Contacts of the helix formed by residues 1026 - 1031 (chain D) in PDB entry 1JPP
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 ASN1026 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354B LYS* 4.2 6.7 - - - +
387B ASN 4.9 0.8 + - - -
390B ASP* 2.9 33.1 + - - +
1024D PRO 4.2 1.2 + - - -
1025D ILE* 1.3 72.7 - - - +
1027D TYR* 1.3 61.2 + - - +
1028D SER* 2.6 33.3 + - - +
1029D LEU* 3.0 37.5 + - + +
1030D LYS* 3.8 8.7 + - - +
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Residues in contact with TYR1027 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B ARG* 3.5 55.7 + - + +
387B ASN* 4.3 5.9 + - - +
389B SER* 4.2 0.2 - - - -
390B ASP* 5.3 1.4 - - - +
422B GLY* 3.6 33.9 + - - -
425B SER* 4.7 3.8 + - - -
426B ASN* 3.7 20.8 + - - -
463B PRO* 4.0 20.2 - - + +
1025D ILE* 2.9 54.7 + - + +
1026D ASN* 1.3 70.2 - - - +
1028D SER* 1.3 66.8 + - - +
1029D LEU 3.2 1.5 + - - -
1030D LYS* 3.5 19.4 + - + +
1031D TYR* 3.6 25.9 + + - +
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Residues in contact with SER1028 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B VAL* 4.1 22.7 + - - +
354B LYS* 3.5 26.3 + - - -
387B ASN* 3.9 24.0 + - - +
1026D ASN* 2.6 36.1 + - - +
1027D TYR* 1.3 80.1 - - - +
1029D LEU* 1.3 64.0 + - - +
1031D TYR* 3.9 10.0 + - - +
1032D SER* 4.3 6.6 + - - -
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Residues in contact with LEU1029 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B VAL* 6.1 2.9 - - + +
1026D ASN* 3.0 31.0 + - + +
1027D TYR 3.2 0.2 - - - -
1028D SER* 1.3 83.4 + - - +
1030D LYS* 1.3 62.6 + - - +
1031D TYR 3.2 2.6 + - - -
1032D SER* 3.5 19.4 + - - +
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Residues in contact with LYS1030 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025D ILE* 5.9 3.4 - - + -
1026D ASN 3.8 8.9 + - - +
1027D TYR* 3.5 15.6 + - + +
1029D LEU* 1.3 78.6 - - - +
1031D TYR* 1.3 83.5 + - + +
1032D SER 3.7 1.5 + - - -
1033D ASP* 5.9 0.5 - - - +
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Residues in contact with TYR1031 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B TRP* 4.6 21.1 - + + -
386B ARG* 2.9 47.4 + - - -
418B THR* 5.5 3.0 - - + +
459B ASP* 4.6 17.5 + - - +
1027D TYR* 3.6 23.1 + + - +
1028D SER 3.9 6.5 + - - +
1029D LEU 3.2 1.2 - - - -
1030D LYS* 1.3 117.0 - - + +
1032D SER* 1.3 54.9 + - - +
1033D ASP* 2.8 16.7 + - + +
1034D GLU* 3.2 15.5 + - - +
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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
------------------------------------------------------------
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