Contacts of the helix formed by residues 78 - 92 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C ARG* 4.4 15.2 - - - +
69C TYR* 2.7 44.2 + - - +
70C PRO* 3.6 14.3 + - + +
76C VAL* 3.5 10.0 - - - +
77C THR* 1.3 83.1 + - - +
79C TRP* 1.3 59.5 + - - +
80C ASP* 3.9 3.9 + - - +
81C ASP* 3.0 8.1 + - - +
82C MET* 3.1 20.4 + - - +
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Residues in contact with TRP 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C VAL* 3.7 42.8 + - + -
77C THR 4.1 5.1 + - - -
78C ASN* 1.3 73.7 - - - +
80C ASP* 1.3 64.3 + - - +
82C MET* 3.9 5.5 - - + +
83C GLU* 3.0 29.3 + - - +
86C TRP* 4.1 19.5 - + - -
115C ASN* 4.1 34.3 - - + +
118C LYS* 3.4 49.0 - - + +
119C MET* 4.2 13.2 - - + -
122C ILE* 3.5 29.2 - - + -
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Residues in contact with ASP 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU 4.4 11.0 - - - +
68C LYS* 5.2 0.9 - - - -
69C TYR* 1.3 67.0 - - + +
78C ASN* 3.6 4.4 + - - +
79C TRP* 1.3 77.6 + - - +
81C ASP* 1.3 48.3 - - - +
83C GLU* 4.0 12.6 - - + +
84C LYS* 5.0 0.2 - - - -
118C LYS* 5.7 0.3 + - - -
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Residues in contact with ASP 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ILE* 1.7 51.5 - - + +
62C ARG* 5.4 0.2 - - - -
67C LEU* 3.2 31.4 - - - +
69C TYR* 0.4 441.3 + - + +
78C ASN* 2.9 10.2 + - - +
80C ASP* 1.3 65.5 - - - +
82C MET* 1.3 51.9 + - - +
84C LYS* 3.4 0.3 - - - +
85C ILE* 3.1 15.2 + - - +
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Residues in contact with MET 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ASN* 3.2 27.6 - - - +
17C CYS* 4.7 0.2 - - - -
69C TYR* 2.3 2.0 - - - -
70C PRO* 3.8 7.0 - - + +
71C ILE* 3.4 37.9 - - + -
76C VAL* 3.5 24.5 - - + -
78C ASN 3.1 20.7 + - - +
79C TRP* 3.9 7.4 - - + +
81C ASP* 1.3 73.3 - - - +
83C GLU* 1.3 63.7 + - - +
85C ILE* 2.8 42.7 + - + +
86C TRP* 3.1 49.4 + - + +
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Residues in contact with GLU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C TYR* 2.9 21.3 - - + +
79C TRP 3.0 20.7 + - - +
80C ASP* 3.3 10.3 - - + +
82C MET* 1.3 74.1 - - - +
84C LYS* 1.3 64.6 + - - +
86C TRP* 3.3 10.1 + - - +
87C HIS* 3.1 20.8 + - - +
118C LYS* 4.5 6.4 + - - -
122C ILE* 3.9 36.5 - - + +
126C THR* 3.9 22.9 + - + +
127C PHE* 4.0 6.3 - - + -
120L LYS* 5.4 7.8 - - - +
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Residues in contact with LYS 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ILE* 2.7 26.1 - - + +
35C VAL* 2.6 19.4 + - - +
67C LEU 2.9 4.8 - - - -
68C LYS* 0.4 255.4 + - + +
69C TYR* 0.8 211.9 - - + +
81C ASP 3.4 0.4 - - - +
83C GLU* 1.3 66.2 - - - +
85C ILE* 1.3 63.0 + - - +
86C TRP 3.2 0.2 + - - -
87C HIS 3.3 0.5 + - - -
88C HIS* 3.0 19.8 + - - +
122L VAL* 3.4 15.4 - - + +
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Residues in contact with ILE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C CYS* 3.9 16.8 - - - -
31C PHE* 4.0 13.0 - - + -
32C PRO 5.1 2.2 - - - +
33C SER* 4.2 29.8 - - - +
34C ILE* 5.1 12.1 - - + +
69C TYR* 4.8 0.4 - - + -
70C PRO* 3.6 26.7 - - + -
71C ILE* 5.0 0.2 - - + -
81C ASP 3.1 9.6 + - - +
82C MET* 2.8 34.5 + - + +
84C LYS* 1.3 74.7 - - - +
86C TRP* 1.3 60.9 + - + +
88C HIS* 3.2 9.3 + - - +
