Contacts of the helix formed by residues 143 - 148 (chain A) in PDB entry 5DGY
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 MET 143 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A LYS 3.3 1.0 - - - -
142A PRO* 1.3 80.6 - - - +
144A SER* 1.3 62.8 + - - +
145A ASN 3.2 0.9 + - - -
146A PHE* 3.2 30.5 + - + +
147A ARG* 3.5 42.5 + - - +
1133A LEU* 4.3 21.1 - - + -
1144A CYS* 5.7 1.6 - - - -
1248A VAL* 4.6 11.0 - - + +
1256A TYR* 3.5 54.1 - - + +
1293A GLY* 4.9 17.0 - - - +
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Residues in contact with SER 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 2.7 27.9 + - - -
138A VAL* 3.3 12.8 - - - +
141A LYS* 2.6 30.2 + - - +
143A MET* 1.3 75.6 - - - +
145A ASN* 1.3 64.3 + - - +
147A ARG* 3.2 21.9 + - - +
148A PHE* 3.0 26.7 + - - +
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Residues in contact with ASN 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 5.3 2.8 - - - +
138A VAL* 3.2 45.0 + - - +
142A PRO* 3.1 24.0 + - - +
143A MET 3.1 0.6 - - - -
144A SER* 1.3 79.5 + - - +
146A PHE* 1.3 62.2 + - - +
148A PHE* 3.7 14.9 + - - +
1068A TYR* 3.2 30.9 - - + -
1069A GLY* 3.9 25.8 - - - +
1073A ILE* 5.6 2.8 - - - +
1074A ASP* 6.0 0.2 - - - -
1142A LYS* 5.1 4.6 - - - +
1143A SER 5.6 0.2 - - - +
1144A CYS* 5.5 2.7 - - + -
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Residues in contact with PHE 146 (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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142A PRO 5.5 0.2 - - - -
143A MET* 3.2 21.2 + - + +
145A ASN* 1.3 79.0 - - - +
147A ARG* 1.3 68.4 + - - +
148A PHE 3.3 4.5 + - - -
149A GLY* 4.3 1.9 + - - -
1133A LEU* 3.8 40.8 - - + -
1134A GLN 4.7 2.5 - - - -
1135A PRO* 3.9 20.4 - - + -
1139A ASP* 4.4 17.3 - - - +
1142A LYS* 3.4 43.1 - - + +
1143A SER* 3.8 2.7 - - - -
1144A CYS* 3.5 43.7 - - + -
1292A ARG* 4.9 15.2 + - + -
1293A GLY* 5.8 5.4 - - - -
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Residues in contact with ARG 147 (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 MET* 3.5 37.8 - - - +
144A SER* 3.2 26.0 + - - +
146A PHE* 1.3 81.9 - - - +
148A PHE* 1.3 58.8 + - + +
149A GLY* 2.8 10.2 + - - -
152A HIS* 3.0 31.0 + - + +
1256A TYR* 4.8 13.3 + - - -
1292A ARG* 4.9 10.1 + - - +
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Residues in contact with PHE 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PRO* 3.4 51.2 - - + +
72A LEU* 3.5 26.2 - - + -
134A GLU* 3.3 37.7 - - + -
137A VAL* 6.4 0.9 - - + -
138A VAL* 4.7 12.6 - - + -
144A SER 3.0 14.7 + - - +
145A ASN* 3.7 10.8 + - - +
146A PHE 3.2 4.5 - - - +
147A ARG* 1.3 73.3 - - + +
149A GLY* 1.3 59.3 + - - +
152A HIS* 3.6 20.6 - + + -
153A ALA* 3.7 26.2 - - + -
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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