Contacts of the helix formed by residues 147 - 161 (chain D) in PDB entry 3IT8
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 LEU 147 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D PHE* 4.2 21.8 - - + +
71D SER* 6.2 0.4 - - - +
72D LEU* 4.3 26.5 - - + -
75D GLU* 5.3 4.5 - - - +
145D ASN* 2.5 19.7 + - - +
146D THR* 1.3 85.2 - - + +
148D TRP* 1.3 54.0 + - - +
149D LYS* 3.1 3.8 - - - -
150D ASP* 2.7 47.6 + - - +
151D VAL* 3.2 11.4 + - - +
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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
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120D TYR* 4.1 11.2 - + - -
125D LYS 3.6 19.5 + - - -
126D ARG* 4.0 8.1 - - + -
127D PHE* 3.7 28.9 - + - -
140D MET 3.4 24.9 - - - -
141D LEU 4.5 2.0 - - - -
142D THR 3.6 18.4 - - - +
143D VAL* 3.5 49.4 - - + +
145D ASN* 3.1 20.4 + - + +
146D THR 3.4 0.6 - - - -
147D LEU* 1.3 76.0 - - - +
149D LYS* 1.3 76.1 + - + +
151D VAL* 2.9 20.2 + - + +
152D LYS* 2.9 60.3 + - + +
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Residues in contact with LYS 149 (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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143D VAL* 4.7 6.8 - - - +
146D THR 5.2 6.5 - - - +
147D LEU 3.0 1.7 + - - -
148D TRP* 1.3 89.9 - - + +
150D ASP* 1.3 63.8 + - - +
152D LYS* 3.5 34.6 + - + +
153D ALA* 3.2 23.0 + - - +
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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
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68D PHE* 3.5 23.7 - - + -
147D LEU* 2.7 39.7 + - - +
149D LYS* 1.3 73.8 - - - +
151D VAL* 1.3 59.0 + - - +
153D ALA* 3.3 4.9 + - - +
154D TYR* 2.8 54.0 + - + +
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Residues in contact with VAL 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D PHE* 4.4 0.7 - - + -
69D TRP* 4.2 21.8 - - + -
72D LEU* 3.7 31.2 - - + -
120D TYR* 5.2 1.8 - - + -
127D PHE* 4.3 10.5 - - + -
140D MET* 4.3 13.5 - - + +
145D ASN* 6.4 0.2 - - - -
147D LEU 3.2 9.1 + - - +
148D TRP* 2.9 39.5 + - + +
150D ASP* 1.3 75.5 - - - +
152D LYS* 1.3 58.9 + - - +
155D LEU* 2.8 41.8 + - + +
156D GLY 3.4 0.2 + - - -
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Residues in contact with LYS 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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86B SER 5.3 0.7 - - - +
120D TYR* 3.8 20.8 + - - +
125D LYS* 3.9 29.5 - - + +
143D VAL* 5.3 1.6 - - - +
148D TRP* 2.9 47.2 + - + +
149D LYS* 3.5 36.3 - - + +
151D VAL* 1.3 76.9 - - - +
153D ALA* 1.3 58.1 + - - +
156D GLY* 2.9 29.1 + - - +
157D GLY 3.1 3.1 + - - -
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Residues in contact with ALA 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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86B SER 5.9 0.4 - - - -
87B TYR* 5.4 1.9 - - - -
149D LYS 3.2 15.4 + - - +
150D ASP* 3.7 7.6 - - - +
151D VAL 3.2 0.2 - - - -
152D LYS* 1.3 80.2 - - - +
154D TYR* 1.3 67.4 + - + +
157D GLY* 3.1 24.2 + - - +
158D PHE 4.2 0.3 + - - -
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Residues in contact with TYR 154 (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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62D ASN* 5.0 4.0 + - - -
65D ASN* 3.5 37.6 + - + +
68D PHE* 3.7 42.4 - + + -
69D TRP* 3.7 18.8 - - + +
150D ASP* 2.8 39.7 + - + +
153D ALA* 1.3 83.0 - - + +
155D LEU* 1.3 61.6 + - - +
158D PHE* 3.3 21.3 + - - +
