Contacts of the helix formed by residues 1005 - 1009 (chain A) in PDB entry 5JP2
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 ASP1005 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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905A CYS* 4.2 2.4 - - - -
907A VAL* 4.7 2.3 - - - +
1003A SER* 3.4 14.3 + - - +
1004A GLN* 1.3 76.9 - - - +
1006A PRO* 1.3 71.9 - - - +
1007A SER* 2.9 30.2 + - - +
1008A ARG* 3.1 20.1 + - - +
1009A ALA 4.5 0.2 + - - -
943B ARG* 3.2 19.2 + - - -
1007B SER* 4.7 0.2 + - - -
1008B ARG* 2.4 35.3 + - - +
1035B ALA 4.4 4.3 - - - +
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Residues in contact with PRO1006 (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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897A PHE* 4.5 12.1 - - + -
903A ASN 6.2 0.2 - - - +
905A CYS* 3.5 27.1 - - + +
1004A GLN 3.5 9.0 - - - +
1005A ASP* 1.3 89.0 - - - +
1007A SER* 1.3 55.2 + - - +
1008A ARG 3.0 1.3 - - - -
1009A ALA* 2.8 31.5 + - + +
1012A LEU* 3.8 10.9 - - + +
1034B PRO 4.7 4.7 - - - +
1035B ALA* 4.2 26.0 - - + +
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Residues in contact with SER1007 (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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943A ARG* 4.7 6.6 + - - -
1005A ASP* 2.9 30.5 + - - -
1006A PRO* 1.3 78.0 - - - +
1008A ARG* 1.3 77.2 + - - +
1009A ALA 3.3 0.4 - - - -
1035A ALA 4.1 2.6 - - - +
1036A THR* 3.5 32.3 - - - +
1005B ASP* 5.2 0.2 - - - -
1007B SER* 3.1 34.8 - - - -
1035B ALA* 4.4 6.0 - - - +
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Residues in contact with ARG1008 (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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893A ILE* 4.2 7.6 - - - +
907A VAL* 4.4 13.8 - - + +
909A ILE* 4.6 11.9 - - + +
943A ARG* 3.5 45.9 + - - +
1003A SER* 3.6 32.5 + - - -
1005A ASP* 3.1 9.9 + - - +
1006A PRO 2.9 1.2 + - - -
1007A SER* 1.3 96.2 + - - +
1009A ALA* 1.3 61.8 + - - +
1010A PRO* 3.7 6.6 - - - +
1036A THR 5.0 3.5 - - - +
1120A LEU* 5.4 4.5 - - - +
1005B ASP* 2.5 31.1 + - - -
1008B ARG* 3.4 17.9 - - - +
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Residues in contact with ALA1009 (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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893A ILE* 4.5 2.2 - - + -
895A ALA* 5.1 0.2 - - + -
897A PHE* 4.1 19.3 - - + -
907A VAL* 3.9 21.7 - - + +
1006A PRO 2.8 14.2 + - - +
1008A ARG* 1.3 79.1 - - - +
1010A PRO* 1.3 70.4 - - + +
1011A LEU 3.3 1.5 + - - +
1012A LEU* 3.6 4.4 - - + +
1036A THR* 3.0 19.1 + - - -
1146A TYR* 3.5 17.7 - - + +
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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