Contacts of the helix formed by residues 185 - 192 (chain 2) in PDB entry 3EPD
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 LEU 185 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2741 PRO* 4.8 1.8 - - - +
2751 PRO 4.7 1.8 + - - -
2771 ALA* 3.8 18.5 - - + +
2931 PRO* 3.9 22.7 - - + -
2941 LEU* 3.9 30.5 - - + -
1782 TYR* 3.6 17.9 - - + +
1792 LEU* 4.2 11.0 - - + -
1802 LEU* 5.2 0.2 - - - +
1842 VAL* 1.3 79.2 - - - +
1862 LEU* 1.3 65.6 + - - +
1872 GLY* 4.4 5.4 - - - +
1882 ASN* 3.0 34.8 + - - +
1892 ALA 4.0 2.1 + - - -
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Residues in contact with LEU 186 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1252 PHE* 4.4 9.0 - - + -
1772 ASP 3.7 15.5 - - - +
1782 TYR* 2.9 24.9 + - + +
1802 LEU* 3.6 33.8 - - + +
1842 VAL 3.7 1.2 + - - -
1852 LEU* 1.3 70.5 - - - +
1872 GLY* 1.3 62.2 + - - +
1892 ALA* 2.9 27.4 + - - +
1902 PHE* 4.5 6.2 - - + -
2312 LEU* 3.9 24.5 - - + -
2332 LEU* 3.9 25.6 - - + -
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Residues in contact with GLY 187 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1852 LEU* 3.0 5.5 + - - +
1862 LEU* 1.3 83.5 - - - +
1882 ASN* 1.3 62.7 + - - +
1902 PHE* 3.2 27.2 + - - +
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Residues in contact with ASN 188 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2741 PRO* 3.5 24.1 - - + +
2751 PRO* 4.3 20.2 + - - +
1852 LEU* 3.0 24.1 + - - +
1872 GLY* 1.3 77.8 - - - +
1892 ALA* 1.3 60.8 + - - +
1902 PHE* 3.0 7.7 + - - -
1912 VAL* 3.1 28.6 + - + +
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Residues in contact with ALA 189 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2741 PRO* 4.0 4.2 - - - +
1252 PHE* 3.5 29.4 - - + -
1802 LEU* 3.8 29.4 - - + -
1852 LEU 4.0 1.6 + - - -
1862 LEU* 2.9 18.0 + - + +
1882 ASN* 1.3 75.7 - - - +
1902 PHE* 1.3 55.9 + - - +
1912 VAL 3.1 0.7 - - - -
1922 TYR* 2.9 38.5 + - + +
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Residues in contact with PHE 190 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1252 PHE* 3.8 18.6 - + - -
1862 LEU* 4.5 6.7 - - + -
1872 GLY* 3.2 27.1 - - - +
1882 ASN 3.0 1.2 + - - +
1892 ALA* 1.3 78.0 - - - +
1912 VAL* 1.3 58.6 + - + +
1922 TYR 3.1 3.0 - - - +
1942 HIS* 3.2 51.3 + + + -
1962 ILE* 3.9 24.7 - - + -
2332 LEU* 3.8 30.1 - - + -
534 PHE 5.5 3.1 - - - +
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Residues in contact with VAL 191 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2721 PRO* 3.8 39.2 - - + +
2731 ARG 4.0 3.4 - - - +
2741 PRO* 3.9 22.4 - - + -
352 TYR* 4.8 2.1 - - - -
1882 ASN* 3.1 21.3 + - + +
1902 PHE* 1.3 77.0 - - + +
1922 TYR* 1.3 64.3 + - + +
1932 PRO* 4.2 2.6 - - - +
534 PHE* 4.7 14.5 - - - +
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Residues in contact with TYR 192 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2721 PRO 3.4 22.2 - - - -
2731 ARG* 3.3 37.5 + - + +
2741 PRO* 3.4 29.1 - - + +
352 TYR* 4.1 4.3 - - - -
1252 PHE* 4.8 2.2 - - + -
1262 ALA 3.5 11.9 - - - +
1272 ILE* 3.6 41.1 - - + +
1282 PRO* 3.8 24.7 - - + -
1802 LEU* 4.2 7.8 - - + +
1892 ALA* 2.9 25.3 + - + +
1902 PHE 3.4 1.9 - - - +
1912 VAL* 1.3 78.8 - - - +
1932 PRO* 1.3 61.8 - - - +
1942 HIS* 2.8 31.5 + - - +
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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