Contacts of the helix formed by residues 1018 - 1026 (chain J) in PDB entry 4XLR
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 ASN1018 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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950I LEU* 4.9 1.8 - - - +
952J ASP 5.0 0.8 + - - -
953J ASP* 2.2 37.3 + - - +
954J ALA* 4.4 1.6 - - - +
955J VAL* 5.4 0.6 - - - +
1011J PHE* 3.3 23.3 - - + -
1015J TYR* 3.0 35.4 + - + +
1016J PRO 3.2 1.0 - - - -
1017J PHE* 1.3 74.6 - - - +
1019J PRO* 1.3 63.3 - - - +
1020J LEU* 3.5 3.3 + - - +
1021J TYR* 3.0 31.1 + - + -
1022J VAL* 2.7 35.7 + - - +
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Residues in contact with PRO1019 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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950I LEU* 5.9 2.9 - - + -
952I LEU* 6.5 0.2 - - + -
971I LYS* 4.9 4.5 - - - +
947J ILE* 3.5 24.0 - - + +
948J THR 3.0 30.5 - - - +
949J ILE* 5.0 0.9 - - + -
953J ASP* 3.4 28.0 - - + +
1017J PHE 3.2 7.5 - - - +
1018J ASN* 1.3 95.1 - - - +
1020J LEU* 1.3 58.3 + - - +
1022J VAL* 4.0 3.6 - - + +
1023J MET* 2.9 38.0 + - + +
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Residues in contact with LEU1020 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877I PRO* 3.5 32.3 - - + -
949J ILE* 5.2 12.7 - - + +
953J ASP* 4.5 6.1 - - + +
954J ALA* 3.6 28.0 - - + -
1011J PHE* 4.0 5.6 - - + -
1018J ASN* 3.4 5.8 + - - +
1019J PRO* 1.3 77.4 - - + +
1021J TYR* 1.3 68.8 + - - +
1023J MET* 3.2 9.7 + - - +
1024J ALA* 3.0 21.2 + - + +
1035J ILE* 3.6 43.5 - - + -
1038J LEU* 4.5 13.7 - - + -
1039J CYS* 5.0 3.4 - - + -
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Residues in contact with TYR1021 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790J TYR* 5.7 4.5 - - - -
794J GLN* 6.1 0.2 - - - -
1008J PHE* 4.6 13.5 - + + -
1011J PHE* 3.4 31.6 - + + -
1012J GLU* 3.1 40.5 + - + +
1015J TYR 4.2 2.7 - - - -
1016J PRO* 3.5 36.1 - - + -
1018J ASN* 3.0 20.6 + - + +
1020J LEU* 1.3 82.4 - - - +
1022J VAL* 1.3 76.9 + - + +
1024J ALA* 3.3 2.1 + - - +
1025J GLN* 2.8 66.7 + - + +
1035J ILE* 5.6 4.9 - - + -
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Residues in contact with VAL1022 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787J LEU* 4.4 17.7 - - + -
790J TYR* 3.5 29.6 - - + +
791J TYR* 5.2 3.6 - - + -
794J GLN* 3.9 12.1 - - - +
947J ILE* 4.9 9.9 - - + -
1016J PRO 3.1 27.8 - - - +
1017J PHE* 3.8 12.6 - - + +
1018J ASN 2.7 21.4 + - - +
1019J PRO* 4.0 3.8 - - + +
1021J TYR* 1.3 76.7 - - + +
1023J MET* 1.3 64.7 + - - +
1025J GLN* 3.1 4.3 + - - +
1026J SER* 2.9 28.3 + - - +
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Residues in contact with MET1023 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873I PRO* 3.0 33.4 - - + +
874I LEU* 3.6 15.5 - - + -
877I PRO* 3.7 23.3 - - + -
787J LEU* 4.7 11.9 - - + -
947J ILE* 4.7 13.0 - - + -
949J ILE* 3.7 20.4 - - + -
1019J PRO 2.9 32.7 + - - +
1020J LEU* 3.3 6.3 - - - +
1022J VAL* 1.3 82.8 - - - +
1024J ALA* 1.3 61.3 + - - +
1026J SER 3.6 0.9 + - - -
1028J ALA* 2.9 36.3 + - + +
1029J ARG 3.9 17.0 - - - +
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Residues in contact with ALA1024 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1020J LEU* 3.0 9.5 + - + +
1021J TYR 4.3 1.6 - - - +
1023J MET* 1.3 78.7 - - - +
1025J GLN* 1.3 61.8 + - - +
1027J GLY* 3.5 10.0 + - - -
1028J ALA 4.8 0.2 - - - +
1029J ARG 3.3 22.2 - - - +
1030J GLY* 3.8 17.6 - - - +
1031J ASN* 4.4 2.0 - - - +
1035J ILE* 3.5 35.0 - - + -
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Residues in contact with GLN1025 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790J TYR* 5.7 4.9 - - + +
907J GLU* 5.0 2.9 - - - +
1008J PHE* 6.4 2.5 - - + -
1012J GLU* 4.0 9.1 + - - -
1021J TYR* 2.8 66.4 + - + +
1022J VAL* 3.4 7.0 - - - +
1024J ALA* 1.3 76.1 - - - +
1026J SER* 1.3 59.8 + - - +
1027J GLY* 3.0 8.8 + - - -
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Residues in contact with SER1026 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786J ILE* 3.5 7.8 + - - +
787J LEU* 4.7 1.9 - - - -
790J TYR* 3.6 41.8 - - - +
907J GLU* 3.7 18.4 - - - -
908J LYS* 3.1 27.2 + - - +
1022J VAL* 2.9 16.8 + - - +
1023J MET* 3.6 5.2 + - - -
1025J GLN* 1.3 75.1 - - - +
1027J GLY* 1.3 58.9 + - - +
1028J ALA* 3.8 10.0 + - - +
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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