Contacts of the helix formed by residues 147 - 164 (chain D) in PDB entry 5AIS
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 147 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D LEU* 3.2 22.4 - - - +
78D ALA 4.2 11.0 - - - +
79D GLY* 4.6 3.1 - - - -
80D ASN* 6.1 0.9 - - - +
84D GLU* 5.5 1.6 - - - +
88D VAL* 4.1 19.7 - - + -
142D ILE* 3.9 21.0 - - + +
145D SER* 3.7 10.8 - - - +
146D VAL* 1.3 84.1 - - - +
148D TRP* 1.3 59.0 + - - +
149D ALA* 3.1 20.5 + - - +
150D ASP* 2.9 35.8 + - - +
151D PHE* 3.5 4.3 + - - -
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Residues in contact with TRP 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ILE* 3.7 15.6 - - + +
21D ILE* 4.5 10.3 - - + -
65D LEU* 3.9 24.0 - - + -
68D ALA* 3.6 25.4 - - + -
69D ARG* 4.1 25.6 - - + +
72D THR* 3.5 37.2 + - + -
77D LEU* 3.1 33.1 + - + +
78D ALA* 4.6 4.1 - - - +
88D VAL* 3.4 21.4 - - + +
89D ASP* 4.0 18.8 + - - -
92D VAL* 3.8 33.4 - - + -
147D THR* 1.3 71.5 - - - +
149D ALA* 1.3 59.4 + - - +
150D ASP 3.3 0.4 - - - -
151D PHE* 3.4 15.2 - - + +
152D TYR* 3.0 26.7 + - + +
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Residues in contact with ALA 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D VAL* 4.2 9.6 - - + +
91D ILE* 4.5 8.7 - - + -
92D VAL* 3.8 23.1 - - + -
95D LEU* 4.4 2.9 - - - +
141D LEU* 3.9 4.9 - - + +
142D ILE* 3.4 32.3 - - + -
147D THR* 3.1 5.4 + - - +
148D TRP* 1.3 78.9 - - - +
150D ASP* 1.3 59.5 + - - +
152D TYR* 3.3 2.3 + - - +
153D TRP* 3.0 28.1 + - - +
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Residues in contact with ASP 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D TRP* 3.7 18.5 - - + +
141D LEU* 2.9 37.2 + - - +
142D ILE 4.9 0.2 + - - -
146D VAL* 3.5 12.7 - - + -
147D THR* 2.9 35.5 + - - +
149D ALA* 1.3 72.6 - - - +
151D PHE* 1.3 66.6 + - - +
153D TRP* 3.4 5.5 + - - +
154D GLU 3.1 17.2 + - - -
177D LEU* 3.5 13.7 - - + +
181D VAL* 3.6 26.9 - - + +
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Residues in contact with PHE 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ILE* 3.7 9.6 - - + -
20D TYR* 3.8 32.7 - + + -
21D ILE* 4.5 5.8 - - + -
24D TYR* 3.8 30.1 - + + -
77D LEU* 3.7 33.2 - - + -
146D VAL* 3.8 21.3 - - + -
147D THR 3.5 6.2 + - - -
148D TRP* 3.4 18.8 - - - +
150D ASP* 1.3 79.2 - - - +
152D TYR* 1.3 56.5 + - - +
154D GLU* 3.2 4.9 + - - +
155D ILE* 2.9 33.6 + - - +
181D VAL* 3.9 16.2 - - + -
184D ILE* 3.9 14.4 - - + -
187D VAL* 4.0 11.4 - - + -
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Residues in contact with TYR 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ARG* 5.7 2.4 - - - +
17D ILE* 3.8 32.3 - - + +
64D SER* 5.2 2.0 + - - -
65D LEU* 3.9 18.2 - - + +
92D VAL* 3.6 39.9 - - + -
95D LEU* 3.8 15.3 - - + -
96D ASP* 2.6 32.7 + - + -
148D TRP* 3.0 17.8 + - + +
149D ALA 3.3 5.1 + - - +
151D PHE* 1.3 73.4 - - - +
153D TRP* 1.3 61.0 + - - +
155D ILE* 3.7 6.4 - - + +
156D CYS* 2.8 54.2 + - - -
1200D CWC 2.8 29.8 + + - -
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Residues in contact with TRP 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D LEU* 3.8 21.2 - - + +
128D MET* 3.6 31.4 - - + -
131D LEU* 3.3 30.7 - - + -
141D LEU* 3.9 13.9 - - + -
149D ALA 3.0 13.3 + - - +
150D ASP 3.6 8.1 - - - +
151D PHE 3.3 0.2 - - - -
152D TYR* 1.3 75.5 - - - +
154D GLU* 1.3 54.4 + - + +
156D CYS* 4.8 0.4 - - + -
157D SER* 2.7 64.5 + - - -
160D LEU* 5.3 3.1 - - + -
167D LEU* 4.9 0.4 - - + -
168D LEU* 4.0 11.4 - - + -
174D LEU* 3.2 46.6 + - + +
177D LEU* 3.5 31.3 - - + +
178D ARG* 3.7 9.3 - - + +
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Residues in contact with GLU 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D TYR* 2.6 37.2 + - - -
150D ASP 3.1 10.6 + - - +
151D PHE 3.5 7.4 - - - +
153D TRP* 1.3 81.6 - - + +
155D ILE* 1.3 55.6 + - - +
157D SER* 3.0 14.7 + - - -
158D THR* 2.7 37.5 + - - -
178D ARG* 3.3 17.0 + - - +
181D VAL* 3.8 26.5 - - + -
182D GLN* 2.7 40.0 + - + +
191D ILE* 4.2 3.2 - - - +
194D ARG* 5.3 2.1 + - - -
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Residues in contact with ILE 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ARG* 5.3 5.3 + - + +
13D GLY 4.5 1.3 - - - +
