Contacts of the helix formed by residues 178 - 194 (chain A) in PDB entry 5ID6
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 GLU 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A SER* 5.3 3.8 - - - -
173A PHE* 3.5 33.6 + - + +
174A ARG* 3.3 29.0 + - - +
176A ILE 3.3 0.8 - - - -
177A ASN* 1.3 87.0 - - - +
179A ASN* 1.3 66.6 + - - +
180A LEU 3.4 0.7 - - - -
181A THR* 3.6 4.7 + - - -
182A ARG* 3.4 29.0 + - - +
277A TYR* 3.1 39.4 - - + -
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Residues in contact with ASN 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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174A ARG* 3.0 11.6 + - - +
175A CYS* 3.3 16.6 - - - +
178A GLU* 1.3 79.8 - - - +
180A LEU* 1.3 57.7 + - - +
182A ARG* 3.3 4.8 + - - +
183A TYR* 2.7 30.0 + - - +
225A PHE* 4.1 9.2 - - + -
228A VAL 4.1 9.7 + - - -
229A LEU* 5.6 1.2 + - - +
234A ILE* 3.8 15.8 - - - +
276A LEU* 3.8 21.9 - - + +
277A TYR* 2.7 55.8 + - - +
279A GLN* 5.2 3.2 + - - -
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 4.1 19.3 - - + -
77A TYR* 3.6 31.0 - - + -
78A ILE* 4.7 0.9 - - + -
101A LEU* 5.0 3.1 - - + -
175A CYS 3.0 15.0 + - - +
176A ILE* 3.1 33.1 + - + +
178A GLU 3.4 0.6 - - - -
179A ASN* 1.3 74.6 - - - +
181A THR* 1.3 60.0 + - - +
183A TYR* 4.2 4.0 - - + -
184A ILE* 2.9 56.4 + - + +
225A PHE* 3.5 39.5 - - + -
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Residues in contact with THR 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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77A TYR* 5.0 2.5 - - - +
81A PHE* 4.2 30.6 - - + -
176A ILE 3.7 14.6 - - - +
177A ASN* 4.0 19.7 + - - +
178A GLU* 3.6 7.1 + - - -
179A ASN 3.4 0.4 - - - -
180A LEU* 1.3 75.2 - - - +
182A ARG* 1.3 64.0 + - - +
184A ILE* 3.7 6.3 - - - +
185A SER* 2.9 30.4 + - - -
477A GLY 5.2 7.5 + - - -
478A LYS 5.9 2.2 - - - +
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Residues in contact with ARG 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A GLU 3.4 19.1 + - - +
179A ASN 3.3 5.0 + - - +
180A LEU 3.2 0.2 - - - -
181A THR* 1.3 82.4 + - - +
183A TYR* 1.3 56.6 + - - +
185A SER* 3.9 5.9 - - - -
186A ASN* 2.7 43.6 + - - +
274A LYS* 4.1 18.9 - - + +
275A PRO* 2.8 44.6 + - - +
276A LEU* 4.0 11.7 - - + +
277A TYR* 2.8 49.4 + - - +
491A VAL* 3.2 25.4 - - - +
495A ASP* 2.9 22.2 + - - -
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Residues in contact with TYR 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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78A ILE* 5.0 2.0 - - + -
179A ASN 2.7 20.8 + - - +
180A LEU* 3.2 8.9 + - + +
182A ARG* 1.3 70.2 - - - +
184A ILE* 1.3 66.2 + - - +
186A ASN* 3.5 9.0 + - - +
187A MSE 3.1 40.3 + - + +
219A PHE* 2.6 36.5 + + + -
220A PHE* 5.7 0.7 - - - -
221A GLU 3.0 27.6 + - - -
222A GLY* 4.5 2.2 - - - -
224A PHE* 3.4 11.8 - - - +
225A PHE* 3.3 41.5 - + + -
228A VAL* 4.0 19.7 - - + -
237A TYR* 3.7 24.2 + + - -
276A LEU* 4.3 4.5 - - + -
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Residues in contact with ILE 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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77A TYR* 3.8 19.1 - - + -
78A ILE* 3.9 22.9 - - + -
81A PHE* 3.8 36.6 - - + -
82A ARG* 3.9 26.2 - - + -
180A LEU* 2.9 46.8 + - + +
181A THR* 3.7 4.3 - - - +
183A TYR* 1.3 76.5 - - - +
185A SER* 1.3 60.2 + - - +
187A MSE 2.8 32.6 + - - +
188A ASP* 3.4 8.5 + - - +
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Residues in contact with SER 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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81A PHE* 6.0 0.6 - - - -
181A THR 2.9 20.0 + - - -
182A ARG* 4.0 7.6 - - - -
184A ILE* 1.3 78.4 - - - +
186A ASN* 1.3 59.2 + - - +
188A ASP* 3.8 8.1 + - - +
189A ILE* 3.1 24.9 + - - +
274A LYS* 3.8 12.6 + - - -
484A GLU* 3.3 30.7 + - - +
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Residues in contact with ASN 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 ARG 2.7 25.7 + - - +
183A TYR 3.7 3.1 - - - +
184A ILE 3.1 0.4 - - - -
