Contacts of the helix formed by residues 168 - 179 (chain A) in PDB entry 5E67
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 ASP 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A TRP* 3.4 40.5 + - + +
166A ILE* 3.3 8.8 + - - +
167A PRO* 1.3 81.0 - - - +
169A PRO* 1.3 75.2 - - - +
170A PHE* 2.9 40.4 + - - +
171A TRP* 2.8 25.5 + - - +
220A TYR* 3.8 4.5 - - - -
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Residues in contact with PRO 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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168A ASP* 1.3 94.5 - - - +
170A PHE* 1.3 59.0 + - - +
172A LEU 3.1 11.3 + - - +
173A ALA 3.2 8.7 + - - -
220A TYR* 3.3 22.7 - - + +
252A PHE* 3.5 29.5 - - + -
256A TYR* 3.4 41.9 - - + +
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Residues in contact with PHE 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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9A ASN* 3.4 48.9 - - + +
11A TRP* 3.8 2.9 - - + -
12A ALA* 3.3 17.8 - - + +
168A ASP* 2.9 22.4 + - - +
169A PRO* 1.3 76.7 - - - +
171A TRP* 1.3 63.7 + - - +
173A ALA* 3.3 9.9 + - + +
174A GLY 3.1 16.6 + - - -
255A GLN 4.5 6.3 - - - -
256A TYR* 3.7 44.0 - + + -
257A LYS* 4.5 7.6 - - + -
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Residues in contact with TRP 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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11A TRP* 3.2 18.7 + + + +
14A VAL* 3.8 13.0 - - + +
15A GLY* 3.4 24.5 - - - +
18A ASP* 2.9 25.9 + - + -
98A SER 5.2 0.4 - - - -
100A ILE* 3.4 33.4 - - + +
101A THR* 4.3 1.3 - - + -
166A ILE* 4.0 25.6 - - + -
167A PRO* 3.9 25.4 - - + -
168A ASP 2.8 16.4 + - - +
170A PHE* 1.3 75.2 - - - +
172A LEU* 1.3 74.0 + - + +
174A GLY 3.1 1.4 + - - -
175A PHE* 2.9 74.0 + + + -
213A LEU* 4.1 10.8 - - + -
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Residues in contact with LEU 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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166A ILE* 4.5 8.1 - - + -
168A ASP 3.7 0.6 + - - -
169A PRO 3.1 10.9 + - - +
171A TRP* 1.3 98.3 - - + +
173A ALA* 1.3 66.3 + - - +
175A PHE* 4.5 3.8 - - + -
176A VAL* 2.9 47.0 + - + +
204A ILE* 4.2 4.9 - - + -
217A LEU* 3.7 25.8 - - + -
220A TYR* 3.8 25.1 - - + -
221A LEU* 3.9 22.7 - - + -
252A PHE* 3.8 22.2 - - + -
253A PHE* 4.4 2.9 - - + -
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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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12A ALA* 5.2 2.0 - - + -
169A PRO 3.2 6.6 + - - +
170A PHE* 3.3 14.5 + - + +
172A LEU* 1.3 75.0 - - - +
174A GLY* 1.3 56.3 + - - +
177A SER* 2.7 34.4 + - - -
252A PHE* 4.6 0.2 - - - -
253A PHE* 4.1 11.5 - - - -
256A TYR* 3.4 37.5 - - + +
257A LYS 3.5 16.8 - - - +
258A ILE* 3.5 4.7 - - - +
259A ILE* 6.2 0.4 - - - -
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Residues in contact with GLY 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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12A ALA* 3.3 27.3 - - - +
16A PHE* 3.3 22.5 - - - -
170A PHE 3.1 7.2 + - - -
171A TRP 3.1 5.9 + - - -
173A ALA* 1.3 77.8 - - - +
175A PHE* 1.3 63.3 + - - +
177A SER* 3.2 20.6 + - - -
178A GLY 3.3 2.9 + - - -
259A ILE* 4.7 3.6 - - - -
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Residues in contact with PHE 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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15A GLY 3.3 19.8 - - - +
18A ASP* 3.9 6.5 - - + -
19A ALA* 3.6 8.1 - - - +
101A THR* 3.9 21.3 - - + -
171A TRP* 2.9 50.4 + + + +
172A LEU* 3.8 10.3 - - + +
174A GLY* 1.3 78.2 - - - +
176A VAL* 1.3 58.6 + - - +
178A GLY* 3.0 2.9 + - - -
179A ASP* 2.8 42.3 + - + +
204A ILE* 3.7 28.0 - - + -
206A GLN* 3.6 31.2 - - + -
213A LEU* 4.7 5.2 - - + -
214A MET* 5.0 4.0 - - - -
217A LEU* 5.5 2.7 - - + -
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Residues in contact with VAL 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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172A LEU* 2.9 27.1 + - + +
175A PHE* 1.3 75.9 - - + +
177A SER* 1.3 60.7 + - - +
179A ASP 4.6 0.4 - - - -
180A GLY* 2.8 35.6 + - - +
182A PHE* 4.0 10.4 - - + -
202A PHE* 3.7 24.5 - - + -
204A ILE* 3.6 30.7 - - + -
253A PHE* 3.7 16.8 - - + -
258A ILE* 3.6 21.5 - - + -
262A ALA* 5.8 0.5 - - - +
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Residues in contact with SER 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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16A PHE* 4.0 8.4 - - - -
173A ALA 2.7 21.0 + - - -
174A GLY 3.2 12.1 - - - -
175A PHE 3.1 0.2 - - - -
176A VAL* 1.3 79.0 - - - +
178A GLY* 1.3 55.2 + - - +
258A ILE* 3.4 13.4 - - - +
259A ILE* 3.0 52.0 + - - +
262A ALA* 4.5 8.2 - - - +
403A MXE 3.2 21.9 + - - +
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Residues in contact with GLY 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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16A PHE* 3.9 9.6 - - - -
19A ALA* 3.7 12.1 - - - -
20A GLU* 4.0 3.4 - - - -
174A GLY 3.3 3.8 + - - -
175A PHE 3.0 5.8 + - - -
177A SER* 1.3 81.5 - - - +
179A ASP* 1.3 64.2 + - - +
180A GLY 3.6 0.9 - - - -
402A MG 2.9 17.3 - - - -
403A MXE 3.3 27.8 - - - +
16C C 4.1 0.9 - - - +
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Residues in contact with ASP 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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19A ALA* 3.4 19.2 - - + +
175A PHE* 2.8 25.0 + - + +
176A VAL* 4.6 0.2 - - - -
178A GLY* 1.3 71.9 - - - -
180A GLY* 1.3 61.0 + - - +
181A SER* 5.0 0.2 + - - -
203A GLN 4.2 0.2 - - - +
204A ILE* 3.5 3.0 - - - -
205A THR* 3.0 35.0 + - - +
206A GLN* 2.3 30.4 - - - +
401A MG 2.2 31.4 - - - -
402A MG 2.6 15.2 - - - -
16C C 3.0 21.7 + - - +
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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