Contacts of the helix formed by residues 32 - 57 (chain R) in PDB entry 1RZZ
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 GLY 32 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15R THR* 5.5 2.0 - - - -
22R PHE* 3.0 25.7 + - - +
30R TYR* 3.9 10.8 - - - -
31R VAL* 1.3 83.8 - - - +
33R PHE* 1.3 61.4 + - - -
34R PHE 3.1 3.4 - - - -
35R GLY 2.8 15.4 + - - -
36R VAL* 3.3 8.3 + - - +
106R GLU* 3.5 14.6 - - - -
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Residues in contact with PHE 33 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15R THR* 6.0 0.8 - - - +
17R VAL* 3.6 54.1 + - + +
22R PHE* 3.5 33.7 - + + +
32R GLY* 1.3 70.8 - - - -
34R PHE* 1.3 94.1 + + + +
36R VAL* 2.8 29.9 - - + +
37R ALA* 3.1 17.1 + - + +
106R GLU* 3.8 5.3 + - - +
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Residues in contact with PHE 34 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16R LEU* 4.3 12.3 - - + -
17R VAL* 4.3 15.0 - - + -
32R GLY 3.1 0.8 - - - -
33R PHE* 1.3 105.0 - + - +
35R GLY* 1.3 56.2 + - - +
37R ALA* 3.7 5.2 - - + -
38R THR* 2.6 36.9 + - - -
99R SER* 3.5 29.3 - - - +
102R LEU* 3.4 47.6 - - + -
103R ARG* 3.9 12.6 - - + +
106R GLU* 3.9 25.7 + - - +
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Residues in contact with GLY 35 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31R VAL* 3.3 27.5 + - - -
32R GLY 2.8 5.5 + - - -
34R PHE* 1.3 80.4 - - - +
36R VAL* 1.3 57.1 + - - +
38R THR* 3.5 4.7 + - - -
39R PHE* 3.2 23.9 + - - +
103R ARG* 3.6 16.1 - - - +
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Residues in contact with VAL 36 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22R PHE* 4.0 27.8 - - + -
24R PHE* 5.9 1.1 - - + -
31R VAL* 3.7 22.4 - - + -
32R GLY 3.3 1.7 + - - +
33R PHE* 2.8 41.5 - - + +
35R GLY* 1.3 76.4 - - - +
37R ALA* 1.3 59.3 + - - +
39R PHE* 3.5 8.7 - - - +
40R PHE* 2.9 27.2 + - - +
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Residues in contact with ALA 37 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R PHE* 3.1 29.1 + - + +
34R PHE* 3.9 12.1 - - + +
36R VAL* 1.3 76.2 - - - +
38R THR* 1.3 65.4 + - - +
40R PHE* 3.2 8.9 + - + +
41R PHE* 3.0 40.8 + - + -
99R SER* 3.7 16.4 - - - +
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Residues in contact with THR 38 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34R PHE 2.6 22.6 + - - -
35R GLY* 3.7 7.1 - - - -
37R ALA* 1.3 77.3 - - - +
39R PHE* 1.3 53.2 + - - +
41R PHE* 3.7 1.0 - - - +
42R ALA* 2.7 40.7 + - + +
96R ALA* 3.7 22.2 - - + +
99R SER* 3.2 18.9 + - - -
100R TRP* 3.5 25.7 + - + -
103R ARG* 4.9 1.5 - - - -
2006R BPH 3.9 22.4 - - + -
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Residues in contact with PHE 39 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35R GLY 3.2 12.4 + - - +
36R VAL* 3.5 11.9 - - - +
37R ALA 3.3 0.2 - - - -
38R THR* 1.3 77.9 - - - +
40R PHE* 1.3 62.3 + - - +
42R ALA* 3.7 5.5 - - - +
43R ALA* 2.8 42.2 + - + +
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Residues in contact with PHE 40 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36R VAL 2.9 14.5 + - - +
37R ALA* 3.2 12.6 - - + +
