Contacts of the helix formed by residues 78 - 92 (chain J) in PDB entry 3LUE
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 ASN 78 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62J ARG* 4.4 15.8 - - - +
69J TYR* 2.7 43.8 + - - +
70J PRO* 3.6 14.3 + - + +
76J VAL* 3.5 10.2 - - - +
77J THR* 1.3 85.3 + - - +
79J TRP* 1.3 60.1 + - - +
80J ASP* 3.9 3.7 + - - +
81J ASP* 3.0 7.3 + - - +
82J MET* 3.1 19.9 + - - +
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Residues in contact with TRP 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76J VAL* 3.7 43.3 + - + -
77J THR 4.1 5.4 + - - -
78J ASN* 1.3 74.3 - - - +
80J ASP* 1.3 64.4 + - - +
82J MET* 3.6 5.4 + - + +
83J GLU* 3.0 29.3 + - - +
86J TRP* 4.1 20.6 - + - -
115J ASN* 4.1 34.6 - - + +
118J LYS* 3.4 46.8 - - + +
119J MET* 4.2 12.8 - - + -
122J ILE* 3.5 28.7 - - + -
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Residues in contact with ASP 80 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J LEU 4.4 10.9 - - - +
68J LYS* 5.2 0.7 - - - -
69J TYR* 1.3 66.1 - - + +
78J ASN* 3.6 4.2 + - - +
79J TRP* 1.3 77.5 + - - +
81J ASP 1.3 46.6 - - - +
83J GLU* 4.0 13.6 - - + +
84J LYS* 5.0 0.4 - - - -
118J LYS* 5.7 0.3 + - - -
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Residues in contact with ASP 81 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J ILE* 1.7 51.0 - - + +
62J ARG* 4.8 0.2 + - - -
67J LEU* 3.2 31.0 - - - +
69J TYR* 0.4 440.8 + - + +
78J ASN* 2.9 9.7 + - - +
80J ASP* 1.3 66.1 - - - +
82J MET* 1.3 51.6 + - - +
84J LYS* 3.4 0.2 - - - +
85J ILE* 3.1 15.8 + - - +
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Residues in contact with MET 82 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J ASN* 3.2 27.1 - - - +
17J CYS* 4.7 0.2 - - - -
69J TYR* 2.3 2.0 - - - -
70J PRO* 3.8 7.7 - - + +
71J ILE* 3.4 38.8 - - + -
76J VAL* 3.5 24.5 - - + -
78J ASN 3.1 19.9 + - - +
79J TRP* 3.9 8.1 - - + +
81J ASP* 1.3 74.2 - - - +
83J GLU* 1.3 62.3 + - - +
85J ILE* 2.8 42.5 + - + +
86J TRP* 3.1 49.7 + - + +
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Residues in contact with GLU 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69J TYR* 2.8 21.3 - - + +
79J TRP 3.0 20.7 + - - +
80J ASP* 3.3 10.5 - - - +
82J MET* 1.3 73.8 - - - +
84J LYS* 1.3 63.9 + - - +
86J TRP* 3.3 9.9 + - - +
87J HIS* 3.1 21.1 + - - +
118J LYS* 4.5 5.5 + - - -
122J ILE* 3.9 37.0 - - + +
126J THR* 3.9 22.8 + - + +
127J PHE* 4.0 7.1 - - + -
120T LYS* 5.3 8.7 - - - +
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Residues in contact with LYS 84 (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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34J ILE* 2.7 26.2 - - + +
35J VAL* 2.6 20.0 + - - +
67J LEU 2.9 5.0 - - - -
68J LYS* 0.4 255.5 + - + +
69J TYR* 0.8 210.9 - - + +
83J GLU* 1.3 65.2 - - - +
85J ILE* 1.3 62.2 + - - +
86J TRP 3.2 0.2 + - - -
87J HIS 3.3 0.5 + - - -
88J HIS* 3.0 20.1 + - - +
122T VAL* 3.3 14.7 - - + +
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Residues in contact with ILE 85 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17J CYS* 3.9 16.4 - - - -
31J PHE* 4.0 12.3 - - + -
32J PRO 5.1 1.6 - - - +
33J SER* 4.2 30.7 - - - +
34J ILE* 5.1 12.1 - - + +
69J TYR* 4.8 0.2 - - + -
70J PRO* 3.6 26.9 - - + -
81J ASP 3.1 10.1 + - - +
82J MET* 2.8 34.3 + - + +
84J LYS* 1.3 75.8 - - - +
86J TRP* 1.3 62.3 + - + +
88J HIS* 3.2 9.3 + - - +
89J THR* 2.8 32.5 + - - +
122T VAL* 5.5 0.2 - - - -
