Contacts of the helix formed by residues 212 - 216 (chain 3) in PDB entry 3EXG
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 ASP 212 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2103 SER* 3.2 15.4 + - - +
2113 THR* 1.3 80.6 + - - +
2133 TYR* 1.3 61.7 + - - +
2143 TYR* 3.5 9.2 - - + -
2153 LYS* 3.3 46.1 + - + +
2163 ARG* 3.5 14.3 + - - +
2243 ARG* 4.0 14.8 + - - +
2543 GLU* 3.9 2.0 - - - -
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Residues in contact with TYR 213 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1653 TYR* 4.8 1.5 + - - +
1673 ASP* 3.8 24.3 + - + +
1703 ALA* 3.5 29.4 - - + -
1933 CYS* 3.9 21.5 - - + -
1953 ASN* 3.7 35.7 - - + -
2053 GLU 4.8 4.5 + - - -
2083 ALA* 3.7 17.8 - - + +
2103 SER 4.2 2.2 - - - -
2113 THR* 3.0 39.3 + - + +
2123 ASP* 1.3 71.7 - - - +
2143 TYR* 1.3 60.7 + - - -
2153 LYS 3.0 1.7 + - - -
2163 ARG* 3.2 41.2 + - + +
2523 LEU* 3.3 14.5 - - - +
2543 GLU* 2.9 19.9 + - + +
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Residues in contact with TYR 214 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133 ASP* 3.5 32.1 - - + +
143 LEU 4.0 14.8 + - - -
153 HIS* 4.0 4.4 - - + +
2123 ASP* 4.4 6.4 - - + -
2133 TYR* 1.3 71.4 - - - +
2153 LYS* 1.3 95.1 + - + +
2163 ARG 3.6 0.2 - - - -
2203 ILE 4.6 1.7 - - - +
2223 GLY* 3.7 34.5 + - - -
2233 LEU 3.8 15.9 - - - +
2243 ARG* 3.4 49.3 + - + -
2523 LEU* 3.8 16.8 - - + +
2533 MET 5.3 0.2 - - - -
2543 GLU* 2.8 39.0 + - + +
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Residues in contact with LYS 215 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143 LEU 5.7 0.7 - - - +
153 HIS* 3.2 47.5 + - + +
2123 ASP* 3.3 41.1 + - + +
2133 TYR 3.0 1.0 - - - -
2143 TYR* 1.3 103.1 + - + +
2163 ARG* 1.3 57.0 + - - +
2173 GLY* 2.9 6.7 - - - -
2183 ASP* 2.9 23.4 + - - -
2185 ASP* 5.1 6.5 - - - +
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Residues in contact with ARG 216 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1653 TYR* 5.7 0.4 - - - +
1703 ALA* 3.2 16.6 + - + +
1713 ASN* 2.5 31.7 + - - -
1763 PHE* 3.6 42.1 - - + -
1793 TYR* 3.6 14.5 - - + +
2083 ALA* 4.3 3.6 - - - +
2093 ALA 5.6 0.2 - - - +
2103 SER* 3.1 36.6 + - - +
2123 ASP 3.5 13.9 - - - +
2133 TYR* 3.2 37.8 + - + +
2153 LYS* 1.3 73.2 - - - +
2173 GLY* 1.3 63.5 + - - +
2183 ASP* 3.1 3.4 + - - +
1805 ASN* 5.0 3.8 + - - +
2185 ASP* 4.0 20.8 + - - +
2195 PHE* 4.3 17.0 - - - -
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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