Contacts of the helix formed by residues 45 - 64 (chain I) in PDB entry 3UF2
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 ASP 45 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I LEU* 3.6 5.0 - - + +
44I LYS* 1.3 79.4 - - - +
46I PRO* 1.3 69.5 - - - +
47I VAL* 3.9 4.4 + - - +
48I CYS* 3.1 31.3 + - + +
49I TYR* 2.8 29.7 + - - +
137I LYS* 2.6 33.2 + - - -
142I SER* 3.8 11.9 + - - +
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Residues in contact with PRO 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I LYS* 3.0 13.2 - - - +
45I ASP* 1.3 91.8 - - - +
47I VAL* 1.3 66.2 + - + +
49I TYR* 3.0 8.6 + - + +
50I LEU* 2.9 34.8 + - + +
123I GLU* 5.6 6.3 - - + +
127I LEU* 5.3 6.1 - - + -
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Residues in contact with VAL 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I ASP* 3.4 2.4 - - - +
46I PRO* 1.3 81.4 - - + +
48I CYS* 1.3 59.1 + - - +
50I LEU* 3.2 6.7 + - - +
51I LYS* 3.1 29.2 + - + +
127I LEU* 4.7 5.8 - - + -
134I ILE* 3.6 46.0 - - + +
135I PHE* 3.8 18.6 - - + -
137I LYS* 3.7 38.1 - - + +
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Residues in contact with CYS 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I LEU* 3.6 6.8 - - + +
45I ASP* 3.1 28.1 + - - +
46I PRO 3.3 0.4 - - - -
47I VAL* 1.3 77.8 - - - +
49I TYR* 1.3 64.9 + - - +
51I LYS* 3.3 1.1 + - - -
52I LYS 3.2 18.2 + - - -
137I LYS* 4.0 7.6 - - - -
139I CYS* 2.0 59.5 - - + -
142I SER* 3.5 21.1 - - - -
143I PHE* 3.5 16.1 - - + -
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Residues in contact with TYR 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I PHE* 3.4 25.0 - + - -
38I VAL* 3.3 36.7 + - + +
39I ASP 4.3 0.7 - - - -
40I GLN* 4.0 34.1 + - + +
43I LEU* 3.5 29.6 - - + +
44I LYS 5.1 0.4 - - - +
45I ASP 2.8 18.4 + - - +
46I PRO* 3.3 9.0 - - + +
48I CYS* 1.3 77.6 - - - +
50I LEU* 1.3 75.0 + - + +
52I LYS* 4.0 1.4 - - - +
53I ALA* 2.9 40.0 + - + +
116I LYS* 5.4 4.2 - - - +
119I ASN* 5.2 7.4 - - - -
120I VAL* 5.0 5.5 - - + +
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Residues in contact with LEU 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I PRO* 2.9 20.9 + - + +
47I VAL 3.5 5.8 - - - +
49I TYR* 1.3 90.8 - - + +
51I LYS* 1.3 59.8 + - - +
53I ALA* 3.9 2.4 - - - +
54I PHE* 2.9 32.7 + - - +
91I PHE* 4.0 3.0 - - + -
119I ASN* 5.1 2.5 - - - +
120I VAL* 4.2 21.5 - - + +
123I GLU* 4.0 22.4 - - + -
124I THR* 3.9 21.1 - - - +
127I LEU* 3.7 30.5 - - + -
135I PHE* 3.7 24.2 - - + -
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Residues in contact with LYS 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I VAL* 3.1 19.5 + - + +
48I CYS* 3.3 7.8 + - - +
50I LEU* 1.3 78.2 - - - +
52I LYS* 1.3 60.8 + - - +
54I PHE* 3.9 2.8 - - - +
55I LEU* 3.5 25.3 + - - +
91I PHE* 3.8 20.3 - - + -
92I THR* 2.8 37.0 + - - +
94I ASP* 3.0 15.0 + - - +
135I PHE* 3.3 34.3 + - + +
137I LYS 2.8 23.2 + - - +
139I CYS* 3.5 21.8 - - - -
143I PHE* 4.5 8.1 - - + -
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Residues in contact with LYS 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I VAL* 3.7 20.0 - - + -
43I LEU* 4.2 3.6 - - + -
48I CYS 3.2 12.8 + - - +
49I TYR 4.0 2.5 - - - +
51I LYS* 1.3 77.8 - - - +
53I ALA* 1.3 65.2 + - - +
55I LEU* 3.2 26.6 + - - +
56I LEU* 3.3 18.2 + - + +
100I LYS 5.9 0.2 - - - +
101I ALA* 3.0 43.2 + - - +
102I CYS* 4.1 9.4 - - + -
103I VAL* 4.1 9.0 - - + -
143I PHE* 3.7 38.0 - - + -
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Residues in contact with ALA 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I PHE* 4.1 7.0 - - + -
38I VAL* 3.3 19.5 - - + +
49I TYR* 2.9 28.0 + - + +
50I LEU* 3.9 5.2 - - - +
52I LYS* 1.3 76.2 - - - +
54I PHE* 1.3 62.1 - - - +
56I LEU* 3.0 6.2 + - - +
57I VAL* 2.9 27.8 + - - +
120I VAL* 3.9 25.4 - - + -
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Residues in contact with PHE 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I LEU 2.9 19.7 + - - +
51I LYS 3.9 4.3 - - - +
52I LYS 3.2 0.2 - - - -
53I ALA* 1.3 77.8 - - - +
55I LEU* 1.3 73.4 + - + +
57I VAL* 3.3 17.2 + - + +
58I GLN* 3.6 13.4 + - + +
84I SER* 3.4 40.4 - - - -
87I LEU* 3.4 39.7 - - + -
88I LYS* 4.1 19.1 - - + -
91I PHE* 3.8 38.4 - + + -
120I VAL* 4.6 13.4 - - + +
