Contacts of the helix formed by residues 1040 - 1047 (chain A) in PDB entry 4X7J
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 PRO1040 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1015A PHE* 4.0 22.2 - - + -
1019A TYR* 3.8 33.9 - - + +
1030A THR* 3.7 26.9 - - + -
1034A VAL* 4.3 1.6 - - + -
1038A LYS 4.2 4.3 - - - +
1039A PHE* 1.3 84.6 - - + +
1041A PRO* 1.3 73.1 - - + +
1042A LEU* 3.2 2.0 - - + +
1043A PHE* 3.0 18.4 + - + +
1044A THR* 3.5 5.7 + - - +
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Residues in contact with PRO1041 (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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1039A PHE 3.4 8.0 - - - +
1040A PRO* 1.3 83.3 - - + +
1042A LEU* 1.3 64.2 + - + +
1044A THR* 2.7 25.4 + - + +
1045A GLN* 3.4 22.7 + - - +
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Residues in contact with LEU1042 (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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1019A TYR* 5.6 7.2 - - + +
1040A PRO* 3.2 2.9 + - + +
1041A PRO* 1.3 78.3 - - + +
1043A PHE* 1.3 59.5 + - - +
1045A GLN* 4.0 18.2 - - + +
1046A LYS* 3.1 30.8 + - - +
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Residues in contact with PHE1043 (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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1015A PHE* 3.7 36.1 - + + -
1018A LEU* 4.0 24.2 - - + -
1019A TYR* 4.2 24.2 - + + -
1039A PHE* 3.9 24.9 - + + -
1040A PRO* 3.0 13.5 + - + +
1042A LEU* 1.3 76.7 - - - +
1044A THR* 1.3 65.7 + - + +
1045A GLN 3.2 0.2 - - - -
1046A LYS* 4.8 2.5 - - - -
1047A TYR* 2.8 58.4 + + + +
1050A GLU 4.5 4.0 - - - -
1051A TYR* 3.8 35.2 - - + -
1054A VAL* 4.6 8.1 - - + -
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Residues in contact with THR1044 (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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1039A PHE* 3.7 20.6 - - + +
1040A PRO 3.5 5.3 + - - +
1041A PRO* 2.7 25.2 + - + +
1043A PHE* 1.3 77.2 - - + +
1045A GLN* 1.3 63.2 + - - +
1048A PRO* 3.6 23.7 - - - +
1051A TYR* 3.7 51.7 - - + +
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Residues in contact with GLN1045 (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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1041A PRO* 3.4 24.0 + - - +
1042A LEU* 4.2 18.0 - - - +
1043A PHE 3.2 0.8 - - - -
1044A THR* 1.3 84.1 + - - +
1046A LYS* 1.3 63.5 + - - +
1048A PRO* 3.6 12.2 - - - +
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Residues in contact with LYS1046 (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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906A ILE* 3.9 31.4 - - + +
911A ARG* 6.2 0.2 - - - +
1042A LEU 3.1 18.3 + - - +
1043A PHE* 4.2 1.1 - - - +
1045A GLN* 1.3 80.0 - - - +
1047A TYR* 1.3 101.4 + - + +
1048A PRO* 3.4 6.9 - - - +
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Residues in contact with TYR1047 (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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906A ILE* 4.7 7.1 - - + +
909A ARG 4.1 16.3 + - - -
911A ARG* 3.7 39.1 + - + +
1018A LEU* 4.0 34.1 + - + +
1043A PHE* 2.8 40.5 + + + +
1044A THR 3.9 0.2 - - - -
1046A LYS* 1.3 121.8 + - + +
1048A PRO* 1.4 59.2 - - - +
1049A CYS 3.4 2.5 - - - -
1050A GLU* 3.4 27.8 - - + +
1051A TYR* 2.8 28.9 + - - +
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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