - - + -
198A MET* 3.1 32.1 - - + -
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Residues in contact with ALA 173 (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 GLU* 3.8 16.6 - - + +
152A LEU* 4.2 16.6 - - + -
169A ILE 3.4 6.7 + - - +
170A LEU 4.0 4.9 - - - +
172A CYS* 1.3 78.2 - - - +
174A PRO* 1.3 70.4 - - + +
176A ASN* 3.1 6.2 + - - +
177A VAL* 3.1 25.3 + - - +
189A TYR* 4.1 6.9 + - - +
306A LEU* 5.3 0.4 - - + -
448A PHE* 3.6 25.1 - - + -
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Residues in contact with PRO 174 (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 LEU 2.8 28.9 - - - +
171A GLY 3.4 6.1 - - - +
173A ALA* 1.3 85.9 - - + +
175A CYS* 1.3 60.9 + - - +
177A VAL* 3.4 3.7 + - + +
178A ILE* 3.3 28.3 + - - +
298A GLY 4.0 7.1 - - - +
299A THR* 4.1 7.2 - - - +
302A THR* 3.8 27.6 - - + -
303A SER* 4.2 8.5 - - - +
306A LEU* 3.9 10.1 - - + -
444A GLU* 3.1 29.1 - - - +
448A PHE* 4.5 0.4 - - + -
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Residues in contact with CYS 175 (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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171A GLY 3.4 18.4 + - - +
172A CYS 3.5 4.7 - - - +
174A PRO* 1.3 79.3 - - - +
176A ASN* 1.3 66.0 + - - +
178A ILE* 3.1 15.1 + - - +
179A CYS* 3.2 13.3 + - - -
194A PHE* 4.0 11.9 - - + -
197A LEU* 5.2 6.3 - - - -
198A MET* 3.6 27.4 - - - -
201A LEU* 4.1 16.4 - - - -
295A PHE* 3.8 11.7 - - - -
299A THR* 3.7 16.5 - - + +
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Residues in contact with ASN 176 (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 GLU* 3.1 34.6 + - - +
172A CYS 2.9 15.2 + - - +
173A ALA 3.1 3.3 + - - +
175A CYS* 1.3 77.6 - - - +
177A VAL* 1.3 59.8 + - - +
178A ILE 3.3 0.2 - - - -
179A CYS* 3.4 3.1 + - - +
180A SER* 3.1 21.8 + - - -
186A ARG* 3.2 13.0 - - - +
187A PHE* 3.1 47.6 + - - +
189A TYR* 3.3 9.5 - - - -
194A PHE* 3.5 23.7 - - - -
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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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144A ARG* 5.0 9.4 - - + +
145A VAL* 3.9 23.6 - - + -
148A GLU* 4.3 13.7 - - + -
173A ALA 3.1 14.8 + - - +
174A PRO 3.6 7.6 - - - +
175A CYS 3.1 0.6 - - - -
176A ASN* 1.3 74.8 - - - +
178A ILE* 1.3 61.6 + - - +
180A SER* 3.1 6.7 + - - -
181A ILE* 2.9 46.0 + - + +
440A LEU* 4.1 2.9 - - + -
444A GLU* 3.6 26.9 - - - +
448A PHE* 4.2 14.1 - - + -
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Residues in contact with ILE 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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174A PRO 3.3 16.4 - - - +
175A CYS 3.1 7.1 + - - +
177A VAL* 1.3 78.4 - - - +
179A CYS* 1.3 59.7 + - - +
181A ILE* 3.6 8.9 - - + +
182A ILE* 2.9 62.6 + - + +
294A LEU* 3.8 21.5 - - + +
295A PHE* 3.4 32.3 - - + +
298A GLY* 4.2 10.5 - - - +
299A THR* 4.5 3.4 - - - +
440A LEU* 4.2 15.9 - - + -
444A GLU* 5.0 0.2 - - - +
1493A HEM 3.9 21.5 - - + -
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Residues in contact with CYS 179 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A CYS* 3.2 18.6 + - - -
176A ASN* 3.5 9.4 - - - +
177A VAL 3.2 0.2 - - - -
178A ILE* 1.3 74.5 - - - +
180A SER* 1.3 55.7 + - - +
183A PHE* 2.4 54.2 + - + +
185A LYS 3.8 15.5 - - - +
187A PHE* 3.6 25.6 - - + -
194A PHE* 4.1 14.8 - - - -
197A LEU* 4.2 11.2 - - - -
295A PHE* 3.7 18.3 - - - -
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Residues in contact with SER 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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139A ARG* 5.0 2.9 + - - -
144A ARG* 2.6 54.7 + - - +
147A GLU* 6.1 0.4 - - - -
176A ASN 3.1 10.7 + - - -
177A VAL* 3.3 11.7 - - - -
178A ILE 3.1 0.2 - - - -
179A CYS* 1.3 83.9 - - - +
181A ILE* 1.3 54.1 + - - +
184A HIS* 2.9 22.0 + - - +
185A LYS 4.3 4.3 - - - +
186A ARG* 4.2 15.0 - - - -
262A ASP* 4.6 0.2 - - - +
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Residues in contact with ILE 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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131A LEU* 3.9 24.9 - - + -
136A MET* 3.8 13.2 - - + +
141A ILE* 3.9 17.5 - - + -
144A ARG* 4.2 14.8 - - - +
177A VAL* 2.9 42.3 + - + +
178A ILE* 3.6 12.8 - - + +
180A SER* 1.3 75.7 - - - +
182A ILE* 1.3 67.9 + - + +
262A ASP* 3.4 6.8 - - - +
263A PHE* 2.8 31.5 + - + -
294A LEU* 5.3 2.2 - - + -
440A LEU* 4.1 24.2 - - + -
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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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178A ILE* 2.9 44.7 + - + +
179A CYS* 3.7 1.6 - - - +
181A ILE* 1.3 89.8 - - + +
183A PHE* 1.3 81.6 + - + +
244A ILE* 5.2 0.2 - - + -
262A ASP* 3.0 21.7 - - - +
263A PHE* 3.9 13.2 - - + -
264A ILE* 3.4 24.1 + - + +
291A ALA* 4.4 19.1 - - + +
294A LEU* 4.0 20.0 - - + -
295A PHE* 4.1 12.3 - - + -
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Residues in contact with PHE 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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179A CYS* 2.4 53.9 + - + +
182A ILE* 1.3 88.0 - - + +
184A HIS* 1.3 69.1 + - - +
185A LYS* 3.2 15.6 + - + +
187A PHE* 4.2 12.8 - + - -
197A LEU* 4.9 0.9 - - + -
243A TYR* 3.6 37.2 - + - -
244A ILE* 4.3 14.8 - - + -
247A LYS* 3.9 28.3 - - + -
251A HIS* 4.1 13.1 + - + -
262A ASP* 3.1 10.4 - - - +
264A ILE* 3.8 13.5 - - + -
295A PHE* 4.2 13.7 - + - -
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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