Contacts of the helix formed by residues 78 - 92 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62F ARG* 4.4 15.6 - - - +
69F TYR* 2.7 43.2 + - - +
70F PRO* 3.6 14.7 + - + +
76F VAL* 3.5 10.4 - - - +
77F THR* 1.3 85.5 + - - +
79F TRP* 1.3 60.9 + - - +
80F ASP* 3.9 4.4 + - - +
81F ASP* 3.0 7.7 + - - +
82F MET* 3.1 20.1 + - - +
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Residues in contact with TRP 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F VAL* 3.7 43.7 + - + -
77F THR 4.1 5.4 + - - -
78F ASN* 1.3 73.9 - - - +
80F ASP* 1.3 65.2 + - - +
82F MET* 3.6 5.5 + - + +
83F GLU* 3.0 29.4 + - - +
86F TRP* 4.1 20.2 - + - -
115F ASN* 4.1 34.2 - - + +
118F LYS* 3.4 47.4 - - + +
119F MET* 4.2 13.0 - - + -
122F ILE* 3.5 28.9 - - + -
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Residues in contact with ASP 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F LEU 4.4 10.6 - - - +
68F LYS* 5.2 0.9 - - - -
69F TYR* 1.3 66.7 - - + +
78F ASN* 3.9 3.6 + - - +
79F TRP* 1.3 77.8 - - - +
81F ASP 1.3 47.4 - - - +
83F GLU* 4.0 13.2 - - + +
84F LYS* 5.0 0.2 - - - -
118F LYS* 5.8 0.3 + - - -
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Residues in contact with ASP 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F ILE* 1.7 50.7 - - + +
62F ARG* 4.8 0.2 + - - -
67F LEU* 3.2 30.0 - - - +
69F TYR* 0.4 442.1 + - + +
78F ASN* 2.9 9.7 + - - +
80F ASP* 1.3 65.7 - - - +
82F MET* 1.3 51.4 + - - +
84F LYS* 3.4 0.3 - - - +
85F ILE* 3.1 14.9 + - - +
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Residues in contact with MET 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F ASN* 3.2 27.1 - - - +
17F CYS* 4.7 0.2 - - - -
69F TYR* 2.3 2.0 - - - -
70F PRO* 3.8 7.2 - - + +
71F ILE* 3.4 39.3 - - + -
76F VAL* 3.5 23.6 - - + -
78F ASN 3.1 20.1 + - - +
79F TRP* 3.9 8.1 - - + +
81F ASP* 1.3 73.9 - - - +
83F GLU* 1.3 62.1 + - - +
85F ILE* 2.8 42.7 + - + +
86F TRP* 3.1 50.6 + - + +
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Residues in contact with GLU 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F TYR* 2.9 20.4 - - + +
79F TRP 3.0 20.6 + - - +
80F ASP* 3.3 11.4 - - - +
82F MET* 1.3 73.7 - - - +
84F LYS* 1.3 64.1 + - - +
86F TRP* 3.3 10.3 + - - +
87F HIS* 3.1 20.6 + - - +
118F LYS* 4.5 5.7 + - - -
122F ILE* 3.9 37.9 - - + +
126F THR* 3.9 22.2 + - - +
127F PHE* 4.0 6.4 - - + -
120Q LYS* 5.3 8.1 - - - +
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Residues in contact with LYS 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F ILE* 2.7 26.4 - - + +
35F VAL* 2.6 20.0 + - - +
67F LEU 2.9 4.8 - - - -
68F LYS* 0.4 254.8 + - + +
69F TYR* 0.8 211.0 - - + +
83F GLU* 1.3 65.4 - - - +
85F ILE* 1.3 62.5 + - - +
86F TRP 3.2 0.3 + - - -
87F HIS 3.3 0.5 + - - -
88F HIS* 3.0 20.1 + - - +
120Q LYS* 4.6 0.2 - - + -
122Q VAL* 3.4 14.5 - - + +
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Residues in contact with ILE 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F CYS* 3.9 17.0 - - - -
31F PHE* 4.0 12.8 - - + -
32F PRO 5.1 2.0 - - - +
33F SER* 4.2 30.1 - - - +
34F ILE* 5.1 11.0 - - + +
69F TYR* 4.8 0.7 - - + -
70F PRO* 3.6 27.1 - - + -
71F ILE* 5.0 0.2 - - + -
81F ASP 3.1 9.8 + - - +
82F MET* 2.8 34.7 + - + +
84F LYS* 1.3 76.0 - - - +
86F TRP* 1.3 61.7 + - + +
