Contacts of the helix formed by residues 78 - 92 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62I ARG* 4.4 15.2 - - - +
69I TYR* 2.7 44.4 + - - +
70I PRO* 3.6 13.9 + - + +
76I VAL* 3.5 10.8 - - - +
77I THR* 1.3 85.1 + - - +
79I TRP* 1.3 60.0 + - - +
80I ASP* 3.9 3.7 + - - +
81I ASP* 3.0 8.3 + - - +
82I MET* 3.1 20.6 + - - +
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Residues in contact with TRP 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76I VAL* 3.7 42.8 + - + -
77I THR 4.1 4.7 + - - -
78I ASN* 1.3 73.4 - - - +
80I ASP* 1.3 65.2 + - - +
82I MET* 3.6 5.3 + - + +
83I GLU* 3.0 29.8 + - - +
86I TRP* 4.1 21.1 - + - -
115I ASN* 4.1 34.5 - - + +
118I LYS* 3.4 49.2 - - + +
119I MET* 4.2 13.0 - - + -
122I ILE* 3.5 28.3 - - + -
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Residues in contact with ASP 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67I LEU 4.4 11.4 - - - +
68I LYS* 5.2 0.9 - - - -
69I TYR* 1.3 66.9 - - + +
78I ASN* 3.6 3.9 + - - -
79I TRP* 1.3 78.2 + - - +
81I ASP* 1.3 47.9 - - - +
83I GLU* 4.0 12.9 - - + +
84I LYS* 5.0 0.2 - - - -
118I LYS* 5.7 0.3 + - - -
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Residues in contact with ASP 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I ILE* 1.7 51.4 - - + +
62I ARG* 4.8 0.4 + - - -
67I LEU* 3.2 30.7 - - - +
69I TYR* 0.4 441.4 + - + +
70I PRO* 4.2 0.2 - - - -
78I ASN* 2.9 9.9 + - - +
80I ASP* 1.3 66.3 - - - +
82I MET* 1.3 51.4 + - - +
84I LYS* 3.4 0.2 - - - +
85I ILE* 3.1 14.9 + - - +
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Residues in contact with MET 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I ASN* 3.2 27.1 - - - +
17I CYS* 4.7 0.4 - - - -
69I TYR* 2.3 2.2 - - - -
70I PRO* 3.8 7.4 - - + +
71I ILE* 3.4 38.6 - - + -
76I VAL* 3.5 24.5 - - + -
78I ASN 3.1 19.0 + - - +
79I TRP* 3.9 8.5 - - + +
81I ASP* 1.3 73.7 - - - +
83I GLU* 1.3 62.6 + - - +
85I ILE* 2.8 42.9 + - + +
86I TRP* 3.1 50.5 + - + +
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Residues in contact with GLU 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69I TYR* 2.8 20.5 - - + +
79I TRP* 3.0 21.6 + - - +
80I ASP* 3.3 10.4 - - - +
82I MET* 1.3 73.1 - - - +
84I LYS* 1.3 64.6 + - - +
86I TRP* 3.3 10.8 + - - +
87I HIS* 3.1 21.1 + - - +
118I LYS* 4.5 6.1 + - - -
122I ILE* 3.9 37.8 - - + +
126I THR* 3.9 22.8 + - - +
127I PHE* 4.0 6.8 - - + -
120R LYS* 5.3 8.5 - - - +
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Residues in contact with LYS 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I ILE* 2.7 24.8 - - + +
35I VAL* 2.6 20.4 + - - +
67I LEU 2.9 5.5 - - - -
68I LYS* 0.4 253.0 + - + +
69I TYR* 0.8 211.5 - - + +
83I GLU* 1.3 65.0 - - - +
85I ILE* 1.3 63.5 + - - +
86I TRP 3.2 0.3 + - - -
87I HIS* 3.3 0.7 + - - +
88I HIS* 3.0 19.9 + - - +
122R VAL* 3.3 15.1 - - + +
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Residues in contact with ILE 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I CYS* 3.9 17.0 - - - -
31I PHE* 4.0 12.1 - - + -
32I PRO 5.1 1.8 - - - +
33I SER* 4.2 31.2 - - - +
34I ILE* 5.1 11.7 - - + +
69I TYR* 4.8 0.4 - - + -
70I PRO* 3.6 26.5 - - + -
71I ILE* 5.0 0.2 - - + -
81I ASP 3.1 10.1 + - - +
82I MET* 2.8 34.5 + - + +
84I LYS* 1.3 76.1 - - - +
86I TRP* 1.3 60.2 + - + +
88I HIS* 3.2 9.9 + - - +
89I THR* 2.8 32.3 + - - +
