Contacts of the helix formed by residues 31 - 45 (chain W) in PDB entry 5FLX
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 SER 31 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6851 A 3.1 30.3 + - - -
6861 U 3.2 11.9 - - - -
6W VAL* 3.5 15.1 - - - +
30W CYS* 1.3 71.6 + - - +
32W LYS* 1.3 59.8 + - - +
33W VAL* 3.1 14.4 - - - -
34W ILE* 2.9 19.5 + - - +
35W VAL* 2.8 33.5 + - - +
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Residues in contact with LYS 32 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6861 U 2.7 33.5 + - - +
6871 C 3.3 28.2 + - - +
6891 U 6.0 2.7 - - - +
8631 U 5.2 9.9 - - - +
123H THR* 6.3 0.8 - - - +
31W SER* 1.3 73.3 - - - +
33W VAL* 1.3 57.7 + - + +
35W VAL* 4.3 14.9 - - + +
36W ARG* 2.9 47.3 + - + +
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Residues in contact with VAL 33 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8621 A 5.4 1.6 - - - +
8631 U 3.9 36.3 - - - +
8641 A 5.8 0.4 - - - +
7W LEU* 4.5 13.5 - - + -
31W SER* 3.1 8.9 - - - -
32W LYS* 1.3 79.5 - - + +
34W ILE* 1.3 57.5 + - + +
36W ARG* 3.6 4.7 + - - +
37W PHE* 2.9 28.8 + - - +
78W ARG* 5.0 9.0 - - - +
105W THR* 6.0 0.4 - - + +
110W ILE* 5.0 9.7 - - + +
126W LEU* 3.6 37.5 - - + +
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Residues in contact with ILE 34 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6W VAL* 3.7 42.8 - - + +
7W LEU* 3.8 26.9 - - + -
10W ALA* 4.5 15.0 - - + -
27W ILE* 5.3 4.0 - - + -
29W PRO* 4.5 10.1 - - + +
30W CYS* 4.5 1.6 - - - -
31W SER* 2.9 24.5 + - - +
33W VAL* 1.3 75.1 - - + +
35W VAL* 1.3 60.7 + - - +
37W PHE* 3.2 7.0 + - + +
38W LEU* 2.9 46.3 + - + +
61W ILE* 4.3 11.9 - - + -
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Residues in contact with VAL 35 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30W CYS* 5.4 3.4 - - + -
31W SER 2.8 27.1 + - - +
32W LYS* 3.9 16.2 - - + +
33W VAL 3.3 0.2 - - - -
34W ILE* 1.3 74.4 - - - +
36W ARG* 1.3 54.4 + - + +
38W LEU* 3.4 5.2 + - - +
39W THR* 2.6 41.5 + - - +
50W PHE* 5.0 3.3 - - + -
52W ILE* 3.9 33.4 - - + -
61W ILE* 4.3 15.3 - - + -
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Residues in contact with ARG 36 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6891 U 2.7 35.8 + - - -
6901 G 5.0 10.7 + - - -
8621 A 5.8 9.4 - - - -
32W LYS* 2.9 31.4 + - + +
33W VAL* 4.1 0.7 - - - +
35W VAL* 1.3 78.6 - - + +
37W PHE* 1.3 57.3 + - - +
39W THR* 3.2 10.5 + - - -
40W VAL* 2.9 33.2 + - - +
109W GLY* 5.5 6.4 - - - -
110W ILE* 3.8 41.5 - - + +
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Residues in contact with PHE 37 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7W LEU* 4.1 23.8 - - + -
11W LEU* 3.4 39.9 - - + -
33W VAL* 2.9 20.6 + - + +
34W ILE* 3.4 7.9 - - + +
35W VAL 3.2 0.2 - - - -
36W ARG* 1.3 72.9 - - - +
38W LEU* 1.3 70.5 + - + +
39W THR 3.0 4.0 - - - -
40W VAL* 3.0 10.2 + - - +
41W MET* 3.0 45.6 + - - +
103W VAL* 3.4 40.8 - - + -
110W ILE* 5.0 3.6 - - - +
126W LEU* 5.3 1.1 - - + -
127W GLY* 5.6 6.5 - - - -
128W PHE 5.4 1.3 - - - -
129W PHE* 3.7 26.2 - + + -
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Residues in contact with LEU 38 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11W LEU* 5.2 5.8 - - + -
