Contacts of the helix formed by residues 168 - 186 (chain A) in PDB entry 5HJS
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 GLN 168 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A GLY 3.9 1.6 + - - -
167A LEU* 1.3 72.2 - - - +
169A VAL* 1.4 61.1 + - - +
170A GLU* 3.1 27.7 + - - +
171A PHE* 3.0 27.6 + - + +
172A ILE* 3.2 11.2 + - - +
256A VAL* 5.1 1.2 - - - +
259A GLU* 4.1 8.7 - - - +
260A GLN* 2.9 43.4 + - - +
263A ALA* 3.6 25.3 - - - +
267A GLN* 5.6 0.8 + - - -
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Residues in contact with VAL 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ALA* 5.2 7.6 - - + -
167A LEU 3.9 1.0 + - - +
168A GLN* 1.4 70.8 - - - +
170A GLU* 1.4 78.1 + - - +
171A PHE 3.1 0.2 - - - -
172A ILE* 3.8 17.7 - - + -
173A ASN* 3.1 45.0 + - - +
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Residues in contact with GLU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A GLN* 3.1 37.2 + - - +
169A VAL* 1.4 89.7 + - + +
171A PHE* 1.4 55.8 + - - +
173A ASN* 5.6 0.2 - - - -
174A PRO* 3.2 21.6 - - - +
256A VAL* 3.4 12.1 - - + +
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Residues in contact with PHE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ILE* 4.6 1.1 - - + -
135A LEU* 4.5 9.2 - - + -
167A LEU* 3.5 21.8 - - + -
168A GLN* 3.0 11.6 + - + +
170A GLU* 1.4 78.5 - - - +
172A ILE* 1.3 63.0 + - - +
173A ASN 3.4 1.3 - - - -
174A PRO* 3.3 2.9 - - - +
175A ILE* 3.3 47.0 + - + +
253A LEU* 4.0 14.8 - - + -
256A VAL* 3.7 21.3 - - + +
257A HIS* 3.7 39.5 - + + -
260A GLN* 3.8 28.5 - - + +
301A 668 3.7 25.4 - - - -
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Residues in contact with ILE 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ARG* 3.7 28.3 - - + +
162A PHE* 3.9 7.4 - - + -
163A ALA* 3.5 31.2 - - + +
167A LEU* 3.3 40.4 - - + +
168A GLN 3.2 15.6 + - - +
169A VAL* 3.4 13.2 + - + +
171A PHE* 1.3 76.0 - - - +
173A ASN* 1.4 65.2 + - - +
175A ILE* 3.3 10.1 + - - +
176A PHE* 3.1 49.5 + - + -
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Residues in contact with ASN 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ARG* 4.0 24.4 + - - +
169A VAL* 3.1 29.3 + - - +
172A ILE* 1.4 77.4 - - - +
174A PRO* 1.4 69.0 - - + +
176A PHE* 3.2 4.2 + - - +
177A GLU* 2.9 43.8 + - - +
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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 GLU 3.2 27.8 - - - +
171A PHE 3.3 7.4 - - - +
173A ASN* 1.4 92.5 - - + +
175A ILE* 1.4 55.2 + - - +
177A GLU* 3.5 14.4 - - + +
178A PHE* 2.9 32.1 + - - +
253A LEU* 3.7 20.8 - - + +
256A VAL* 4.4 13.9 - - + -
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Residues in contact with ILE 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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135A LEU* 3.9 19.5 - - + -
138A THR* 4.1 25.6 - - + -
149A ILE* 4.6 1.3 - - + -
162A PHE* 4.2 17.0 - - + -
167A LEU* 4.1 12.8 - - + -
171A PHE* 3.3 60.3 + - + +
172A ILE* 3.6 5.8 - - - +
173A ASN 3.3 0.4 - - - -
174A PRO* 1.4 75.4 - - - +
176A PHE* 1.3 64.6 + - + +
178A PHE* 3.8 2.8 - - - +
179A SER* 2.6 38.1 + - - +
253A LEU* 4.2 10.1 - - + -
301A 668 5.3 3.4 - - + -
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Residues in contact with PHE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TYR* 4.1 16.5 - + + -
147A GLU 3.4 28.7 - - - -
148A SER* 4.2 3.6 - - - -
149A ILE* 3.5 25.6 - - + -
157A TYR 4.0 1.3 - - - -
158A ASN 3.6 6.5 - - - -
159A ARG* 3.4 61.2 + - + +
162A PHE* 3.8 27.8 - + - -
172A ILE* 3.1 40.6 + - + +
173A ASN 3.9 1.1 - - - +
175A ILE* 1.3 78.3 - - + +
177A GLU* 1.3 59.2 + - - +
179A SER* 3.5 4.7 + - - -
180A ARG* 3.0 30.1 + - - +
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Residues in contact with GLU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ARG* 4.9 9.1 + - - +
173A ASN* 2.9 43.0 + - - +
174A PRO* 3.5 13.6 - - + +
176A PHE* 1.3 75.0 - - - +
178A PHE* 1.4 61.8 + - - +
180A ARG* 3.5 19.6 + - - +
181A ALA* 3.2 23.0 + - - +
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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
