Contacts of the helix formed by residues 152 - 164 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A ARG* 3.6 37.6 - - + +
132A THR* 4.5 13.2 - - + -
141A TYR* 4.4 2.9 - - - -
150A PHE* 3.3 4.1 - - - +
151A THR* 1.3 91.2 + - - +
153A LYS* 1.3 56.9 + - - +
154A ASP* 2.9 31.3 + - - +
155A ASN* 2.7 44.2 + - - +
156A MET* 3.0 10.2 + - - +
7B A 3.4 26.2 + - - +
8B G 2.7 53.5 + - - -
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Residues in contact with LYS 153 (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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141A TYR* 3.4 52.8 - - + -
152A ARG* 1.3 70.5 - - - +
154A ASP* 1.3 56.6 + - - +
156A MET* 3.3 12.8 + - + +
157A THR* 2.8 40.7 + - - +
30C A 3.9 30.0 + - - +
31C T 3.4 24.1 + - - -
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Residues in contact with ASP 154 (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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152A ARG* 2.9 54.8 + - - +
153A LYS* 1.3 75.7 - - - +
155A ASN* 1.3 69.0 + - - +
157A THR* 3.3 7.2 + - - -
158A ALA* 3.1 21.3 + - - +
161A LYS* 5.7 0.2 + - - -
31C T 3.8 27.4 - - + +
32C C 3.0 28.0 + - + -
33C C 4.1 1.6 + - - -
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Residues in contact with ASN 155 (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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150A PHE* 4.3 17.7 - - + -
151A THR* 5.8 0.8 + - - +
152A ARG* 2.7 36.3 + - + +
154A ASP* 1.3 79.2 + - - +
156A MET* 1.3 57.7 + - - +
158A ALA* 2.9 10.6 + - - +
159A HIS* 2.8 28.1 + - - +
6B A 3.7 22.4 - - + +
7B A 3.0 47.0 + - - +
33C C 4.9 0.7 + - - -
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Residues in contact with MET 156 (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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141A TYR* 3.5 34.3 - - + +
142A PRO 4.1 7.9 - - - +
143A CYS* 4.1 11.4 - - + -
144A PRO* 4.0 25.8 - - + -
150A PHE* 3.7 36.1 - - + -
152A ARG 3.0 7.2 + - - +
153A LYS* 3.7 22.4 - - + +
155A ASN* 1.3 76.7 - - - +
157A THR* 1.3 66.5 + - - +
159A HIS* 3.4 2.1 + - - +
160A VAL* 3.0 28.5 + - - +
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Residues in contact with THR 157 (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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153A LYS* 2.8 33.4 + - - +
154A ASP* 3.7 7.3 - - - -
156A MET* 1.3 82.9 - - - +
158A ALA* 1.3 62.9 + - - +
160A VAL* 3.6 5.8 + - + +
161A LYS* 3.0 53.7 + - + +
32C C 6.0 0.7 - - - +
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Residues in contact with ALA 158 (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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154A ASP 3.1 12.6 + - - +
155A ASN* 2.9 13.3 + - - +
157A THR* 1.3 75.4 - - - +
159A HIS* 1.3 66.1 + - - +
161A LYS* 3.1 18.2 + - - +
162A ILE* 2.9 31.4 + - + +
5B T 6.3 2.5 - - + -
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Residues in contact with HIS 159 (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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143A CYS* 3.7 10.5 - - - -
146A CYS* 3.4 9.9 - - - -
148A LYS* 4.4 1.8 - - + -
150A PHE* 3.3 32.3 - + + -
155A ASN 2.8 9.9 + - - +
156A MET 3.5 7.2 - - - +
158A ALA* 1.3 74.6 - - - +
160A VAL* 1.3 73.7 + - + +
162A ILE* 2.9 11.9 + - - +
163A ILE* 2.8 56.1 + - + +
164A HIS* 3.2 1.4 + - - -
172A ZN 2.0 36.7 - - - -
5B T 3.0 35.8 + - - +
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Residues in contact with VAL 160 (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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143A CYS* 3.7 13.7 - - - -
144A PRO* 3.6 32.8 - - + -
145A PHE* 3.9 19.5 - - + -
156A MET* 3.0 22.4 + - - +
157A THR* 3.7 8.7 - - + +
159A HIS* 1.3 83.9 - - + +
161A LYS* 1.3 62.1 + - + +
164A HIS* 3.0 14.5 + - - +
165A LYS 3.0 31.4 + - - +
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Residues in contact with LYS 161 (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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154A ASP 5.7 0.4 + - - -
157A THR* 3.0 44.4 + - + +
158A ALA* 3.1 14.4 + - - +
159A HIS 3.1 0.8 - - - -
160A VAL* 1.3 84.5 - - + +
162A ILE* 1.3 63.0 + - + +
164A HIS 4.2 2.6 - - - +
165A LYS* 4.1 22.2 - - - +
32C C 4.6 12.3 + - - -
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Residues in contact with ILE 162 (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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158A ALA* 2.9 17.4 + - + +
159A HIS* 2.9 16.9 + - - +
161A LYS* 1.3 81.1 - - + +
163A ILE* 1.3 78.8 + - + +
164A HIS 3.5 4.2 + - - +
4B A 4.2 45.7 + - + +
5B T 4.4 18.4 - - + +
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Residues in contact with ILE 163 (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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146A CYS* 5.7 0.4 - - - -
159A HIS* 2.8 48.2 + - + +
162A ILE* 1.3 76.2 - - + +
164A HIS* 1.3 83.3 + - + +
4B A 3.7 42.6 - - - +
5B T 3.8 6.1 - - - +
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Residues in contact with HIS 164 (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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143A CYS* 3.4 3.2 - - - -
145A PHE* 3.6 46.2 - + + +
146A CYS* 4.1 10.1 - - + -
159A HIS* 3.2 8.1 + - - -
160A VAL* 3.0 19.0 + - - +
161A LYS 4.2 3.3 - - - +
162A ILE 4.0 5.0 - - - +
163A ILE* 1.3 97.3 + - + +
165A LYS* 1.3 60.2 + - - +
172A ZN 2.0 37.1 - - - -
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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