Contacts of the helix formed by residues 182 - 199 (chain A) in PDB entry 1DI8
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 THR 182 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A HIS* 3.3 57.3 + - + +
122A ARG* 5.6 2.9 - - - -
124A LEU* 3.1 28.6 - - + +
181A SER* 1.3 77.2 - - - +
183A ALA* 1.3 64.1 + - - +
184A VAL* 3.1 0.4 - - - -
185A ASP* 3.0 14.7 + - - +
186A ILE* 3.7 3.4 + - - +
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Residues in contact with ALA 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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172A GLU* 4.5 0.4 - - - +
181A SER* 3.0 16.2 + - - +
182A THR* 1.3 82.3 + - - +
184A VAL* 1.3 60.6 + - - +
185A ASP 3.2 0.2 - - - -
186A ILE* 3.3 11.2 + - - -
187A TRP 3.2 13.5 + - - -
271A PRO* 3.5 28.9 - - + +
274A ARG* 2.8 37.2 + - + +
275A ILE 6.0 0.4 - - - +
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Residues in contact with VAL 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 5.2 0.9 - - + -
126A ARG* 4.3 24.2 - - + -
170A ALA* 4.1 8.3 + - + +
172A GLU* 3.7 15.5 - - - +
173A ILE* 3.9 24.5 - - + -
180A TYR* 3.5 31.6 - - + -
181A SER 3.1 15.0 + - - +
183A ALA* 1.3 78.6 - - - +
185A ASP* 1.3 76.4 + - - +
187A TRP* 3.5 3.8 + - - +
188A SER* 3.2 25.1 + - - -
274A ARG* 4.0 4.7 - - - +
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Residues in contact with ASP 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 4.0 16.4 - - + +
119A HIS* 2.8 29.0 + - + +
124A LEU* 3.6 4.1 - - - +
125A HIS* 2.9 31.9 + - - +
126A ARG* 2.8 29.2 + - - -
127A ASP 4.6 0.2 + - - -
128A LEU* 3.9 8.5 + - + +
182A THR 3.0 9.4 + - - +
184A VAL* 1.3 81.4 - - - +
186A ILE* 1.3 59.8 + - - +
188A SER* 3.4 7.2 + - - -
189A LEU* 3.0 29.5 + - - +
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Residues in contact with ILE 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 4.3 13.0 - - + -
115A LEU* 4.5 9.4 - - + -
119A HIS* 4.7 5.8 - - + -
182A THR 3.7 10.1 + - - +
183A ALA* 3.3 13.0 + - - +
185A ASP* 1.3 78.3 - - - +
187A TRP* 1.3 56.4 + - - +
189A LEU* 3.3 4.3 + - - +
190A GLY* 2.8 25.3 + - - -
266A MET* 3.7 38.1 - - + +
274A ARG* 4.1 4.9 - - + -
275A ILE* 3.3 26.0 - - + +
276A SER* 4.2 1.6 - - - -
277A ALA* 3.7 37.7 - - + +
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Residues in contact with TRP 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A TRP 5.2 0.6 + - - -
168A TYR 3.6 12.3 + - - -
169A ARG 3.4 11.7 + - - -
170A ALA* 3.5 17.0 - - + -
171A PRO* 3.4 37.9 - - + -
183A ALA 3.2 3.2 + - - -
184A VAL 3.6 9.6 - - - +
185A ASP 3.2 0.2 - - - -
186A ILE* 1.3 78.6 - - - +
188A SER* 1.3 65.1 + - - +
190A GLY* 2.9 11.6 + - - -
191A CYS* 3.0 24.9 + - - -
203A PHE* 4.0 15.4 - + - -
211A GLN* 6.2 0.2 - - - +
215A ILE* 3.9 19.8 - - + +
219A LEU* 3.6 23.1 - - + -
266A MET 3.7 10.5 + - - -
267A LEU* 3.4 42.8 - - + +
268A HIS 4.1 5.4 - - - -
269A TYR* 4.9 2.5 - + - -
274A ARG* 3.8 28.9 - - - +
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Residues in contact with SER 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ARG 5.6 2.6 - - - -
127A ASP* 5.6 1.4 + - - -
128A LEU* 3.8 28.0 + - - +
168A TYR* 2.5 37.2 + - - +
169A ARG* 4.8 0.2 - - - -
170A ALA 4.9 0.5 + - - -
184A VAL 3.2 11.9 + - - -
185A ASP* 3.7 8.9 + - - -
186A ILE 3.4 0.2 - - - -
187A TRP* 1.3 79.0 - - - +
189A LEU* 1.3 62.3 + - - +
191A CYS* 3.1 5.4 + - - +
192A ILE* 3.0 27.9 + - - +
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Residues in contact with LEU 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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108A LEU* 3.9 13.5 - - + -
111A LEU* 3.7 37.0 - - + -
112A LEU* 3.6 37.2 - - + -
115A LEU* 3.7 17.9 - - + -
128A LEU* 4.7 9.3 - - + +
133A LEU* 5.2 0.9 - - + -
185A ASP 3.0 17.4 + - - +
186A ILE* 3.6 5.6 - - + +
188A SER* 1.3 76.0 - - - +
190A GLY* 1.3 64.4 + - - +
192A ILE* 3.2 18.8 + - + +
193A PHE* 2.9 25.1 + - - +
266A MET* 3.9 11.0 - - + -
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Residues in contact with GLY 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 ILE 2.8 15.3 + - - -
187A TRP 2.9 5.3 + - - -
189A LEU* 1.3 78.4 - - - +
191A CYS* 1.3 60.2 + - - +
193A PHE* 3.4 1.8 - - - +
194A ALA* 3.1 19.1 + - - +
263A LEU* 3.3 27.6 - - - +
266A MET* 3.8 17.7 - - - +
267A LEU* 4.4 5.4 - - - -
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Residues in contact with CYS 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A TRP 4.1 10.8 - - - +