122R VAL* 5.5 0.2 - - - -
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Residues in contact with TRP 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I VAL* 3.7 20.5 - - + +
12I ASN* 2.9 37.1 + - - -
76I VAL* 5.6 1.3 - - + -
79I TRP* 4.1 16.6 - + - -
82I MET* 3.1 48.3 + - + +
83I GLU* 3.8 6.3 - - - +
85I ILE* 1.3 77.9 - - + +
87I HIS* 1.3 64.0 + - - +
89I THR* 2.8 29.0 + - - -
90I PHE* 3.1 14.6 + + + -
105I LEU* 4.4 11.2 - - + +
119I MET* 4.2 27.8 - - + -
122I ILE* 4.0 21.5 - - + -
123I MET* 3.5 27.4 - - + -
127I PHE* 3.9 12.6 - + + -
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Residues in contact with HIS 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69I TYR 4.6 2.2 - - - +
83I GLU 3.1 13.6 + - - +
84I LYS* 3.4 9.6 - - - +
86I TRP* 1.3 72.3 - - - +
88I HIS* 1.3 57.5 + - - +
90I PHE* 4.5 0.4 - - - -
91I TYR* 2.9 77.6 + + + +
92I ASN* 5.4 2.2 - - - -
127I PHE* 3.7 18.1 - - + -
118R GLY 5.6 1.1 - - - -
119R VAL* 4.4 9.0 - - + -
120R LYS* 4.0 44.9 + - + +
122R VAL* 4.2 7.4 - - + -
143R THR* 4.1 18.6 - - + +
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Residues in contact with HIS 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I PHE* 4.2 22.2 - + - +
84I LYS 3.0 11.7 + - - +
85I ILE* 3.3 10.1 - - - +
87I HIS* 1.3 72.9 - - - +
89I THR* 1.3 58.6 + - - +
92I ASN* 3.0 46.1 + - + +
93I GLU* 2.7 65.6 + - - +
122R VAL* 4.3 19.6 + - + +
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Residues in contact with THR 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I VAL* 3.9 22.5 - - + +
17I CYS* 5.7 0.3 - - - +
19I ALA* 3.7 31.4 - - + -
31I PHE* 3.5 17.2 - - + -
85I ILE* 2.8 17.7 + - - +
86I TRP* 2.8 27.7 + - - -
88I HIS* 1.3 72.8 - - - +
90I PHE* 1.3 58.1 + - + +
93I GLU* 3.3 8.5 + - - +
94I LEU* 2.7 41.3 + - + +
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Residues in contact with PHE 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I LEU* 3.3 34.8 - - + -
10I VAL* 4.5 17.9 - - + -
86I TRP* 3.1 30.2 + + + -
87I HIS* 4.1 2.2 - - - +
89I THR* 1.3 79.1 - - + +
91I TYR* 1.3 61.4 + + + +
94I LEU* 4.8 1.1 - - + -
95I ARG 2.8 30.5 + - - -
96I VAL* 2.8 23.4 + - + +
98I PRO* 3.6 32.3 - - + -
103I VAL* 4.0 17.9 - - + -
105I LEU* 5.6 0.2 - - + -
123I MET* 4.0 29.6 - - + -
127I PHE* 4.2 18.8 - + + -
142R TRP* 3.6 1.1 - - - -
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Residues in contact with TYR 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87I HIS* 2.9 69.8 + + + +
90I PHE* 1.3 65.3 - - + +
92I ASN* 1.3 64.3 + - - +
98I PRO* 3.7 25.2 - - + +
99I GLU* 4.8 3.6 + - - -
127I PHE* 4.1 20.2 + + - -
142R TRP* 1.2 58.0 - - + +
143R THR* 4.5 6.5 - - - +
146R LEU* 1.0 129.5 - - + +
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Residues in contact with ASN 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87I HIS* 5.4 2.5 - - - -
88I HIS* 3.0 43.6 + - + +
91I TYR* 1.3 94.4 + - - +
93I GLU* 1.3 72.0 + - - +
94I LEU 3.9 0.2 - - - -
95I ARG* 3.5 18.3 - - - +
43R TRP* 4.6 4.9 - - - -
47R GLN* 4.3 4.0 + - - +
122R VAL* 5.0 5.9 - - - +
124R ILE* 4.1 13.9 - - - +
139R GLY* 2.6 45.3 + - - -
142R TRP* 3.7 0.9 - - - -
143R 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
------------------------------------------------------------
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