38R THR 3.2 0.2 - - - -
39R PHE* 1.3 82.9 - - - +
41R PHE* 1.3 98.4 + + - +
43R ALA* 3.7 2.2 - - - +
44R LEU* 2.9 53.9 + - + +
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Residues in contact with PHE 41 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37R ALA* 3.0 30.7 + - + +
40R PHE* 1.3 105.9 - + - +
42R ALA* 1.3 58.1 + - - +
44R LEU* 4.5 5.6 - - + -
45R GLY* 2.9 28.1 + - - -
91R ILE* 4.8 9.0 - - + -
92R CYS* 3.2 45.0 - - + +
95R GLY* 3.5 32.3 - - - -
96R ALA* 3.7 7.6 - - + -
99R SER* 4.0 7.6 - - - -
2006R BPH 3.7 2.1 - - - +
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Residues in contact with ALA 42 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38R THR* 2.7 26.4 + - + +
39R PHE* 3.8 6.1 - - - +
41R PHE* 1.3 72.9 - - - +
43R ALA* 1.3 58.8 + - - +
45R GLY 4.2 0.2 - - - -
46R ILE* 2.9 38.6 + - + +
96R ALA* 4.2 0.8 - - + +
2006R BPH 3.7 41.7 - - + -
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Residues in contact with ALA 43 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39R PHE* 2.8 37.8 + - + +
40R PHE* 3.7 3.1 - - - +
42R ALA* 1.3 77.7 - - - +
44R LEU* 1.3 65.5 + - - +
46R ILE* 3.4 4.5 + - - +
47R ILE* 2.9 38.5 + - + +
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Residues in contact with LEU 44 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40R PHE* 2.9 44.6 + - + +
41R PHE* 4.0 5.4 - - + +
43R ALA* 1.3 77.4 - - - +
45R GLY* 1.3 56.4 + - - +
47R ILE* 3.1 15.1 + - + +
48R LEU* 2.8 52.0 + - + +
88R ILE* 5.3 3.8 - - + -
92R CYS* 3.6 24.7 - - - -
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Residues in contact with GLY 45 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41R PHE 2.9 17.3 + - - -
44R LEU* 1.3 78.4 - - - +
46R ILE* 1.3 56.6 + - - +
48R LEU* 3.2 7.5 + - - +
49R ILE* 3.0 36.4 + - - +
89R ILE* 4.1 7.5 - - - +
92R CYS* 3.9 17.2 - - - +
2006R BPH 4.3 8.1 - - - -
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Residues in contact with ILE 46 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42R ALA* 2.9 27.7 + - + +
43R ALA* 3.4 5.5 + - - +
44R LEU 3.4 0.4 - - - -
45R GLY* 1.3 75.7 - - - +
47R ILE* 1.3 59.4 + - + +
49R ILE* 3.3 10.3 + - + +
50R ALA* 2.8 29.7 + - + +
2006R BPH 4.0 21.5 - - + -
2004S BCL 4.1 28.3 - - + -
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Residues in contact with ILE 47 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43R ALA* 2.9 35.4 + - + +
44R LEU* 3.3 14.1 - - + +
46R ILE* 1.3 78.5 - - + +
48R LEU* 1.3 63.9 + - + +
50R ALA* 3.3 6.7 + - - +
51R TRP* 2.9 31.1 + - + +
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Residues in contact with LEU 48 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44R LEU* 2.8 35.1 + - + +
45R GLY 3.2 1.1 + - - +
47R ILE* 1.3 83.0 - - + +
49R ILE* 1.3 56.9 + - - +
51R TRP* 3.9 9.1 - - + +
52R SER* 3.1 25.8 + - - -
85R LEU* 3.5 25.7 - - + +
88R ILE* 3.3 42.6 - - + -
89R ILE* 3.5 25.4 - - + +
92R CYS* 4.2 10.5 - - - -
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Residues in contact with ILE 49 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45R GLY 3.0 23.8 + - - +
46R ILE* 3.5 9.6 - - + +
47R ILE 3.1 0.2 - - - -
