Contacts of the helix formed by residues 119 - 128 (chain J) in PDB entry 4XLN
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 SER 119 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118J LEU* 1.3 75.0 - - - +
120J ALA* 1.3 64.1 + - - +
121J THR* 3.1 12.7 + - - -
122J GLU* 2.8 33.4 + - - +
123J LEU* 3.0 20.6 + - - +
46R T 3.8 17.7 - - - -
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Residues in contact with ALA 120 (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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105J VAL* 4.7 15.2 - - + +
106J LYS* 5.3 12.3 + - + +
110J SER* 4.9 11.2 - - - -
113J GLY* 5.6 0.8 - - - -
118J LEU 3.7 1.4 + - - -
119J SER* 1.3 72.8 - - - +
121J THR* 1.3 56.4 + - - +
123J LEU* 4.3 9.2 - - - -
124J GLU* 2.9 30.5 + - - +
46R T 3.9 11.4 + - - +
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Residues in contact with THR 121 (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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119J SER* 3.0 13.4 + - - -
120J ALA* 1.3 78.8 + - - +
122J GLU* 1.3 60.3 + - - +
124J GLU* 3.4 14.0 - - - +
125J GLN* 3.4 25.2 - - - +
46R T 5.0 14.4 + - - -
47R G 5.2 5.4 + - - +
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Residues in contact with GLU 122 (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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117J ASP 4.5 0.5 - - - +
118J LEU* 3.3 29.2 - - + +
119J SER* 2.8 42.9 + - - +
121J THR* 1.3 74.3 - - - +
123J LEU* 1.3 60.2 + - - +
124J GLU 3.1 2.0 - - - -
125J GLN* 2.9 28.9 + - - +
126J VAL* 2.9 19.3 + - + +
152J LEU* 3.2 33.6 - - + +
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Residues in contact with LEU 123 (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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105J VAL* 5.1 4.7 - - + +
110J SER* 4.3 5.4 - - - +
112J ILE* 3.9 24.0 - - + -
113J GLY* 3.7 31.9 - - - +
116J LEU* 5.0 3.4 - - + -
118J LEU* 4.3 20.4 - - + -
119J SER 3.0 16.5 + - - +
120J ALA* 4.1 7.0 - - - +
122J GLU* 1.3 78.2 - - - +
124J GLU* 1.3 56.2 + - - +
126J VAL* 4.2 4.7 - - + -
127J LEU* 2.9 47.5 + - + +
461J ILE* 3.7 37.0 - - + -
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Residues in contact with GLU 124 (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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105J VAL* 5.6 5.0 - - + +
106J LYS* 3.7 20.6 + - - +
120J ALA 2.9 20.2 + - - +
121J THR* 3.4 10.3 - - - +
123J LEU* 1.3 76.9 - - - +
125J GLN* 1.3 67.7 + - + +
127J LEU* 5.1 0.9 - - - -
128J TYR* 3.2 40.6 + - - +
587J ARG* 2.5 47.2 + - - +
93L SER* 3.3 17.2 - - - -
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Residues in contact with GLN 125 (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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121J THR* 3.4 20.7 + - - +
122J GLU* 2.9 13.6 + - - +
124J GLU* 1.3 80.6 - - + +
126J VAL* 1.3 59.7 + - - +
129J PHE 3.6 1.2 + - - -
130J ASN* 2.8 55.0 + - + +
131J LYS* 3.2 33.4 + - + +
152J LEU* 3.3 22.0 - - + +
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Residues in contact with VAL 126 (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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118J LEU* 6.2 2.2 - - + -
122J GLU* 2.9 19.0 + - + +
123J LEU* 3.8 7.6 - - + +
124J GLU 3.2 0.2 - - - -
125J GLN* 1.3 75.1 - - - +
127J LEU* 1.3 67.8 + - - +
128J TYR 3.1 2.0 - - - -
129J PHE* 2.9 14.4 + - - -
131J LYS 3.8 10.9 - - - +
133J ILE* 3.5 42.2 - - + -
152J LEU* 4.1 9.2 - - + -
456J MET* 4.7 0.2 - - - -
457J GLY* 3.2 30.2 + - - +
461J ILE* 3.6 28.3 - - + -
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Residues in contact with LEU 127 (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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100J ALA* 3.8 16.4 - - + -
105J VAL* 3.7 39.3 - - + -
112J ILE* 4.4 2.7 - - + -
123J LEU* 2.9 39.6 + - + +
124J GLU* 5.4 0.2 - - - -
126J VAL* 1.3 74.4 - - - +
128J TYR* 1.3 68.1 + - + +
129J PHE* 3.3 21.2 - - - -
457J GLY 4.1 0.2 - - - -
458J ALA* 3.7 30.2 + - + +
461J ILE* 3.6 31.6 - - + -
513J ILE* 4.4 0.4 - - + -
575J GLN* 4.0 15.4 - - - +
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Residues in contact with TYR 128 (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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102J ILE* 4.0 11.4 - - - +
105J VAL* 4.9 14.5 - - + +
106J LYS* 5.7 0.7 - - + -
124J GLU* 3.2 39.4 + - - +
125J GLN 4.2 0.4 - - - +
126J VAL 3.0 1.2 + - - -
127J LEU* 1.3 85.3 - - + +
129J PHE* 1.3 77.1 + - - +
130J ASN* 3.7 2.5 - - + -
572J ARG* 3.5 27.7 - - + -
575J GLN* 3.6 20.8 + - + -
576J GLU* 4.4 9.6 - - + -
579J ASP* 2.2 35.0 + - - +
587J ARG* 3.1 54.4 + - - +
98L GLN* 3.7 6.6 - - - +
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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