121I PHE* 4.8 8.5 - + - -
124I THR* 5.6 3.1 - - + +
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Residues in contact with LEU 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I LYS 3.5 17.7 + - - +
52I LYS* 3.2 22.3 + - - +
54I PHE* 1.3 89.4 - - + +
56I LEU* 1.3 63.1 + - + +
58I GLN* 3.3 22.1 - - - +
59I ASP* 4.1 6.2 + - - +
88I LYS* 4.6 13.2 - - + +
91I PHE* 6.2 3.1 - - + -
93I LYS* 4.1 25.6 - - + +
143I PHE* 6.1 2.2 - - + -
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Residues in contact with LEU 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I GLU* 4.5 19.1 - - + +
37I PHE* 3.8 15.7 - - + -
38I VAL* 3.3 46.9 - - + +
52I LYS* 3.3 10.7 + - + +
53I ALA 3.0 6.8 + - - +
55I LEU* 1.3 77.0 - - + +
57I VAL* 1.3 66.4 + - - +
58I GLN 3.0 2.5 - - - -
59I ASP* 2.9 26.6 + - + +
60I ILE* 3.2 13.4 + - + +
100I LYS* 6.3 2.5 - - + -
103I VAL* 4.0 24.0 - - + -
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Residues in contact with VAL 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I PHE* 4.0 17.5 - - + -
53I ALA 2.9 22.5 + - - +
54I PHE* 3.3 10.5 + - + +
56I LEU* 1.3 74.9 - - - +
58I GLN* 1.3 58.0 + - - +
60I ILE* 4.3 8.1 - - + -
61I MET* 2.8 61.3 + - + +
84I SER* 5.5 0.4 - - - +
117I VAL* 4.2 17.7 - - + -
120I VAL* 4.3 21.5 - - + -
121I PHE* 4.0 16.2 - - + -
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Residues in contact with GLN 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I PHE* 3.8 11.9 - - + +
55I LEU* 3.3 16.4 - - - +
56I LEU 3.0 0.4 + - - -
57I VAL* 1.3 79.3 - - - +
59I ASP* 1.3 64.3 + - - +
61I MET* 3.0 35.5 + - - +
62I GLU* 3.4 21.1 + - - +
81I GLN* 4.2 10.1 + - - +
84I SER* 3.0 33.8 + - - -
85I LEU* 4.2 9.9 - - - +
88I LYS* 4.0 28.5 - - - +
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Residues in contact with ASP 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I LEU 4.4 7.5 - - - +
56I LEU* 2.9 19.6 + - + +
58I GLN* 1.3 78.7 - - - +
60I ILE* 1.3 58.9 + - + +
62I GLU* 3.3 2.8 + - - -
63I ASP* 2.8 49.6 + - - +
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Residues in contact with ILE 60 (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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35I PHE* 4.4 9.4 - - + -
36I GLU 3.4 26.9 - - - +
37I PHE* 3.8 23.6 - - + -
56I LEU 3.2 9.3 + - - +
57I VAL* 3.1 10.6 + - - +
59I ASP* 1.3 79.3 - - + +
61I MET* 1.3 58.4 + - + +
63I ASP* 5.1 0.2 - - - -
64I THR* 2.9 45.7 + - - +
65I MET* 2.9 27.9 + - - -
113I LEU* 4.0 27.6 - - + -
117I VAL* 4.8 4.9 - - + -
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Residues in contact with MET 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57I VAL* 2.8 43.9 + - + +
58I GLN* 3.0 31.9 - - - +
60I ILE* 1.3 72.9 - - - +
62I GLU* 1.3 59.3 + - - +
65I MET* 3.0 47.0 - - + +
77I ILE* 3.9 12.6 - - + +
80I LEU* 3.8 30.3 - - - +
81I GLN* 3.9 30.7 + - + +
84I SER* 3.8 10.8 - - - +
117I VAL* 5.2 1.8 - - + -
121I PHE* 4.4 6.5 - - - -
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Residues in contact with GLU 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D LEU* 4.8 2.1 - - - +
88D LYS* 2.8 41.2 + - - +
93D LYS* 5.2 10.4 + - - -
58I GLN 3.4 14.5 + - - +
59I ASP* 3.3 5.5 + - - +
60I ILE 3.2 0.2 - - - -
61I MET* 1.3 81.8 - - - +
63I ASP* 1.3 71.2 + - - +
65I MET 5.1 1.1 - - - +
66I ARG* 5.4 5.4 - - - +
81I GLN* 3.7 22.4 + - - +
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Residues in contact with ASP 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I ASP* 2.8 34.4 + - - +
62I GLU* 1.3 92.5 - - - +
64I THR* 1.3 67.0 + - - +
65I MET 5.4 0.4 - - - -
66I ARG* 5.3 4.4 - - - +
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Residues in contact with THR 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I ILE* 4.1 16.6 - - + -
34I THR 5.1 4.1 + - - +
35I PHE* 4.6 10.8 - - + +
60I ILE* 2.9 31.3 + - - +
63I ASP* 1.3 83.1 - - - +
65I MET* 1.3 60.4 + - + +
66I ARG* 3.1 9.3 + - - +
113I LEU* 3.8 24.9 - - + -
27J MET* 4.3 7.3 - - + +
28J GLU 4.1 12.3 - - - +
29J THR* 5.3 2.0 - - + +
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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) + - + + + + + -
------------------------------------------------------------
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