Contacts of the helix formed by residues 152 - 161 (chain D) in PDB entry 1A9B
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 VAL 152 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97D ARG* 4.9 4.0 - - - +
133D TRP* 4.1 9.6 - - + -
147D TRP* 2.9 39.0 + - + +
150D ALA* 4.0 7.0 - - + +
151D ARG* 1.3 73.9 - - - +
153D ALA* 1.3 68.4 + - - +
155D GLN* 3.0 18.1 + - + +
156D LEU* 2.9 43.1 + - + +
7F THR* 3.8 30.7 - - - +
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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
----------------------------------------------------------
126D LEU* 4.2 6.4 - - + +
130D LEU 3.5 11.1 - - - +
131D SER* 3.6 31.9 - - - +
133D TRP* 3.8 28.6 - - + +
147D TRP 4.0 2.1 + - - +
148D GLU* 6.1 2.2 - - + -
151D ARG* 5.1 1.3 - - - -
152D VAL* 1.3 79.4 - - - +
154D GLU* 1.3 65.1 + - + +
156D LEU* 3.3 4.0 + - - +
157D ARG* 3.0 19.7 + - - +
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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
----------------------------------------------------------
151D ARG* 2.8 64.2 + - + +
152D VAL 3.2 0.6 - - - -
153D ALA* 1.3 77.4 - - + +
155D GLN* 1.3 64.9 + - + +
157D ARG* 3.3 32.6 + - - +
158D ALA* 3.2 21.5 + - - +
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Residues in contact with GLN 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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155A GLN* 5.7 4.4 - - - +
150D ALA 4.6 7.0 + - - +
151D ARG* 3.3 16.6 - - + +
152D VAL* 3.0 21.7 + - + +
154D GLU* 1.3 77.2 - - + +
156D LEU* 1.3 62.2 + - + +
158D ALA* 3.3 10.5 + - - +
159D TYR* 3.0 21.1 + - - +
6F ILE* 5.4 9.5 - - - +
7F THR* 5.2 2.8 + - - -
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Residues in contact with LEU 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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97D ARG* 4.0 7.0 - - - +
99D TYR* 5.6 7.4 - - + -
114D ASP* 3.4 33.4 - - + +
126D LEU* 4.0 14.8 - - + -
133D TRP* 4.0 18.8 - - + -
152D VAL* 2.9 26.2 + - + +
153D ALA 3.7 4.5 - - - +
155D GLN* 1.3 74.9 - - + +
157D ARG* 1.3 66.3 + - - +
159D TYR* 3.0 16.3 + - + +
160D LEU* 2.9 45.2 + - + +
3F PRO* 5.1 10.5 - - + -
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Residues in contact with ARG 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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129D ASP 4.4 4.9 + - - -
130D LEU* 3.0 59.5 + - + +
131D SER* 3.6 17.4 - - - +
153D ALA* 3.0 7.2 + - - +
154D GLU* 3.3 42.1 + - - +
156D LEU* 1.3 73.5 - - - +
158D ALA* 1.3 65.5 + - - +
160D LEU* 3.8 0.7 - - - +
161D GLU* 3.0 59.8 + - - +
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Residues in contact with ALA 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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151A ARG* 5.5 13.7 - - - +
154D GLU 3.2 10.4 + - - +
155D GLN* 3.3 13.5 - - - +
157D ARG* 1.3 79.8 - - - +
159D TYR* 1.3 61.4 + - - +
161D GLU* 4.1 5.4 - - - +
162D GLY* 3.1 21.0 + - - -
163D LEU 4.2 0.9 + - - -
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Residues in contact with TYR 159 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D MET* 3.7 18.2 - - - +
7D TYR* 4.0 5.0 - - - -
99D TYR* 4.1 9.9 - + - -
155D GLN 3.0 12.0 + - - +
156D LEU* 3.0 15.3 + - + +
158D ALA* 1.3 77.3 - - - +
160D LEU* 1.3 82.1 + - + +
162D GLY 3.3 5.4 + - - -
163D LEU* 3.3 24.8 + - + +
164D CYS* 2.9 54.1 + - + -
167D TRP* 5.9 0.4 - + - +
1F LEU* 2.7 30.7 + - + -
2F PRO 4.9 0.2 - - - -
3F PRO* 3.6 42.7 - - + +
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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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99D TYR* 5.1 2.0 - - + -
100D GLY* 3.8 23.6 - - - +
101D CYS* 4.1 1.1 - - + -
109D LEU* 3.6 19.2 - - + +
112D GLY* 4.0 17.7 - - - -
113D HIS 4.3 9.6 - - - +
114D ASP* 5.7 0.4 - - + -
126D LEU* 5.0 8.3 - - + -
130D LEU* 4.4 4.5 - - + -
156D LEU* 2.9 56.2 + - + +
157D ARG* 4.0 2.7 - - - +
159D TYR* 1.3 85.4 - - + +
161D GLU* 1.3 62.3 + - - +
162D GLY 3.3 0.5 + - - -
164D CYS* 3.4 30.4 - - - +
165D VAL* 3.2 20.3 - - - +
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Residues in contact with GLU 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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108D ARG* 5.6 2.6 - - - +
109D LEU* 3.5 27.6 + - + +
130D LEU* 4.1 5.9 - - + +
157D ARG* 3.0 49.7 + - + +
158D ALA* 4.4 4.0 - - - +
160D LEU* 1.3 75.3 - - - +
162D GLY* 1.3 60.3 + - - +
165D VAL* 3.8 11.1 - - - +
169D ARG* 6.0 0.2 + - - -
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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