Contacts of the helix formed by residues 28 - 45 (chain U) 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 ASN 28 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26U SER* 3.4 19.4 - - - -
27U ARG* 1.3 82.5 + - + +
29U VAL* 1.3 63.5 + - + +
30U LYS* 4.2 12.2 - - + +
31U SER* 3.2 38.5 + - - +
32U LEU* 3.5 4.5 + - - +
83U ARG 5.3 0.9 - - - -
85U HIS* 5.1 4.7 - - - -
109U GLY* 5.3 1.9 - - - +
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Residues in contact with VAL 29 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14471 G 3.3 51.8 - - - +
14481 A 5.7 2.9 - - - +
28U ASN* 1.3 73.1 - - - +
30U LYS* 1.3 73.8 + - + +
32U LEU* 3.3 6.2 + - + +
33U GLU* 2.9 34.5 + - + +
85U HIS* 4.4 16.2 - - + +
87U ARG* 5.1 0.4 - - - +
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Residues in contact with LYS 30 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D LYS* 3.4 35.8 - - - +
28U ASN* 3.4 13.3 - - + +
29U VAL* 1.3 86.6 - - + +
31U SER* 1.3 64.0 + - - +
33U GLU* 3.1 7.7 + - - +
34U LYS* 2.9 35.2 + - + +
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Residues in contact with SER 31 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26U SER* 4.5 1.3 - - - -
28U ASN* 3.2 28.9 + - - -
29U VAL 3.5 0.2 - - - -
30U LYS* 1.3 78.2 - - - +
32U LEU* 1.3 56.0 + - - +
34U LYS* 3.8 14.6 + - - +
35U VAL* 2.9 32.9 + - - +
107U GLU* 3.4 40.0 + - - +
109U GLY 5.9 0.4 - - - -
110U VAL* 4.5 6.6 - - - +
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Residues in contact with LEU 32 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14471 G 4.5 1.6 - - - +
24U LEU* 3.7 23.1 - - + +
26U SER* 3.3 27.2 + - - +
28U ASN 3.5 11.3 + - - +
29U VAL* 3.3 8.9 + - - +
30U LYS 3.1 1.0 - - - -
31U SER* 1.3 76.2 - - - +
33U GLU* 1.3 60.2 + - - +
35U VAL* 3.3 6.2 - - + +
36U CYS* 2.9 32.4 + - + +
85U HIS* 3.6 32.1 - - + +
87U ARG* 3.5 53.2 - - + +
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Residues in contact with GLU 33 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14471 G 3.6 33.9 + - - +
29U VAL* 2.9 28.8 + - + +
30U LYS* 3.6 6.3 - - - +
32U LEU* 1.3 76.3 - - - +
34U LYS* 1.3 59.2 + - + +
36U CYS* 3.7 5.2 - - - +
37U ALA* 2.9 30.8 + - - +
55U ARG* 4.0 12.8 + - - -
87U ARG* 2.4 38.1 + - - -
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Residues in contact with LYS 34 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30U LYS* 2.9 28.7 + - + +
31U SER* 3.8 12.4 + - - +
33U GLU* 1.3 75.9 - - + +
35U VAL* 1.3 61.1 + - - +
37U ALA* 3.4 3.9 + - - +
38U ASP* 2.9 41.8 + - - +
107U GLU* 5.2 8.5 + - - -
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Residues in contact with VAL 35 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24U LEU* 4.1 22.2 - - + +
31U SER 2.9 21.8 + - - +
32U LEU* 3.3 15.3 - - + +
34U LYS* 1.3 76.1 - - - +
36U CYS* 1.3 60.9 + - - +
38U ASP* 4.4 6.5 - - + -
39U LEU* 2.9 34.4 + - + +
104U ILE* 5.4 8.3 - - + -
105U SER 5.6 0.7 - - - +
106U ILE* 3.6 37.9 - - + -
107U GLU* 5.5 3.1 - - + +
110U VAL* 4.2 15.7 - - + -
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Residues in contact with CYS 36 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24U LEU* 5.1 6.1 - - + -
32U LEU* 2.9 23.5 + - + +
33U GLU* 3.7 9.0 - - - +
35U VAL* 1.3 77.1 - - + +
37U ALA* 1.3 60.6 + - - +
39U LEU* 3.3 4.5 + - - +
40U ILE* 2.9 44.5 + - - +
53U PRO* 3.8 33.2 - - - -
55U ARG* 5.7 1.3 - - - -