185A SER* 1.3 74.8 - - - +
187A MSE 1.3 59.6 + - - +
188A ASP 3.3 0.4 - - - -
189A ILE* 3.7 7.8 - - - +
190A PHE* 2.8 29.8 + - - +
220A PHE* 3.8 5.9 - - + -
237A TYR* 2.6 33.5 + - - +
273A PHE* 3.4 25.1 - - + -
274A LYS* 3.0 47.5 + - - +
276A LEU* 4.2 0.6 - - - +
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Residues in contact with MSE 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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78A ILE* 4.0 26.5 - - + -
82A ARG* 4.5 23.8 - - - +
183A TYR* 3.1 24.0 - - + +
184A ILE* 2.8 22.7 + - - +
186A ASN* 1.3 76.6 - - - +
188A ASP* 1.3 54.8 - - - +
190A PHE* 3.0 8.0 + - - +
191A GLU* 2.7 44.1 + - + +
220A PHE* 3.3 26.0 - - + +
221A GLU* 3.7 1.3 - - - +
222A GLY* 3.2 33.9 - - - +
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Residues in contact with ASP 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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82A ARG* 2.3 58.7 + - - +
184A ILE* 3.4 10.4 + - - +
185A SER* 4.0 9.9 - - - +
186A ASN 3.3 0.2 - - - -
187A MSE 1.3 74.9 - - - +
189A ILE* 1.3 63.6 + - + +
191A GLU* 3.9 8.5 - - - +
192A LYS* 3.4 26.2 + - - +
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Residues in contact with ILE 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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185A SER* 3.1 19.2 + - - +
186A ASN* 3.7 16.4 - - - +
187A MSE 3.2 0.6 - - - -
188A ASP* 1.3 75.0 - - + +
190A PHE* 1.3 64.6 + - - +
192A LYS* 3.2 5.1 + - - +
193A VAL* 3.0 28.9 + - + +
271A PRO* 3.6 44.4 - - + +
272A LYS 3.5 15.0 - - - +
273A PHE* 3.6 18.8 - - + -
274A LYS* 3.5 27.4 - - - +
484A GLU* 4.3 10.5 - - + -
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Residues in contact with PHE 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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186A ASN 2.8 19.4 + - - +
187A MSE 3.0 5.1 + - - +
189A ILE* 1.3 78.9 - - - +
191A GLU* 1.3 64.7 + - + +
193A VAL* 5.1 0.7 - - - -
194A ASP* 3.0 58.3 + - - +
197A PHE* 4.2 21.3 - + - -
202A VAL* 6.2 2.2 - - + -
216A VAL* 4.6 8.1 - - + -
217A GLU* 4.3 26.5 - - + -
220A PHE* 3.4 55.9 - + + -
221A GLU* 6.1 0.7 - - - -
273A PHE* 3.6 17.9 - + + -
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Residues in contact with GLU 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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82A ARG* 2.8 35.3 + - - -
187A MSE 2.7 24.9 + - + +
188A ASP* 3.9 8.2 - - - +
189A ILE 3.2 0.4 - - - -
190A PHE* 1.3 78.6 - - + +
192A LYS* 1.3 62.1 + - - +
193A VAL 3.5 0.2 + - - -
194A ASP* 3.9 17.4 + - - +
220A PHE 6.1 1.1 - - - +
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Residues in contact with LYS 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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188A ASP 3.4 17.1 + - - +
189A ILE* 3.2 5.9 + - - +
191A GLU* 1.3 80.6 - - - +
193A VAL* 1.3 66.6 + - + +
194A ASP 3.6 0.2 - - - -
196A ILE* 5.9 0.7 - - - +
270A LEU* 5.0 9.5 - - + +
271A PRO* 3.7 29.7 - - - +
484A GLU* 5.9 2.8 - - - +
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Residues in contact with VAL 193 (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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189A ILE* 3.0 23.6 + - + +
190A PHE* 3.9 1.8 - - - -
192A LYS* 1.3 89.5 - - + +
194A ASP* 1.3 65.9 + - - +
195A ALA 3.5 2.0 - - - -
196A ILE* 3.0 35.8 + - + +
197A PHE* 4.1 11.4 - - + -
259A ILE* 4.1 27.1 - - + -
270A LEU* 3.9 27.8 - - + -
271A PRO* 4.2 16.6 - - + +
273A PHE* 5.5 2.0 - - + -
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Residues in contact with ASP 194 (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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190A PHE* 3.0 55.3 + - - +
191A GLU* 4.0 13.5 - - - +
192A LYS 3.6 1.4 + - - -
193A VAL* 1.3 77.2 - - - +
195A ALA* 1.3 60.6 + - + +
196A ILE 3.0 6.1 + - - -
197A PHE* 3.3 25.8 + - - +
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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