48R LEU* 1.3 75.6 - - - +
50R ALA* 1.3 61.9 + - - +
52R SER* 3.0 6.6 + - - -
53R ALA* 2.8 27.0 + - - +
64R ILE* 4.4 22.4 - - + +
66R VAL* 4.7 8.7 - - + -
89R ILE* 3.7 23.1 - - + -
148R TYR* 5.6 4.7 - - + -
2006R BPH 3.8 30.1 - - + -
2004S BCL 4.1 18.6 - - + -
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Residues in contact with ALA 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46R ILE* 2.8 22.1 + - + +
47R ILE* 3.6 8.1 - - - +
49R ILE* 1.3 79.3 - - - +
51R TRP* 1.3 61.0 + - - +
53R ALA* 3.1 17.9 - - - +
54R VAL* 3.2 12.7 + - - +
59R TRP* 3.3 24.0 - - + -
64R ILE* 6.2 0.4 - - - -
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Residues in contact with TRP 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47R ILE* 2.9 18.6 + - + +
48R LEU* 4.0 10.8 - - + +
50R ALA* 1.3 72.6 - - - +
52R SER* 1.3 61.7 + - - +
53R ALA 3.0 1.8 - - - -
54R VAL* 2.9 41.7 + - + +
55R LEU* 3.1 36.4 + - + +
80R LEU* 4.4 14.1 - - + -
85R LEU* 3.4 42.2 - - + -
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Residues in contact with SER 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48R LEU 3.1 20.2 + - - -
49R ILE 3.0 6.5 + - - -
51R TRP* 1.3 76.0 - - - +
53R ALA* 1.3 62.3 + - - +
55R LEU* 3.5 7.4 + - - +
56R GLN* 3.1 22.3 + - - +
64R ILE* 5.5 0.8 - - - +
65R SER 4.5 3.8 + - - -
66R VAL* 3.4 33.1 - - - +
85R LEU* 3.4 22.1 - - - +
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Residues in contact with ALA 53 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49R ILE 2.8 12.1 + - - +
50R ALA* 3.1 12.6 - - - +
52R SER* 1.3 77.7 - - - +
54R VAL* 1.3 56.8 + - - +
56R GLN* 3.0 9.1 + - - +
57R GLY 2.9 24.3 + - - -
58R THR 3.2 28.4 + - - +
59R TRP* 3.6 16.8 - - + -
64R ILE* 4.0 23.1 - - + +
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Residues in contact with VAL 54 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50R ALA 3.3 15.0 - - - +
51R TRP* 2.9 27.1 + - + +
53R ALA* 1.3 76.2 - - - +
55R LEU* 1.3 61.5 + - + +
57R GLY* 2.9 21.0 + - - -
58R THR 5.1 0.9 - - - +
59R TRP* 3.9 22.4 - - + -
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Residues in contact with LEU 55 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51R TRP* 3.1 43.9 + - + +
52R SER* 3.8 5.6 - - - +
53R ALA 3.4 0.2 - - - -
54R VAL* 1.3 79.0 - - + +
56R GLN* 1.3 60.1 + - - +
80R LEU* 5.7 0.2 - - + -
81R ALA* 4.2 26.9 - - + +
85R LEU* 4.1 25.8 - - + -
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Residues in contact with GLN 56 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52R SER* 3.1 12.6 + - - +
53R ALA 3.0 11.8 + - - +
55R LEU* 1.3 77.6 - - - +
57R GLY* 1.3 60.4 + - - +
58R THR* 3.3 23.2 - - + +
63R LEU* 2.9 28.5 + - - +
64R ILE* 3.7 4.8 - - - +
65R SER* 2.9 36.3 + - - +
67R TYR* 6.2 0.9 - - - -
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Residues in contact with GLY 57 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53R ALA 2.9 3.8 + - - -
54R VAL* 2.9 13.6 + - - -
55R LEU 3.3 0.2 - - - -
56R GLN* 1.3 78.5 - - - +
58R THR* 1.3 63.6 + - - +
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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