Contacts of the helix formed by residues 9 - 21 (chain X) 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 THR 9 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6811 U 3.2 41.5 - - - +
101L ARG* 3.2 4.9 + - - -
4X CYS* 3.1 40.5 + - - -
6X GLY* 2.5 30.1 + - - -
7X LEU 3.3 0.2 - - - -
8X ARG* 1.3 75.0 - - - +
10X ALA* 1.3 64.9 + - - +
11X ARG 3.1 2.9 - - - -
12X LYS* 3.0 20.8 + - - +
13X LEU* 3.0 11.1 + - - +
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Residues in contact with ALA 10 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96L ILE* 3.7 25.6 - - + -
99L TYR* 3.8 14.8 - - + -
101L ARG* 3.7 25.7 - - + +
102L PHE 3.9 6.7 - - - +
103L GLU* 4.3 1.8 - - + -
7X LEU 4.4 1.0 + - - -
8X ARG 3.3 2.8 - - - -
9X THR* 1.3 78.0 + - - +
11X ARG* 1.3 57.3 + - - +
13X LEU* 3.1 15.4 + - - +
14X ARG* 2.9 29.7 + - - +
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Residues in contact with ARG 11 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3991 C 3.6 44.7 + - - -
4001 C 3.9 11.9 + - - -
6801 G 5.8 1.6 + - - -
6811 U 5.7 1.6 + - - -
103L GLU* 3.2 39.5 + - + +
104L LYS* 2.4 42.2 + - - +
105L ARG* 3.4 20.2 - - - +
8X ARG 5.2 3.7 + - - +
9X THR 3.0 1.3 + - - -
10X ALA* 1.3 79.0 - - - +
12X LYS* 1.3 56.5 + - - +
14X ARG* 3.3 12.3 - - + +
15X SER* 2.9 35.3 + - - -
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Residues in contact with LYS 12 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6801 G 5.9 3.1 - - - +
11611 U 4.3 19.5 - - - +
11621 C 3.1 40.0 + - - -
4X CYS* 5.2 9.9 - - + -
9X THR* 3.0 16.8 + - - +
11X ARG* 1.3 79.2 - - - +
13X LEU* 1.3 58.9 + - + +
15X SER* 4.4 7.2 + - - -
16X HIS* 2.9 49.5 + - + +
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Residues in contact with LEU 13 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6601 C 4.5 21.5 - - - +
99L TYR* 3.5 39.3 - - + -
101L ARG* 3.2 42.0 - - - +
3X LYS* 5.7 2.2 - - + -
4X CYS* 3.8 18.4 - - + +
9X THR 3.0 15.0 + - - +
10X ALA* 3.2 11.9 - - - +
11X ARG 3.1 0.2 - - - -
12X LYS* 1.3 77.8 - - + +
14X ARG* 1.3 58.6 + - - +
16X HIS* 4.1 1.7 - - - +
17X ARG* 2.9 39.3 + - + +
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Residues in contact with ARG 14 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3561 C 5.1 4.0 + - - -
3571 C 4.1 17.6 + - - -
96L ILE* 3.3 49.2 - - - +
99L TYR* 3.4 22.4 - - + +
103L GLU* 4.4 8.3 + - - -
105L ARG* 4.4 11.7 - - - +
10X ALA 2.9 13.8 + - - +
11X ARG* 3.3 17.7 - - + +
13X LEU* 1.3 73.5 - - - +
15X SER* 1.3 61.3 + - - +
17X ARG* 4.2 1.3 - - - +
18X ARG* 2.9 39.5 + - - +
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Residues in contact with SER 15 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4001 C 5.9 0.5 + - - -
11X ARG* 2.9 21.5 + - - -
12X LYS* 4.0 11.2 + - - +
14X ARG* 1.3 76.9 - - - +
16X HIS* 1.3 60.5 + - - +
18X ARG* 3.3 22.1 + - - +
19X ASP* 2.9 44.1 + - - +
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Residues in contact with HIS 16 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6591 G 5.9 4.5 + - - -
11621 C 5.8 1.5 + - - -
11631 C 2.9 47.4 + + - -
11641 G 5.4 1.6 + - - -
12X LYS* 2.9 40.4 + - + +
13X LEU* 4.1 2.2 - - - +
15X SER* 1.3 76.2 + - - +
17X ARG* 1.3 65.5 + - + +
19X ASP* 3.3 6.9 + - - +
20X GLN* 2.9 64.4 + - + +
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Residues in contact with ARG 17 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6581 U 2.2 65.5 + - - +
6591 G 3.1 52.3 + - - +
6601 C 2.9 28.5 + - - +
98L LYS* 5.4 7.3 - - - +
99L TYR* 3.5 19.6 + - + +
13X LEU* 2.9 25.6 + - + +
14X ARG* 4.2 1.6 - - - +
16X HIS* 1.3 84.2 - - + +
18X ARG* 1.3 59.3 + - - +
20X GLN* 3.3 4.8 + - - +
21X LYS* 2.9 33.1 + - - +
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Residues in contact with ARG 18 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3581 C 3.2 42.3 + - - +
3591 U 3.0 36.3 + - - +
14X ARG* 2.9 28.3 + - - +
15X SER* 3.3 22.8 + - - +
17X ARG* 1.3 76.7 - - - +
19X ASP* 1.3 65.7 + - - +
21X LYS* 3.7 12.4 + - - +
22X TRP* 3.0 22.7 + - - +
27X TYR* 5.0 4.5 + - - +
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Residues in contact with ASP 19 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3591 U 3.9 12.6 + - - -
3601 A 5.3 3.5 + - - -
15X SER* 2.9 30.0 + - - +
16X HIS* 3.8 6.8 - - - +
18X ARG* 1.3 84.3 + - - +
20X GLN* 1.3 70.5 + - + +
21X LYS 3.1 1.1 + - - -
22X TRP* 3.4 23.0 + - - +
23X HIS* 3.7 10.7 + - - -
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Residues in contact with GLN 20 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6581 U 3.2 22.8 + - - +
6591 G 5.8 2.7 - - - +
11631 C 4.7 13.9 + - - -
11641 G 3.9 22.9 + - - +
11651 G 3.1 41.1 + - - +
16X HIS* 2.9 54.1 + - + +
17X ARG* 3.8 5.4 - - - +
19X ASP* 1.3 79.1 - - - +
21X LYS* 1.3 64.3 + - - +
22X TRP 3.2 1.4 + - - -
23X HIS* 3.5 22.5 + - - +
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Residues in contact with LYS 21 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4221 U 4.4 14.8 + - - -
4231 U 4.2 16.6 + - - -
6581 U 3.9 31.2 + - + +
17X ARG 2.9 18.1 + - - +
18X ARG* 3.9 11.4 - - - +
19X ASP 3.1 0.8 - - - -
20X GLN* 1.3 77.2 - - - +
22X TRP* 1.3 63.2 + - - +
23X HIS 3.2 0.7 + - - -
24X ASP* 3.6 10.7 + - + +
27X TYR* 3.1 51.4 - - + +
31X HIS* 5.7 0.6 + - - -
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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
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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