88F HIS* 3.2 8.8 + - - +
89F THR* 2.8 32.7 + - - +
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Residues in contact with TRP 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F VAL* 3.7 20.3 - - + +
12F ASN* 2.9 38.7 + - - -
76F VAL* 5.6 1.3 - - + -
79F TRP* 4.1 17.9 - + - -
82F MET* 3.1 47.0 + - + +
83F GLU* 3.8 5.8 - - - +
85F ILE* 1.3 76.6 - - + +
87F HIS* 1.3 65.4 + - - +
89F THR* 2.8 29.3 + - - -
90F PHE* 3.1 15.5 + + + -
105F LEU* 4.4 11.0 - - + -
119F MET* 4.2 27.1 - - + -
122F ILE* 4.0 20.2 - - + -
123F MET* 3.5 27.8 - - + -
127F PHE* 3.9 12.6 - + + -
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Residues in contact with HIS 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F TYR 4.6 2.5 - - - +
83F GLU 3.1 12.7 + - - +
84F LYS* 3.4 10.3 - - - +
86F TRP* 1.3 73.0 - - - +
88F HIS* 1.3 58.2 + - - +
90F PHE* 4.5 0.9 - - - -
91F TYR* 2.9 77.5 + + + +
92F ASN* 5.4 2.5 - - - -
127F PHE* 3.7 18.5 - - + -
118Q GLY 5.6 0.9 - - - -
119Q VAL* 4.4 8.7 - - + -
120Q LYS* 4.0 44.9 + - + +
122Q VAL* 4.2 7.9 - - + -
143Q THR* 4.1 19.1 - - + +
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Residues in contact with HIS 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F PHE* 4.2 22.4 - + - +
84F LYS 3.0 11.9 + - - +
85F ILE* 3.3 9.0 - - - +
87F HIS* 1.3 73.1 - - - +
89F THR* 1.3 57.7 + - - +
92F ASN* 3.0 45.7 + - + +
93F GLU* 2.7 64.2 + - - +
122Q VAL* 4.3 19.0 + - + +
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Residues in contact with THR 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F VAL* 3.9 22.1 - - + +
17F CYS* 5.7 0.2 - - - -
19F ALA* 3.7 30.7 - - + -
31F PHE* 3.5 17.5 - - + -
85F ILE* 2.8 18.0 + - - +
86F TRP* 2.8 27.9 + - - -
88F HIS* 1.3 71.8 - - - +
90F PHE* 1.3 57.8 + - + +
93F GLU* 3.3 8.6 + - - +
94F LEU* 2.7 41.6 + - + +
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Residues in contact with PHE 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F LEU* 3.3 34.5 - - + -
10F VAL* 4.5 17.0 - - + -
86F TRP* 3.1 30.3 + + + -
87F HIS* 4.1 2.5 - - - +
89F THR* 1.3 78.0 - - + +
91F TYR* 1.3 61.8 + - + +
94F LEU* 4.8 0.4 - - - -
95F ARG 2.8 30.7 + - - -
96F VAL* 2.8 23.4 + - + +
98F PRO* 3.6 32.8 - - + -
103F VAL* 4.0 17.5 - - + -
105F LEU* 5.6 0.2 - - + -
123F MET* 4.0 31.0 - - + -
127F PHE* 4.2 18.2 - + - -
142Q TRP* 3.6 0.9 - - - -
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Residues in contact with TYR 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F HIS* 2.9 70.5 + + + +
90F PHE* 1.3 65.7 - - + +
92F ASN* 1.3 64.9 + - - +
96F VAL 4.0 0.7 - - - -
98F PRO* 3.7 25.0 - - + +
99F GLU* 4.8 4.0 + - - -
127F PHE* 4.1 20.9 + + - -
142Q TRP* 1.2 58.7 - - + +
143Q THR* 4.5 6.5 - - + +
146Q LEU* 1.0 127.6 - - + +
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Residues in contact with ASN 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F HIS* 5.4 3.4 - - - -
88F HIS* 3.0 43.6 + - + +
91F TYR* 1.3 96.1 + - - +
93F GLU* 1.3 71.7 + - - +
95F ARG* 3.5 17.7 - - - +
43Q TRP* 4.6 4.9 - - - -
47Q GLN* 4.3 4.7 + - - +
122Q VAL* 5.0 5.4 - - - +
124Q ILE* 4.2 14.0 - - - +
139Q GLY* 2.7 44.7 + - - -
142Q TRP* 3.7 0.7 - - - -
143Q THR* 3.3 9.8 + - - -
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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