87U ARG* 4.0 19.1 - - + +
89U ILE* 5.9 1.8 - - - -
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Residues in contact with ALA 37 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33U GLU 2.9 18.8 + - - +
34U LYS* 4.0 4.7 - - - +
36U CYS* 1.3 77.2 - - - +
38U ASP* 1.3 63.0 + - - +
40U ILE* 4.3 3.9 - - - +
41U ARG* 2.9 31.1 + - - +
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Residues in contact with ASP 38 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34U LYS* 2.9 27.5 + - - +
35U VAL* 4.1 6.9 - - + +
37U ALA* 1.3 80.6 - - - +
39U LEU* 1.3 59.9 + - - +
41U ARG* 3.7 30.5 + - - +
42U GLY* 2.9 24.6 + - - -
104U ILE* 6.5 1.1 - - + -
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Residues in contact with LEU 39 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22U ILE* 4.6 13.7 - - + -
24U LEU* 3.6 28.5 - - + -
35U VAL* 2.9 22.1 + - + +
36U CYS* 3.9 4.0 - - - +
38U ASP* 1.3 75.2 - - - +
40U ILE* 1.3 61.1 + - + +
42U GLY* 3.4 2.5 + - - -
43U ALA* 2.9 28.0 + - + +
89U ILE* 3.6 30.7 - - + -
91U LEU* 6.0 2.9 - - + -
101U ILE* 4.4 16.6 - - + -
104U ILE* 3.6 32.1 - - + -
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Residues in contact with ILE 40 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36U CYS* 2.9 32.7 + - - +
37U ALA* 4.3 3.6 - - - +
39U LEU* 1.3 74.4 - - + +
41U ARG* 1.3 61.9 + - - +
42U GLY 3.1 1.6 - - - -
43U ALA* 2.8 19.3 + - + +
44U LYS* 2.9 47.2 + - + +
50U VAL* 4.3 20.9 - - + -
51U LYS 4.9 1.6 - - - +
53U PRO* 5.4 9.4 - - + -
89U ILE* 4.2 34.3 - - + -
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Residues in contact with ARG 41 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37U ALA 2.9 21.6 + - - +
38U ASP* 3.8 33.4 + - - +
40U ILE* 1.3 76.0 - - - +
42U GLY* 1.3 56.3 + - - +
44U LYS* 4.1 5.9 + - - +
45U GLU* 2.7 17.5 + - - +
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Residues in contact with GLY 42 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38U ASP 2.9 16.7 + - - -
39U LEU* 3.6 3.8 - - - -
41U ARG* 1.3 74.7 - - - +
43U ALA* 1.3 57.4 + - - +
45U GLU* 2.7 32.1 - - - +
46U LYS* 4.7 9.7 - - - +
101U ILE* 6.0 5.2 - - - +
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Residues in contact with ALA 43 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39U LEU* 2.9 17.8 + - + +
40U ILE* 2.8 17.4 + - + +
42U GLY* 1.3 81.0 - - - +
44U LYS* 1.3 62.5 + - - +
45U GLU 3.4 0.6 + - - -
46U LYS* 3.4 18.1 + - - +
48U LEU* 5.3 4.9 - - - +
50U VAL* 4.2 31.8 - - + +
89U ILE* 6.1 1.3 - - + -
91U LEU* 5.1 12.3 - - + -
101U ILE* 6.2 6.5 - - + -
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Residues in contact with LYS 44 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14011 A 6.0 0.2 + - - -
40U ILE* 2.9 38.9 + - + +
41U ARG* 4.9 4.9 - - - +
43U ALA* 1.3 79.5 - - + +
45U GLU* 1.3 62.1 + - - +
46U LYS 2.8 14.0 - - - +
50U VAL* 5.2 12.1 - - + -
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Residues in contact with GLU 45 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41U ARG 2.7 22.6 + - - +
42U GLY* 2.7 32.7 - - - +
44U LYS* 1.3 74.6 - - - +
46U LYS* 1.3 75.2 + - + +
47U ASN* 3.9 0.5 + - - +
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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
------------------------------------------------------------
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