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Residues in contact with LEU 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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69D TRP* 3.9 17.5 - - + -
93D LEU* 4.3 21.8 - - + -
95D THR* 3.6 33.0 - - + +
108D GLY* 4.1 12.3 - - - +
120D TYR* 3.9 22.0 - - + -
127D PHE* 3.6 32.1 - - + -
151D VAL* 2.8 23.1 + - + +
154D TYR* 1.3 72.0 - - - +
156D GLY* 1.3 66.9 + - - +
158D PHE* 3.4 2.9 + - - +
159D GLU* 3.0 26.2 + - - +
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Residues in contact with GLY 156 (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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86B SER* 4.3 2.5 - - - -
120D TYR* 3.3 30.4 - - - -
122D THR* 4.1 2.1 + - - -
151D VAL 3.4 1.6 + - - -
152D LYS* 2.9 16.0 + - - +
155D LEU* 1.3 79.7 - - - +
157D GLY* 1.3 51.9 + - - +
159D GLU* 3.3 2.1 + - - +
160D TYR* 2.7 38.8 + - - +
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Residues in contact with GLY 157 (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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86B SER 3.2 20.8 + - - -
87B TYR* 3.4 18.3 - - - -
152D LYS 3.1 9.7 + - - -
153D ALA* 3.1 14.9 + - - -
156D GLY* 1.3 76.6 - - - +
158D PHE* 1.3 62.1 + - - +
160D TYR* 3.1 1.6 + - - +
161D MET 3.0 19.9 + - - -
162D GLY 3.2 5.5 + - - -
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Residues in contact with PHE 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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87B TYR* 4.5 2.4 - - - -
3D LEU* 4.6 2.0 - - + -
5D TYR* 3.1 49.8 - + - -
58D HIS 4.1 9.6 - - - -
60D PRO* 4.1 22.0 - - + -
95D THR* 3.7 28.5 - - + -
96D GLY* 4.3 4.0 - - - -
153D ALA 4.2 0.2 + - - -
154D TYR 3.3 20.6 + - - +
155D LEU* 3.4 4.2 + - - +
156D GLY 3.4 0.2 - - - -
157D GLY* 1.3 73.3 - - - +
159D GLU* 1.3 63.1 + - - +
161D MET 3.6 0.3 + - - -
162D GLY* 3.3 9.5 + - - +
163D CYS* 2.8 78.7 + - + +
164D SER 4.6 0.2 + - - -
166D ALA* 4.8 2.2 - - + -
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Residues in contact with GLU 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D THR* 4.7 3.4 - - - +
96D GLY 5.8 0.2 - - - -
106D SER* 2.7 42.0 + - - +
107D TYR* 3.6 22.3 - - - +
108D GLY* 3.3 28.9 + - - -
120D TYR* 3.2 38.8 - - - +
122D THR* 4.2 13.5 + - - +
155D LEU* 3.0 17.3 + - - +
156D GLY* 3.7 3.4 - - - +
158D PHE* 1.3 79.3 - - - +
160D TYR* 1.3 63.5 + - - +
161D MET* 3.5 0.5 + - - -
163D CYS* 5.2 0.7 - - - -
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Residues in contact with TYR 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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82B ARG* 3.3 29.0 + - - -
84B ALA* 4.1 5.6 - - + -
86B SER* 3.7 27.1 - - - +
87B TYR* 4.1 5.2 - - + -
125B GLN 5.5 0.3 + - - -
127B GLU* 3.2 43.5 - - + +
122D THR* 3.3 35.0 + - + +
156D GLY 2.7 21.2 + - - +
157D GLY 3.1 4.2 + - - +
159D GLU* 1.3 76.6 - - - +
161D MET* 1.3 77.8 + - + +
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Residues in contact with MET 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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33A ALA* 4.9 9.2 - - + +
34A ASN* 3.7 17.0 - - - +
82B ARG* 3.2 34.5 - - - +
84B ALA* 4.9 4.3 - - + -
87B TYR* 4.1 12.6 - - + -
91B VAL* 4.0 26.7 - - + -
157D GLY 3.0 3.2 + - - -
158D PHE 3.8 0.2 - - - -
159D GLU 3.4 1.8 - - - -
160D TYR* 1.3 98.7 - - + +
162D GLY* 1.3 70.2 + - - +
163D CYS 3.3 2.7 - - - -
164D SER* 2.7 30.0 + - - +
165D LEU* 3.1 28.7 + - + +
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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