16D GLU* 3.7 25.1 - - + +
17D ILE* 3.4 46.7 - - + +
20D TYR* 3.7 33.0 - - + -
151D PHE 2.9 20.2 + - - +
152D TYR* 3.7 8.7 - - + +
154D GLU* 1.3 75.9 - - - +
156D CYS* 1.3 65.7 + - - +
158D THR* 3.4 13.8 + - - -
159D THR* 3.4 16.2 + - - +
1200D CWC 4.3 20.0 - - + -
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Residues in contact with CYS 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D LEU* 4.2 17.0 - - + -
99D MET* 3.7 36.4 - - + +
152D TYR* 2.8 58.0 + - - +
153D TRP* 4.1 2.9 - - + +
155D ILE* 1.3 74.1 - - - +
157D SER* 1.3 58.0 + - - +
159D THR* 3.3 5.4 + - - -
160D LEU* 3.0 34.6 + - + +
1200D CWC 4.0 7.6 - - - -
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Residues in contact with SER 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D TRP* 2.7 53.4 + - - -
154D GLU* 3.0 4.7 + - - -
156D CYS* 1.3 74.7 - - - +
158D THR* 1.3 58.1 + - - +
160D LEU* 3.8 10.4 - - - +
161D LEU* 2.9 36.3 + - - +
167D LEU* 4.7 2.5 - - - -
168D LEU* 4.6 4.5 - - - -
178D ARG* 2.8 36.5 + - - +
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Residues in contact with THR 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ARG* 3.9 26.2 - - - +
20D TYR* 6.0 0.2 - - - -
154D GLU* 2.7 32.6 + - - -
155D ILE* 3.5 7.6 - - - -
157D SER* 1.3 80.4 + - - +
159D THR* 1.3 60.9 + - - +
161D LEU* 3.5 7.3 + - - +
162D VAL* 3.4 24.2 + - + +
178D ARG* 3.1 17.7 + - - +
182D GLN* 4.7 0.2 + - - -
194D ARG* 4.6 12.7 + - - +
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Residues in contact with THR 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ARG* 3.4 22.8 + - - +
13D GLY 5.5 1.4 + - - -
99D MET* 3.9 15.4 - - + +
104D TRP* 3.8 28.7 - - + -
155D ILE* 3.4 10.1 + - - +
156D CYS 3.3 8.3 + - - -
158D THR* 1.3 75.6 - - - +
160D LEU* 1.3 65.3 + - + +
162D VAL* 3.2 18.8 + - - +
163D PHE* 3.4 15.5 - - + -
199D LEU* 4.4 13.0 + - + -
1200D CWC 4.2 15.0 + - - +
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Residues in contact with LEU 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D LEU* 6.3 1.6 - - + -
98D PHE* 3.8 34.8 - - + -
99D MET* 3.8 23.6 - - + -
102D PHE* 4.0 16.6 - - + -
104D TRP* 6.2 0.9 - - + -
120D LEU* 4.2 11.4 - - + +
124D ALA* 5.6 0.7 - - + -
127D LEU* 5.5 0.7 - - + -
128D MET* 4.5 12.8 - - + -
153D TRP* 5.3 3.1 - - + -
156D CYS* 3.0 25.5 + - + +
157D SER* 3.9 2.5 - - - +
159D THR* 1.3 77.1 - - + +
161D LEU* 1.3 51.2 + - - +
163D PHE* 3.3 5.9 + - + +
164D LYS* 2.8 37.6 + - - +
167D LEU* 3.6 29.6 - - + -
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Residues in contact with LEU 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D SER 2.9 24.6 + - - +
158D THR* 3.7 6.1 - - - +
159D THR 3.3 0.4 - - - -
160D LEU* 1.3 74.2 - - - +
162D VAL* 1.3 65.1 + - - +
164D LYS 3.5 3.4 - - - -
165D PRO* 3.2 48.6 - - + +
167D LEU* 3.7 26.0 - - + +
168D LEU* 4.4 16.2 - - + +
178D ARG* 3.6 36.8 - - - +
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Residues in contact with VAL 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ARG* 4.5 2.5 - - - +
158D THR* 3.4 17.2 + - + +
159D THR* 3.2 11.2 + - - +
160D LEU 3.2 0.8 - - - -
161D LEU* 1.3 79.5 - - - +
163D PHE* 1.3 64.8 + - + +
165D PRO* 4.4 6.2 - - - +
198D LYS* 3.6 59.4 - - + +
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Residues in contact with PHE 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D PHE* 6.1 0.4 - + - -
104D TRP* 3.9 11.7 - + - -
112D LYS* 6.2 1.8 - - - -
116D PHE* 3.7 39.7 - + + -
120D LEU* 3.4 28.7 - - + +
159D THR* 3.4 17.7 - - + -
160D LEU* 3.3 4.9 + - + +
161D LEU 3.3 0.2 - - - -
162D VAL* 1.3 79.3 - - + +
164D LYS* 1.3 60.1 + - - +
165D PRO* 3.6 6.8 - - - +
198D LYS* 3.9 24.2 - - - -
199D LEU* 3.5 36.3 - - + -
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Residues in contact with LYS 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D LEU* 3.1 46.8 + - + +
121D THR* 4.4 13.7 + - - +
124D ALA* 4.5 0.4 - - + -
125D PRO* 4.2 16.7 - - - +
160D LEU 2.8 12.1 + - - +
161D LEU* 3.4 8.5 - - - -
163D PHE* 1.3 78.7 - - - +
165D PRO* 1.3 65.5 - - + +
166D ASP* 3.0 36.5 + - - +
167D LEU* 3.1 42.4 + - + +
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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