Contacts of the helix formed by residues 152 - 164 (chain D) in PDB entry 2DRP
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 ARG 152 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128D ARG* 3.6 37.6 - - + +
132D THR* 4.9 13.2 - - + +
141D TYR* 4.4 2.0 - - - -
150D PHE* 4.1 4.3 - - - +
151D THR* 1.3 86.2 + - - +
153D LYS* 1.3 60.4 + - - +
154D ASP* 2.8 35.2 + - - +
155D ASN* 2.8 39.7 + - - +
156D MET 3.2 8.1 + - - -
7E A 3.4 30.6 + - - +
8E G 2.8 50.9 + - - -
31F T 6.3 0.2 - - + -
32F C 3.5 5.3 - - - +
33F C 3.9 1.4 - - - +
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Residues in contact with LYS 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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141D TYR* 3.9 42.4 - - + -
152D ARG* 1.3 71.4 - - - +
154D ASP* 1.3 53.9 + - - +
156D MET* 3.1 13.7 + - + +
157D THR* 2.7 49.2 + - - +
30F A 5.0 19.5 + - - +
31F T 3.3 26.5 + - - +
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Residues in contact with ASP 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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152D ARG* 2.8 52.6 + - - +
153D LYS* 1.3 76.1 + - - +
155D ASN* 1.3 64.2 + - - +
157D THR* 3.7 8.1 - - - +
158D ALA* 3.2 21.8 + - - +
31F T 3.9 28.2 - - + +
32F C 3.0 28.9 + - + +
33F C 4.2 2.9 + - - -
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Residues in contact with ASN 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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150D PHE* 4.3 13.8 - - + -
151D THR* 5.6 1.6 + - - -
152D ARG* 2.8 29.9 + - + +
154D ASP* 1.3 81.8 - - - +
156D MET* 1.3 59.9 + - - +
158D ALA* 3.2 8.2 + - - +
159D HIS* 2.8 28.4 + - - +
5E T 6.1 0.7 - - + -
6E A 3.7 22.2 + - + +
7E A 2.9 51.2 + - - -
33F C 4.7 1.2 + - - -
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Residues in contact with MET 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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141D TYR* 3.6 31.4 - - + +
142D PRO 3.9 12.8 - - - +
143D CYS* 4.0 9.9 - - + -
144D PRO* 4.4 6.1 - - + -
150D PHE* 3.3 45.4 - - + -
152D ARG 3.2 4.0 + - - +
153D LYS* 3.1 18.3 + - + +
155D ASN* 1.3 76.7 - - - +
157D THR* 1.3 64.4 + - - +
159D HIS* 3.2 3.7 + - - +
160D VAL* 2.8 44.2 + - - +
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Residues in contact with THR 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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153D LYS* 2.7 33.6 + - - +
154D ASP* 3.7 9.3 - - - +
156D MET* 1.3 84.9 - - - +
158D ALA* 1.3 59.1 + - - +
160D VAL* 3.4 5.8 + - - +
161D LYS* 2.9 44.3 + - + +
32F C 5.5 9.2 - - - +
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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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136A ARG* 4.5 14.8 - - - +
154D ASP 3.2 11.8 + - - +
155D ASN* 3.2 10.7 + - - +
157D THR* 1.3 77.6 - - - +
159D HIS* 1.3 68.1 + - - +
161D LYS* 3.1 8.2 + - - +
162D ILE* 2.9 32.2 + - + +
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Residues in contact with HIS 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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136A ARG* 5.1 2.9 - - - +
143D CYS* 3.6 10.5 - - + -
146D CYS* 3.6 7.7 - - - -
148D LYS* 4.8 2.7 - - - -
150D PHE* 3.2 32.3 - + + -
155D ASN 2.8 11.4 + - - +
156D MET 3.3 6.7 - - - +
158D ALA* 1.3 75.9 - - - +
160D VAL* 1.3 60.0 + - + +
162D ILE* 5.2 0.2 - - - -
163D ILE* 2.7 70.2 + - + +
164D HIS* 3.1 2.0 + - - -
174D ZN 2.0 37.8 - - - -
5E T 2.9 36.0 + - - +
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Residues in contact with VAL 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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143D CYS* 3.6 29.8 - - - -
144D PRO* 4.3 5.2 - - + -
145D PHE* 3.8 27.6 - - + -
156D MET* 2.8 34.5 + - - +
157D THR* 3.5 7.0 - - - +
159D HIS* 1.3 78.1 - - + +
161D LYS* 1.3 67.4 + - + +
164D HIS* 3.0 30.8 + - - +
165D LYS 3.6 0.9 + - - -
166D ILE* 4.3 12.7 + - + -
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Residues in contact with LYS 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 THR* 2.9 35.3 + - + +
158D ALA* 3.1 6.5 + - - +
160D VAL* 1.3 77.9 - - + +
162D ILE* 1.3 64.7 + - + +
165D LYS* 3.1 24.3 - - - -
166D ILE* 3.9 26.7 + - + +
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Residues in contact with ILE 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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136A ARG* 3.4 64.2 - - + +
137A ASN* 5.1 8.3 - - - +
158D ALA* 2.9 19.2 + - + +
161D LYS* 1.3 83.3 - - + +
163D ILE* 1.3 73.4 + - + +
165D LYS* 3.5 7.4 + - - -
4E A 4.2 8.7 - - - +
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Residues in contact with ILE 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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136A ARG* 3.6 26.9 - - - +
159D HIS* 2.7 52.2 + - + +
162D ILE* 1.3 79.5 - - + +
164D HIS* 1.3 74.2 + - + +
165D LYS 3.5 0.5 + - - -
4E A 3.9 22.2 - - - +
5E T 3.8 15.3 - - - +
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Residues in contact with HIS 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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143D CYS* 3.3 6.1 - - - -
145D PHE* 3.6 48.5 - + + +
146D CYS* 4.0 5.4 - - + -
159D HIS* 3.1 8.4 + - - -
160D VAL* 3.0 19.4 + - - +
163D ILE* 1.3 89.1 + - + +
165D LYS* 1.3 66.1 + - - +
166D ILE* 2.8 11.2 + - + +
174D ZN 2.0 37.4 - - - -
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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
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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