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Residues in contact with TRP 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J VAL* 3.7 21.2 - - + +
12J ASN* 2.9 37.6 + - - -
76J VAL* 5.6 1.8 - - + -
79J TRP* 4.1 17.5 - + - -
82J MET* 3.1 46.5 + - + +
83J GLU* 3.8 6.1 - - - +
85J ILE* 1.3 76.4 - - + +
87J HIS* 1.3 64.5 + - - +
89J THR* 2.8 28.3 + - - -
90J PHE* 3.1 15.4 + + + -
105J LEU* 4.4 10.8 - - + -
119J MET* 4.2 27.1 - - + -
122J ILE* 4.0 20.4 - - + -
123J MET* 3.5 26.9 - - + -
127J PHE* 3.9 12.3 - + + -
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Residues in contact with HIS 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69J TYR 4.6 2.5 - - - -
83J GLU 3.1 13.2 + - - +
84J LYS* 3.4 10.1 - - - +
86J TRP* 1.3 71.9 - - - +
88J HIS* 1.3 58.2 + - - +
90J PHE* 4.5 0.4 - - - -
91J TYR* 2.9 78.1 + + + +
92J ASN* 5.4 2.9 - - - -
127J PHE* 3.7 19.1 - - + -
118T GLY 5.6 0.9 - - - -
119T VAL* 4.4 9.0 - - + -
120T LYS* 4.0 44.3 + - + +
122T VAL* 4.2 8.1 - - + -
143T THR* 4.1 18.6 - - + +
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Residues in contact with HIS 88 (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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31J PHE* 4.2 22.0 - + - +
84J LYS 3.0 11.9 + - - +
85J ILE* 3.3 9.4 - - - +
87J HIS* 1.3 72.2 - - - +
89J THR* 1.3 57.7 + - - +
92J ASN* 3.0 45.7 + - + +
93J GLU* 2.7 65.6 + - - +
122T VAL* 4.3 19.8 + - + +
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Residues in contact with THR 89 (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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10J VAL* 3.9 22.7 - - + +
17J CYS* 5.7 0.3 - - - +
19J ALA* 3.7 30.3 - - + -
31J PHE* 3.5 17.8 - - + -
85J ILE* 2.8 17.6 + - - +
86J TRP* 2.8 28.1 + - - -
88J HIS* 1.3 72.5 - - - +
90J PHE* 1.3 57.4 + - + +
93J GLU* 3.3 8.8 + - - +
94J LEU* 2.7 41.6 + - + +
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Residues in contact with PHE 90 (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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8J LEU* 3.3 35.2 - - + -
10J VAL* 4.5 17.3 - - + -
86J TRP* 3.1 30.7 + + + -
87J HIS* 4.1 1.8 - - - +
89J THR* 1.3 79.1 - - + +
91J TYR* 1.3 61.2 + + + +
94J LEU* 4.8 0.7 - - - -
95J ARG 2.8 30.8 + - - -
96J VAL* 2.8 23.2 + - + +
98J PRO* 3.6 32.5 - - + -
103J VAL* 4.0 17.7 - - + -
105J LEU* 5.6 0.2 - - + -
123J MET* 4.0 30.7 - - + -
127J PHE* 4.2 17.5 - + - -
142T TRP* 3.6 0.9 - - - -
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Residues in contact with TYR 91 (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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87J HIS* 2.9 69.9 + + + +
90J PHE* 1.3 65.1 - - + +
92J ASN* 1.3 65.2 + - - +
95J ARG* 4.6 0.2 - - - -
96J VAL 4.0 0.2 - - - -
98J PRO* 3.7 23.6 - - + +
99J GLU* 4.8 3.8 + - - -
127J PHE* 4.1 20.5 + + - -
142T TRP* 1.2 56.7 - - + +
143T THR* 4.5 7.0 - - + +
146T LEU* 1.0 129.3 - - + +
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Residues in contact with ASN 92 (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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87J HIS* 5.2 3.3 - - - -
88J HIS* 3.0 44.2 + - + +
91J TYR* 1.3 95.1 + - - +
93J GLU* 1.3 70.2 + - - +
94J LEU 3.9 0.2 - - - -
95J ARG* 3.5 18.6 - - - +
43T TRP* 4.6 4.5 - - - -
47T GLN* 4.3 5.0 + - - +
122T VAL* 5.0 5.4 - - - +
124T ILE* 4.1 14.6 - - - +
139T GLY* 2.6 45.0 + - - -
142T TRP* 3.7 0.2 - - - -
143T THR* 3.3 10.4 + - - -
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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