Contacts of the helix formed by residues 109 - 119 (chain J) in PDB entry 1J0B
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 LYS 109 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107J GLU* 3.1 48.8 + - + +
108J LEU* 1.3 77.4 - - - +
110J GLY* 1.3 66.4 + - - +
111J ASN 3.4 0.5 + - - -
112J TYR* 3.5 3.5 + - - +
113J LEU* 3.2 25.4 + - + +
315J PHE 5.3 1.8 + - - +
316J HIS* 3.4 42.6 + - - +
319J ASP* 4.4 16.4 + - - -
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Residues in contact with GLY 110 (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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315I PHE* 3.9 17.5 - - - -
109J LYS* 1.3 78.7 - - - +
111J ASN* 1.3 60.0 + - - -
113J LEU* 3.6 9.2 - - - +
114J LEU* 3.1 23.0 - - - +
312J SER* 4.5 2.2 - - - -
315J PHE* 5.5 0.8 - - - +
316J HIS* 3.2 32.4 - - - +
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Residues in contact with ASN 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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50J ILE* 3.3 12.6 - - - +
79J VAL 5.0 0.4 - - - +
80J HIS* 2.9 26.9 + - - +
81J SER 3.7 11.7 - - - +
82J ASN* 2.7 27.7 - - - +
85J PHE* 4.0 7.0 - - + +
109J LYS 3.4 0.6 + - - -
110J GLY* 1.3 68.9 - - - -
112J TYR* 1.3 51.6 + - - +
113J LEU 3.0 4.7 - - - -
114J LEU* 2.7 32.1 + - - +
115J ASP* 2.4 26.8 + - - +
312J SER* 2.3 34.7 + - - -
313J GLY* 4.2 3.8 - - - +
316J HIS* 4.0 4.8 - - - -
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Residues in contact with TYR 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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79J VAL* 3.2 31.9 + - + +
80J HIS* 4.9 0.2 - - - +
102J LEU* 4.2 15.9 - - + -
106J GLU* 3.7 40.2 + - + +
107J GLU 2.9 24.2 - - - +
108J LEU* 4.1 16.4 - - + +
109J LYS 3.5 6.7 + - - +
111J ASN* 1.3 76.7 - - - +
113J LEU* 1.3 60.3 + - - +
115J ASP* 3.5 18.9 - - + +
116J LYS* 3.6 35.0 + - - +
122J THR* 3.5 31.8 - - + +
124J VAL* 4.6 2.0 - - + +
316J HIS* 5.4 1.6 - - - +
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Residues in contact with LEU 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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314I THR 4.7 0.4 - - - +
315I PHE* 3.6 30.5 - - + +
318I GLY* 3.2 37.5 - - - +
319I ASP* 4.8 1.6 - - - +
322I LEU* 4.1 6.1 - - + -
108J LEU* 3.1 28.3 - - - +
109J LYS* 3.2 34.1 + - + +
110J GLY 3.6 6.1 - - - +
111J ASN 3.0 0.4 - - - -
112J TYR* 1.3 77.0 - - - +
114J LEU* 1.3 64.3 + - + +
116J LYS* 3.6 5.2 + - - +
117J ILE* 3.4 25.9 + - + +
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Residues in contact with LEU 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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277I ILE* 5.4 7.0 - - + -
311I ILE* 6.1 0.4 - - + -
314I THR* 3.8 28.5 - - + -
315I PHE* 3.5 29.2 - - + +
50J ILE* 4.4 10.3 - - + -
85J PHE* 3.7 20.2 - - + -
110J GLY 3.1 18.2 - - - +
111J ASN* 2.7 16.2 + - - +
113J LEU* 1.3 77.9 - - + +
115J ASP* 1.3 64.5 + - - +
116J LYS 3.2 0.2 - - - -
117J ILE* 3.1 8.6 + - + +
118J MET* 3.1 26.8 + - + +
312J SER* 3.3 26.0 - - - +
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Residues in contact with ASP 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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79J VAL 5.5 0.8 - - - +
81J SER 5.3 0.6 - - - +
84J ALA* 4.8 2.4 - - - +
85J PHE* 3.7 23.0 + - - +
100J LEU* 3.7 22.0 - - - +
102J LEU* 4.5 8.5 - - - +
111J ASN* 2.4 40.9 + - - +
112J TYR* 3.6 19.5 - - + +
114J LEU* 1.3 75.3 - - - +
116J LYS* 1.3 59.3 + - + +
118J MET 3.2 1.0 + - - -
119J GLY 3.0 20.8 + - - -
120J ILE* 3.0 33.1 + - + +
122J THR* 4.2 14.6 + - - +
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Residues in contact with LYS 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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268I ARG* 2.7 23.0 + - - -
322I LEU* 3.2 24.9 - - + -
108J LEU* 4.3 13.0 - - + -
112J TYR* 3.6 40.2 + - - +
113J LEU 3.9 4.9 - - - +
114J LEU 3.2 0.4 - - - -
115J ASP* 1.3 72.7 - - - +
117J ILE* 1.3 60.0 + - - +
118J MET 3.0 1.8 - - - -
119J GLY* 2.8 13.1 + - - +
120J ILE 3.4 14.7 + - - +
121J GLU* 4.7 0.6 - - - +
122J THR* 3.3 31.7 + - - +
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Residues in contact with ILE 117 (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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264I ALA* 5.3 2.9 - - + +
267I ILE* 3.8 21.3 - - + +
268I ARG* 2.5 36.5 + - - +
314I THR* 3.7 29.8 - - + +
318I GLY* 4.2 3.4 - - - +
321I LEU* 4.1 21.3 - - + +
322I LEU* 4.3 12.8 - - + +
325I LEU* 4.7 6.8 - - + +
113J LEU* 3.4 33.0 + - + +
114J LEU* 3.1 11.9 + - + +
116J LYS* 1.3 76.1 - - - +
118J MET* 1.3 72.1 + - + +
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Residues in contact with MET 118 (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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267I ILE* 3.5 31.9 - - + +
268I ARG* 3.4 10.1 - - - +
271I GLY* 3.7 19.1 - - - -
272I THR* 2.7 26.9 - - + +
277I ILE* 4.2 31.9 - - + -
314I THR* 5.4 3.8 - - + -
85J PHE* 3.8 10.8 - - + -
89J LEU* 3.5 25.1 - - + -
92J LYS* 4.7 0.2 + - - -
114J LEU* 3.1 13.1 + - + +
115J ASP 3.6 7.6 - - - +
116J LYS 3.0 0.6 - - - -
117J ILE* 1.3 98.5 - - + +
119J GLY* 1.3 60.7 + - - +
120J ILE* 4.0 11.2 - - + -
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Residues in contact with GLY 119 (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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268I ARG* 4.0 11.0 - - - -
92J LYS* 3.1 19.1 + - - -
115J ASP 3.0 0.4 + - - -
116J LYS* 2.8 18.3 + - - -
118J MET* 1.3 79.4 - - - +
120J ILE* 1.3 64.3 + - - +
121J GLU 3.7 1.6 + - - -
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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