Contacts of the helix formed by residues 42 - 51 (chain d) 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 CYS 42 (chain d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14951 G 3.2 25.6 - - + +
23d VAL* 3.6 10.1 - - - -
38d MET* 3.6 16.6 - - - -
39d CYS* 3.4 10.5 - - - -
41d GLN* 1.3 74.9 - - - +
43d PHE* 1.3 59.2 + - - +
44d ARG 3.0 2.9 - - - -
45d GLN* 2.9 36.6 + - + +
46d TYR* 3.3 17.5 + - + +
101d ZN 3.4 29.6 - - - -
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Residues in contact with PHE 43 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63U ILE* 3.5 36.6 - - + -
65U THR* 3.6 18.4 - - + +
80U PHE* 3.7 29.6 - + - -
32d ARG* 4.2 8.5 - - - +
36d LEU* 3.9 13.7 - - + -
38d MET* 3.6 42.4 - - + +
40d ARG* 4.9 12.1 - - - +
41d GLN 3.2 2.9 - - - +
42d CYS* 1.3 78.0 - - - +
44d ARG* 1.3 61.9 + - - +
46d TYR* 3.5 2.0 + - + +
47d ALA* 3.1 21.1 + - + +
50d ILE* 3.6 24.0 - - + -
52d PHE* 4.0 14.6 - + - -
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Residues in contact with ARG 44 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13361 C 2.7 38.3 + - - -
13371 C 2.5 32.6 + - - -
65U THR* 4.1 11.7 - - + -
67U LYS* 3.6 34.4 - - - +
78U ASP* 3.2 29.7 + - - +
80U PHE* 5.0 4.4 - - + -
40d ARG 5.7 0.7 - - - -
41d GLN 4.0 13.7 + - - +
42d CYS 3.0 0.8 - - - -
43d PHE* 1.3 79.1 - - - +
45d GLN* 1.3 69.0 + - - +
46d TYR 3.5 0.2 + - - -
47d ALA* 3.6 16.4 + - - +
48d LYS* 4.8 1.6 + - - +
54d LYS* 5.2 9.7 - - - +
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Residues in contact with GLN 45 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13351 G 4.2 8.7 + - - -
13361 C 3.5 35.2 - - - -
14951 G 5.6 5.5 + - - +
23D GLU* 5.6 1.7 - - - +
172D VAL* 5.7 5.4 - - - +
41d GLN 5.3 0.8 + - - +
42d CYS* 2.9 27.0 + - + +
44d ARG* 1.3 87.0 - - + +
46d TYR* 1.3 72.8 + - + +
47d ALA 3.7 0.2 + - - -
48d LYS* 4.1 20.8 - - - +
49d ASP* 4.2 4.2 - - - +
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Residues in contact with TYR 46 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ALA* 4.2 9.4 - - + -
23D GLU* 3.0 42.1 + - - -
27D ARG* 4.7 6.2 + - - -
64K TRP* 3.4 36.7 - + - -
23d VAL* 4.1 8.2 - - + +
38d MET* 3.4 35.2 - - + -
42d CYS* 3.3 22.7 + - + +
43d PHE 3.5 3.3 + - - +
44d ARG 3.3 0.4 - - - -
45d GLN* 1.3 82.2 - - + +
47d ALA* 1.3 56.1 + - - +
48d LYS 3.2 2.7 - - - -
49d ASP* 2.8 17.3 + - + -
50d ILE* 2.7 53.5 + - + +
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Residues in contact with ALA 47 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80U PHE* 3.5 39.9 - - + -
43d PHE* 3.1 16.6 + - + +
44d ARG 3.6 8.9 + - - +
45d GLN 3.4 1.8 - - - -
46d TYR* 1.3 76.8 - - - +
48d LYS* 1.3 60.8 + - - +
50d ILE* 4.0 8.3 - - - -
51d GLY 3.2 3.8 + - - -
52d PHE* 2.8 38.0 + - + +
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Residues in contact with LYS 48 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D THR* 3.8 25.7 + - - +
27U ARG* 4.5 5.2 + - - -
44d ARG 4.8 1.9 + - - +
45d GLN 4.1 17.0 - - - +
47d ALA* 1.3 80.3 - - - +
49d ASP* 1.3 78.1 + - - +
51d GLY* 3.9 6.3 + - - -
52d PHE 3.9 5.4 + - - -
53d ILE* 5.9 2.7 - - + -
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Residues in contact with ASP 49 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLY* 4.2 1.8 - - - -
18D LYS* 4.0 19.9 - - + +
19D ALA* 4.2 23.1 - - + +
22D ASN* 4.4 20.4 + - - -
23D GLU* 4.4 8.8 - - - +
27U ARG* 4.1 8.3 + - - -
45d GLN 4.2 3.9 - - - +
46d TYR* 2.8 26.9 + - - +
48d LYS* 1.3 100.1 - - - +
50d ILE* 1.3 60.4 + - - +
51d GLY 3.5 0.7 + - - -
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Residues in contact with ILE 50 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PHE 4.3 6.2 - - - +
12D VAL* 4.5 4.4 - - + +
15D GLY* 3.4 40.9 - - - +
16D ILE* 3.9 6.3 - - + +
19D ALA* 4.2 8.3 - - + -
27U ARG* 4.3 1.7 - - - -
82U MET* 4.2 7.8 - - - +
36d LEU* 3.6 19.7 - - + -
38d MET* 5.6 1.1 - - + -
43d PHE* 3.6 23.3 - - + -
46d TYR* 2.7 41.8 + - + +
47d ALA* 3.9 1.8 - - - +
49d ASP* 1.3 71.7 - - - +
51d GLY* 1.3 58.6 + - - +
52d PHE* 3.4 39.1 - - + -
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Residues in contact with GLY 51 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27U ARG* 3.2 27.6 + - - -
81U GLN 4.8 0.5 - - - +
82U MET* 3.2 23.2 - - - +
47d ALA 3.2 3.0 + - - -
48d LYS* 3.9 3.3 + - - -
49d ASP 3.3 4.6 + - - -
50d ILE* 1.3 79.4 - - - +
52d PHE* 1.3 61.5 + - - +
53d ILE* 3.9 8.1 + - - +
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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