Contacts of the helix formed by residues 110 - 116 (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 110 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104J PHE 2.7 23.1 + - - -
105J VAL* 3.2 18.4 + - - -
107J ASP* 3.2 13.5 + - - -
108J VAL 3.3 3.4 + - - -
109J PRO* 1.3 69.4 - - - +
111J LYS* 1.3 51.8 + - - +
112J ILE* 3.8 3.5 - - - +
113J GLY* 3.5 17.8 + - - -
114J THR* 2.4 42.9 + - - -
120J ALA* 4.9 13.6 - - - +
123J LEU* 4.3 4.3 - - - +
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Residues in contact with LYS 111 (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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104J PHE* 3.3 18.3 + - + -
107J ASP* 4.1 11.0 - - - +
109J PRO* 3.7 18.2 + - - +
110J SER* 1.3 69.4 - - - +
112J ILE* 1.3 61.8 + - - +
114J THR* 3.8 3.3 - - - -
115J LEU* 2.9 31.7 + - - +
498J VAL* 4.0 39.5 - - + +
502J PHE* 5.3 1.0 - - + -
512J MET* 3.7 19.1 - - + -
1448J THR* 5.2 2.5 - - + -
1449J GLU* 3.0 50.0 + - - +
1452J ILE* 4.2 21.6 - - + +
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Residues in contact with ILE 112 (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* 5.3 0.7 - - + -
101J HIS 5.1 0.7 - - - +
104J PHE* 3.4 18.2 - - + +
105J VAL* 3.6 38.1 - - + +
110J SER* 3.8 1.8 - - - +
111J LYS* 1.3 73.4 - - - +
113J GLY* 1.3 58.0 + - - +
115J LEU* 4.5 3.6 - - - -
116J LEU* 2.8 42.2 + - + +
123J LEU* 3.9 17.7 - - + -
127J LEU* 4.4 5.2 - - + -
461J ILE* 4.3 5.6 - - + -
465J LEU* 3.5 37.0 - - + -
512J MET* 3.4 20.8 - - + +
513J ILE* 4.8 9.9 - - + -
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Residues in contact with GLY 113 (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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110J SER* 3.4 15.8 + - - -
111J LYS 3.3 0.4 - - - -
112J ILE* 1.3 79.2 - - - +
114J THR* 1.3 56.9 + - - +
117J ASP* 3.2 7.6 - - - -
118J LEU* 2.8 45.4 + - - +
119J SER 5.4 0.4 - - - -
120J ALA 5.6 0.4 - - - -
123J LEU* 3.7 12.3 - - - +
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Residues in contact with THR 114 (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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109J PRO* 3.9 13.3 + - + +
110J SER 2.4 33.3 + - - -
111J LYS* 3.9 4.0 - - - -
113J GLY* 1.3 73.4 - - - +
115J LEU* 1.3 63.9 + - - +
117J ASP* 3.8 3.5 + - - -
494J LYS* 3.8 17.7 - - + +
495J ARG* 3.2 35.5 + - + +
498J VAL* 3.8 25.8 - - + -
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Residues in contact with LEU 115 (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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111J LYS 2.9 17.1 + - - +
112J ILE* 3.8 4.3 - - - +
114J THR* 1.3 74.2 - - - +
116J LEU* 1.3 60.9 + - + +
117J ASP 3.0 5.3 + - - -
465J LEU* 5.2 2.5 - - + -
468J LEU* 3.6 30.1 - - + -
470J LEU* 4.2 11.2 - - + -
473J LEU* 4.1 15.3 - - + -
495J ARG* 3.0 31.9 + - - +
498J VAL* 3.6 27.8 - - + -
499J VAL* 3.7 29.2 - - + +
502J PHE* 4.1 15.7 - - + -
509J PRO* 5.2 3.8 - - + -
512J MET* 6.2 0.4 - - + -
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Residues in contact with LEU 116 (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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112J ILE* 2.8 22.6 + - + +
115J LEU* 1.3 74.0 - - - +
117J ASP* 1.3 68.8 + - - +
118J LEU* 3.2 21.1 - - + +
123J LEU* 5.0 2.9 - - + -
150J ARG* 3.3 26.0 + - - +
461J ILE* 3.8 22.0 - - + -
464J LEU* 4.0 28.7 - - + -
465J LEU* 3.7 28.9 - - + -
468J LEU* 3.6 38.4 - - + -
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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