14W ILE* 5.6 4.5 - - + -
27W ILE* 4.8 8.1 - - + -
34W ILE* 2.9 27.3 + - + +
35W VAL* 3.7 2.7 - - - +
37W PHE* 1.3 90.3 - - + +
39W THR* 1.3 56.8 + - - +
41W MET* 3.8 12.0 - - - -
42W MET* 2.9 25.6 + - - +
47W ILE* 3.7 18.3 - - + +
50W PHE* 3.3 27.2 - - + -
61W ILE* 3.9 25.8 - - + -
63W VAL* 3.7 27.8 - - + -
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Residues in contact with THR 39 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149H ASP 6.0 0.7 - - - +
35W VAL* 2.6 26.6 + - - +
36W ARG* 3.3 14.3 - - + -
37W PHE 3.0 0.2 - - - -
38W LEU* 1.3 77.7 - - - +
40W VAL* 1.3 61.3 + - + +
42W MET* 3.1 17.7 + - + +
43W LYS* 2.9 27.3 + - + +
50W PHE* 4.9 5.3 - - - -
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Residues in contact with VAL 40 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36W ARG* 2.9 19.7 + - + +
37W PHE* 3.0 8.5 + - - +
39W THR* 1.3 76.2 - - + +
41W MET* 1.3 56.9 + - - +
43W LYS* 3.1 8.7 + - + +
44W HIS* 2.9 52.9 + - + +
103W VAL* 4.6 11.7 - - + -
110W ILE* 3.9 28.5 - - + +
111W MET 5.2 4.5 - - - -
112W ASP* 4.3 13.0 - - + +
129W PHE* 4.2 8.5 - - + -
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Residues in contact with MET 41 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11W LEU* 5.0 4.0 - - + -
14W ILE* 5.7 1.6 - - + -
37W PHE* 3.0 46.6 + - + +
38W LEU* 3.8 13.7 - - - +
40W VAL* 1.3 76.2 - - - +
42W MET* 1.3 53.5 + - - +
44W HIS* 4.2 7.2 - - - -
45W GLY* 2.6 29.1 + - - -
46W TYR* 3.3 14.9 + - + +
47W ILE* 3.7 25.1 + - + -
69W LEU* 3.6 42.6 - - + -
72W CYS* 5.9 1.1 - - + -
129W PHE* 3.6 33.0 - - + -
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Residues in contact with MET 42 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146H VAL* 3.5 22.0 - - + +
147H LYS 3.3 17.5 - - - +
148H LEU* 3.6 35.8 - - + +
149H ASP* 3.2 34.5 - - - +
38W LEU 2.9 18.4 + - - +
39W THR* 3.2 20.2 - - - +
40W VAL 3.1 0.4 - - - -
41W MET* 1.3 76.5 - - - +
43W LYS* 1.3 63.8 + - - +
45W GLY* 3.2 12.6 + - - -
47W ILE* 4.8 2.2 - - - -
50W PHE* 3.4 28.9 - - + -
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Residues in contact with LYS 43 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39W THR* 2.9 13.0 + - + +
40W VAL* 3.1 9.8 + - - +
42W MET* 1.3 76.4 - - - +
44W HIS* 1.3 70.0 + - + +
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Residues in contact with HIS 44 (chain W).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256C TRP* 4.9 5.0 - - - -
40W VAL* 2.9 32.1 + - + +
41W MET* 3.9 4.0 - - - +
43W LYS* 1.3 91.5 - - + +
45W GLY* 1.3 59.9 + - - +
46W TYR* 3.5 25.0 + - + -
101W PHE* 3.7 29.2 - + + -
112W ASP* 2.9 38.5 + - - +
129W PHE* 3.3 23.4 - + - -
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Residues in contact with GLY 45 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C TRP* 3.3 21.1 - - - -
148H LEU* 5.4 5.2 - - - -
41W MET 2.6 16.2 + - - -
42W MET 3.2 11.1 + - - -
44W HIS* 1.3 75.2 - - - +
46W TYR* 1.3 60.3 + - - -
47W ILE 3.2 9.8 + - - +
66W THR* 3.9 5.9 + - - -
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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