168A TYR* 3.7 19.5 - - + -
187A TRP* 3.0 43.0 + - - -
188A SER 3.1 7.6 + - - +
190A GLY* 1.3 75.2 - - - +
192A ILE* 1.3 64.8 + - - +
194A ALA* 3.5 2.9 + - - +
195A GLU* 3.1 24.1 + - - +
202A LEU* 4.3 17.2 + - + +
203A PHE* 4.1 23.3 - - - -
267A LEU* 4.3 5.4 - - - -
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Residues in contact with ILE 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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87A LEU* 4.2 18.6 - - + -
91A MET* 5.6 1.8 - - - -
128A LEU* 4.4 11.2 - - + -
129A LYS* 4.0 25.1 - - - +
130A PRO* 4.2 7.4 - - + -
133A LEU* 3.8 24.7 - - + -
168A TYR* 3.8 19.5 - - + -
188A SER 3.0 15.7 + - - +
189A LEU* 3.2 17.0 + - + +
191A CYS* 1.3 74.1 - - - +
193A PHE* 1.3 66.5 + - - +
195A GLU* 3.2 7.8 + - + +
196A MET* 2.9 41.4 + - + +
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Residues in contact with PHE 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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104A ILE* 4.1 16.8 - - + -
108A LEU* 3.9 33.9 - - + -
189A LEU 2.9 17.3 + - - +
190A GLY* 3.4 4.7 - - - +
192A ILE* 1.3 76.9 - - - +
194A ALA* 1.3 61.1 + - - +
196A MET* 3.3 12.9 + - + +
197A VAL* 3.3 36.1 + - + +
255A LEU* 3.6 22.9 - - + -
259A GLY 3.8 17.5 - - - -
262A LEU* 4.3 8.7 - - + -
263A LEU* 3.8 22.4 - - + -
266A MET* 4.4 8.3 - - - -
285A PHE* 3.8 25.6 - + - -
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Residues in contact with ALA 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 GLY 3.1 12.6 + - - +
191A CYS 3.8 4.5 - - - +
192A ILE 3.3 0.2 - - - -
193A PHE* 1.3 81.5 - - - +
195A GLU* 1.3 58.4 + - - +
197A VAL* 3.3 4.7 + - - +
198A THR* 3.0 35.8 + - - +
200A ARG 4.7 0.4 - - - -
202A LEU* 4.0 27.4 - - + -
252A VAL* 3.9 24.7 - - + -
255A LEU* 6.2 0.7 - - - -
263A LEU* 4.3 8.3 - - + -
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Residues in contact with GLU 195 (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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88A LYS* 5.0 9.4 - - - +
91A MET* 3.4 25.0 - - + +
130A PRO* 4.5 7.5 - - - +
167A TRP* 5.1 3.1 - - - -
168A TYR* 2.6 39.2 + - - -
191A CYS 3.1 11.9 + - - +
192A ILE* 3.2 10.5 + - - +
194A ALA* 1.3 75.3 - - - +
196A MET* 1.3 60.6 + - - +
199A ARG* 2.7 32.8 + - - -
200A ARG* 3.5 25.6 - - - +
201A ALA* 3.8 20.8 + - - +
202A LEU 4.8 0.6 - - - +
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Residues in contact with MET 196 (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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87A LEU* 4.1 19.1 - - + -
91A MET* 3.7 25.2 - - + +
99A ILE* 4.5 26.0 + - + +
104A ILE* 3.8 48.3 - - + +
107A TYR* 4.8 13.0 - - + -
108A LEU* 4.9 11.2 - - + +
111A LEU* 5.1 5.8 - - + -
189A LEU* 6.0 0.2 - - + -
192A ILE* 2.9 25.5 + - + +
193A PHE* 3.3 23.3 + - - +
195A GLU* 1.3 77.1 - - - +
197A VAL* 1.3 62.5 + - - +
199A ARG* 4.0 10.9 + - - +
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Residues in contact with VAL 197 (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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101A LEU* 5.0 3.1 - - + -
104A ILE* 4.1 19.3 - - + -
193A PHE* 3.3 34.6 + - + +
194A ALA* 3.7 8.3 - - - +
195A GLU 3.2 0.2 - - - -
196A MET* 1.3 79.7 - - - +
198A THR* 1.3 65.3 + - + +
199A ARG* 4.6 7.8 + - - +
252A VAL* 5.1 2.7 - - + -
254A PRO* 3.5 31.7 - - + +
255A LEU* 4.0 31.9 - - + +
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Residues in contact with THR 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ALA 3.0 18.3 + - - +
197A VAL* 1.3 81.9 - - + +
199A ARG* 1.3 72.1 + - - +
200A ARG* 3.2 30.1 + - - +
251A VAL 4.0 8.7 - - - +
252A VAL* 3.9 32.5 - - + -
253A PRO* 4.6 2.2 - - + -
254A PRO* 4.5 10.5 - - + -
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Residues in contact with ARG 199 (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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91A MET* 5.2 5.4 - - + +
95A ALA* 3.2 34.2 + - - +
96A LEU 3.4 17.2 + - - -
97A THR* 3.5 13.3 + - - +
98A GLY* 3.5 25.0 - - - -
99A ILE 5.4 0.4 - - - +
195A GLU* 2.7 22.5 + - - -
196A MET 4.2 10.1 - - - +
197A VAL 3.5 6.4 + - - +
198A THR* 1.3 77.8 + - - +
200A ARG* 1.3 69.4 + - + +
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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
------------------------------------------------------------
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