Contacts of the helix formed by residues 1026 - 1030 (chain B) in PDB entry 3PT6
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 ARG1026 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994B PRO* 3.2 26.4 + - - +
995B TYR* 2.6 36.4 + - - +
996B ARG* 5.4 0.8 - - - +
997B ILE* 3.6 20.8 - - + +
1024B PHE 3.6 3.3 + - - +
1025B TYR* 1.3 75.5 - - - +
1027B PRO* 1.3 71.9 - - + +
1028B GLU* 3.4 32.5 + - - +
1029B ASN* 2.8 36.7 + - - +
1030B THR* 3.7 5.9 - - - +
1042B ILE 4.6 7.3 + - - -
1045B LEU* 3.8 16.1 - - + +
1086B PHE* 4.2 11.1 - - - -
1364B PRO 2.9 29.3 + - - -
1365B PHE* 4.3 4.4 - - - +
1366B ARG* 4.8 1.8 - - - +
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Residues in contact with PRO1027 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025B TYR 4.2 1.8 - - - +
1026B ARG* 1.3 86.6 - - + +
1028B GLU* 1.3 65.3 + - - +
1030B THR* 3.1 23.0 + - - -
1032B ARG* 4.3 2.9 - - - +
1033B SER 3.8 6.4 + - - +
1036B GLY 5.3 1.3 - - - +
1037B SER* 3.6 21.2 - - - -
1040B THR* 3.7 20.0 - - + +
1041B ASP 5.1 1.8 - - - +
1044B MET* 3.1 48.5 - - + +
1045B LEU* 4.6 0.9 - - - -
1046B TYR* 3.9 18.8 - - + -
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Residues in contact with GLU1028 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994B PRO* 4.5 6.2 - - - +
1026B ARG* 3.0 37.5 + - - +
1027B PRO* 1.3 86.9 - - - +
1029B ASN* 1.3 64.7 + - - +
1030B THR 3.2 5.6 + - - +
1033B SER* 3.5 27.2 + - - +
1034B TYR* 4.3 30.0 - - + -
1037B SER* 4.0 13.9 - - - +
1040B THR* 5.7 0.3 + - - -
1366B ARG* 4.4 35.9 + - - +
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Residues in contact with ASN1029 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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952B PHE* 3.2 46.7 - - + +
954B ILE* 5.0 4.3 - - - +
993B GLU* 4.2 17.0 + - - -
996B ARG* 4.3 5.3 + - - +
1025B TYR* 2.8 29.6 - - + -
1026B ARG* 2.8 37.3 + - - +
1028B GLU* 1.3 85.9 + - - +
1030B THR* 1.3 60.9 + - - +
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Residues in contact with THR1030 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025B TYR* 3.9 4.3 - - + -
1026B ARG 3.7 14.8 - - - +
1027B PRO* 3.1 12.9 + - - +
1028B GLU 3.2 4.4 - - - +
1029B ASN* 1.3 83.5 - - - +
1031B HIS* 1.3 63.6 + - - +
1032B ARG* 3.0 20.3 + - - +
1033B SER* 3.2 10.7 + - - -
1046B TYR* 4.0 20.8 - - + -
1092B TYR* 3.5 40.8 - - + -
1099B PHE* 4.4 6.0 - - + -
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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