89C THR* 2.8 31.3 + - - +
122L VAL* 5.5 0.2 - - - -
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Residues in contact with TRP 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C VAL* 3.7 20.4 - - + +
12C ASN* 2.9 38.8 + - - -
76C VAL* 5.6 2.0 - - + -
79C TRP* 4.1 17.3 - + - -
82C MET* 3.1 46.5 + - + +
83C GLU* 3.8 6.7 - - - +
85C ILE* 1.3 77.1 - - + +
87C HIS* 1.3 64.5 + - - +
89C THR* 2.8 28.3 + - - -
90C PHE* 3.1 14.3 + + + -
105C LEU* 4.4 10.5 - - + -
119C MET* 4.2 26.7 - - + -
122C ILE* 4.1 20.2 - - + -
123C MET* 3.5 27.8 - - + -
127C PHE* 3.9 11.7 - + + -
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Residues in contact with HIS 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C TYR 4.6 2.7 - - - +
83C GLU 3.1 13.0 + - - +
84C LYS* 3.4 9.6 - - - +
86C TRP* 1.3 72.9 - - - +
88C HIS* 1.3 57.1 + - - +
90C PHE* 4.5 0.4 - - - -
91C TYR* 2.9 76.7 + + + +
92C ASN* 5.4 2.9 - - - -
127C PHE* 3.7 17.9 - - + -
118L GLY 5.6 1.1 - - - -
119L VAL* 4.5 8.5 - - + -
120L LYS* 4.0 44.7 + - + +
122L VAL* 4.2 7.6 - - + -
143L THR* 4.2 18.6 - - + +
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Residues in contact with HIS 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C PHE* 4.2 22.9 - + - +
84C LYS 3.0 12.5 + - - +
85C ILE* 3.3 9.9 - - - +
87C HIS* 1.3 73.0 - - - +
89C THR* 1.3 58.4 + - - +
92C ASN* 3.0 44.3 + - + +
93C GLU* 2.7 64.2 + - - +
122L VAL* 4.3 18.3 + - + +
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Residues in contact with THR 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C VAL* 3.9 22.5 - - + +
17C CYS* 5.7 0.2 - - - -
19C ALA* 3.7 30.7 - - + -
31C PHE* 3.5 17.2 - - + -
85C ILE* 2.8 18.1 + - - +
86C TRP* 2.8 26.1 + - - -
88C HIS* 1.3 72.6 - - - +
90C PHE* 1.3 58.7 + - + +
93C GLU* 3.4 8.6 - - - +
94C LEU* 2.7 42.0 + - + +
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Residues in contact with PHE 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LEU* 3.3 34.8 - - + -
10C VAL* 4.5 17.7 - - + -
86C TRP* 3.1 30.2 + + + -
87C HIS* 4.1 2.0 - - - +
89C THR* 1.3 78.1 - - + +
91C TYR* 1.3 61.1 + + + +
94C LEU* 4.8 1.1 - - + -
95C ARG 2.8 30.5 + - - -
96C VAL* 2.8 23.6 + - + +
98C PRO* 3.6 33.7 - - + -
103C VAL* 4.0 17.5 - - + -
105C LEU* 5.6 0.2 - - + -
123C MET* 4.0 31.0 - - + -
127C PHE* 4.2 17.7 - + - -
142L TRP* 3.6 0.7 - - - -
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Residues in contact with TYR 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C HIS* 2.9 71.2 + + + +
90C PHE* 1.3 65.8 - - + +
92C ASN* 1.3 64.2 + - - +
96C VAL 4.0 0.9 - - - -
98C PRO* 3.7 24.3 - - + +
99C GLU* 4.8 3.6 + - - -
127C PHE* 4.1 20.8 + + - -
142L TRP* 1.2 87.4 - - + +
143L THR* 4.6 7.2 - - + +
146L LEU* 1.0 129.7 - - + +
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Residues in contact with ASN 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C HIS* 5.4 2.3 - - - -
88C HIS* 3.0 44.7 + - + +
90C PHE 3.4 0.2 - - - -
91C TYR* 1.3 96.1 + - - +
93C GLU* 1.3 71.1 + - - +
95C ARG* 3.5 18.2 - - - +
43L TRP* 4.6 5.0 - - - -
47L GLN* 4.3 4.2 + - - +
122L VAL* 5.0 5.9 - - - +
124L ILE* 4.2 13.3 - - - +
139L GLY* 2.7 44.6 + - - -
142L TRP* 3.7 1.1 - - - -
143L 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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