----------------------------------------------------------
135A LEU* 3.9 18.4 - - + -
136A LEU* 4.1 6.3 - - + -
139A SER* 4.0 9.0 - - - -
174A PRO 2.9 18.5 + - - +
175A ILE 3.8 4.3 - - - +
177A GLU* 1.4 76.8 - - - +
179A SER* 1.3 58.1 + - - +
181A ALA* 3.4 7.0 + - + +
182A MET* 2.9 59.7 + - + +
246A LYS* 3.7 29.8 - - + -
249A SER* 3.9 21.1 - - - -
250A LEU* 3.7 30.5 - - + -
253A LEU* 3.6 24.2 - - + -
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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
----------------------------------------------------------
135A LEU 5.0 0.3 + - - -
138A THR* 4.3 4.9 - - - +
139A SER* 3.7 30.7 + - - +
142A TYR* 3.7 31.6 - - - +
149A ILE* 4.5 2.6 - - - +
175A ILE* 2.6 30.3 + - - +
176A PHE* 3.7 4.9 - - - -
177A GLU 3.4 0.2 - - - -
178A PHE* 1.3 76.1 - - - +
180A ARG* 1.3 57.0 + - - +
182A MET* 3.7 1.7 - - - +
183A ASN* 3.0 29.5 + - - +
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Residues in contact with ARG 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TYR* 3.9 27.3 - - + +
147A GLU* 6.0 2.2 - - - +
159A ARG* 6.0 2.9 - - - +
176A PHE 3.0 17.7 + - - +
177A GLU* 3.7 16.7 + - - +
179A SER* 1.3 72.8 - - - +
181A ALA* 1.4 83.6 + - - +
183A ASN* 3.2 12.5 + - - +
184A GLU* 2.7 45.6 + - + +
211B GLN* 4.2 22.6 + - - +
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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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177A GLU 3.2 16.8 + - - +
178A PHE* 3.7 7.2 - - + +
180A ARG* 1.4 92.2 - - - +
182A MET* 1.3 62.0 + - - +
184A GLU* 3.4 23.0 + - - +
185A LEU* 3.8 5.7 + - - +
246A LYS* 3.9 26.3 + - + +
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Residues in contact with MET 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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136A LEU* 4.3 8.3 - - + -
139A SER* 3.7 13.9 - - - +
178A PHE* 2.9 48.9 + - + +
179A SER 3.7 5.2 - - - +
181A ALA* 1.3 73.0 - - - +
183A ASN* 1.3 65.7 + - - +
185A LEU* 3.2 22.1 + - + +
186A GLN* 3.6 3.6 + - - -
187A LEU* 3.6 28.7 + - + -
192A PHE* 3.6 35.6 - - + -
195A LEU* 4.7 0.7 - - + -
246A LYS* 3.6 36.8 - - + +
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Residues in contact with ASN 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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139A SER 5.0 5.7 + - - +
142A TYR* 3.9 37.0 + - + +
144A PRO* 3.7 24.7 - - - +
179A SER 3.0 19.7 + - - +
180A ARG 3.2 5.8 + - - +
182A MET* 1.3 76.4 - - - +
184A GLU* 1.4 60.8 + - - +
186A GLN* 2.7 47.0 + - - +
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Residues in contact with GLU 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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180A ARG* 2.7 43.2 + - + +
181A ALA* 3.4 14.9 - - - +
182A MET 3.2 0.6 - - - -
183A ASN* 1.4 76.3 + - - +
185A LEU* 1.4 60.2 + - - +
186A GLN* 3.4 7.7 + - - +
242A ARG* 5.2 12.0 + - - +
212B LEU* 5.8 3.3 - - - +
215B GLU* 5.5 2.3 - - - +
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Residues in contact with LEU 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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181A ALA 3.8 6.7 + - - +
182A MET* 3.2 17.1 + - - +
184A GLU* 1.4 77.3 - - - +
186A GLN* 1.4 67.2 + - - +
187A LEU* 3.5 21.6 + - + +
233A HIS* 4.9 2.3 + - - -
239A MET* 3.4 32.8 - - + +
242A ARG* 3.6 56.3 - - + +
243A MET* 4.3 7.2 - - + +
246A LYS* 3.7 38.4 - - + +
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Residues in contact with GLN 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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144A PRO* 6.1 0.2 - - - +
182A MET 3.6 2.8 + - - -
183A ASN* 2.7 48.7 + - - +
184A GLU* 4.0 7.9 - - - +
185A LEU* 1.4 79.7 - - - +
187A LEU* 1.3 64.6 + - - +
188A ASN 3.9 1.4 + - - -
191A GLU* 4.4 2.4 - - - +
232A HIS* 4.6 9.0 - - - -
233A HIS* 5.1 2.8 + - - -
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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
------------------------------------------------------------
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