Contacts of the helix formed by residues 16 - 32 (chain I) in PDB entry 5TJ4
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 16 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I ILE* 5.2 2.2 - - - +
15I LYS* 1.3 72.7 - - - +
17I TYR* 1.3 60.1 + - - -
19I GLY 3.5 1.2 + - - -
20I LEU* 3.1 23.9 + - - +
293I VAL* 3.6 18.4 - - - +
296I ASP* 3.2 27.4 - - - -
297I LYS* 3.7 19.5 + - - +
299I LEU* 5.9 0.8 - - - +
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Residues in contact with TYR 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I ILE* 3.7 27.8 - - + -
12I ASN 4.4 1.1 - - - -
13I GLY* 3.3 23.3 - - - -
15I LYS* 3.1 17.1 + - - +
16I GLY* 1.3 69.0 - - - -
18I ASN* 1.3 99.9 + - - +
20I LEU* 3.2 6.1 + - - +
21I ALA* 2.9 28.5 + - - +
37I VAL* 3.8 14.6 - - + +
39I HIS* 3.4 47.7 + + - +
296I ASP* 3.5 1.0 + - - -
297I LYS* 4.9 8.9 + - - -
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Residues in contact with ASN 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I TYR* 1.3 104.5 + - - +
19I GLY* 1.3 60.7 + - - +
21I ALA* 3.1 9.5 + - - +
22I GLU* 2.9 37.5 + - - +
296I ASP* 3.1 18.7 + - - +
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Residues in contact with GLY 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I GLY 3.5 3.8 + - - -
17I TYR 3.3 0.2 - - - -
18I ASN* 1.3 75.4 - - - +
20I LEU* 1.3 61.2 + - - +
22I GLU* 3.3 17.3 + - - +
23I VAL* 3.2 22.9 + - - +
292I ALA* 3.7 22.4 - - - +
293I VAL* 4.1 7.6 - - - -
296I ASP* 3.0 18.5 + - - -
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Residues in contact with LEU 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I ILE* 3.9 26.0 - - + -
11I ILE* 3.8 26.7 - - + -
16I GLY 3.1 14.9 + - - +
17I TYR* 3.2 9.4 + - - +
19I GLY* 1.3 75.5 - - - +
21I ALA* 1.3 57.4 + - - +
23I VAL* 3.1 9.1 + - + +
24I GLY* 2.8 23.0 + - - -
37I VAL* 4.3 16.8 - - + +
61I PHE* 4.1 8.1 - - + -
279I PHE* 4.1 19.8 - - + -
284I LEU* 4.0 33.2 - - + -
293I VAL* 4.0 9.7 - - + +
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Residues in contact with ALA 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I TYR 2.9 14.2 + - - +
18I ASN* 3.1 12.8 + - - +
20I LEU* 1.3 73.4 - - - +
22I GLU* 1.3 55.3 + - - +
24I GLY* 3.0 4.1 + - - +
25I LYS* 2.7 34.2 + - - +
35I VAL 5.6 2.6 - - - +
37I VAL* 4.0 20.8 - - + +
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Residues in contact with GLU 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I ASN* 2.9 22.6 + - - +
19I GLY* 3.3 19.0 + - - +
21I ALA* 1.3 74.6 - - - +
23I VAL* 1.3 60.1 + - - +
25I LYS* 3.3 9.4 + - - +
26I LYS* 3.1 21.0 + - - +
292I ALA* 4.5 18.3 - - + +
296I ASP* 5.8 1.2 - - - +
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Residues in contact with VAL 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I GLY 3.2 13.9 + - - +
20I LEU* 3.1 10.6 + - + +
22I GLU* 1.3 72.3 - - - +
24I GLY* 1.3 66.5 + - - +
26I LYS* 3.3 8.3 + - + +
27I PHE* 3.0 20.1 + - - +
279I PHE* 3.8 21.8 - - + -
283I TYR* 3.8 29.2 - - + +
284I LEU* 4.1 7.0 - - + +
289I GLY* 3.5 31.2 - - - +
292I ALA* 3.9 6.7 - - + -
293I VAL* 4.2 8.5 - - + -
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Residues in contact with GLY 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I LEU 2.8 14.4 + - - -
21I ALA* 3.0 7.5 + - - -
23I VAL* 1.3 75.8 - - - +
25I LYS* 1.3 55.0 + - - +
27I PHE* 3.1 5.5 + - - +
28I GLU* 2.9 26.1 + - - +
35I VAL* 3.3 37.0 - - - +
37I VAL* 5.7 0.2 - - - -
279I PHE* 4.2 6.6 - - - -
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Residues in contact with LYS 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I ALA 2.7 14.3 + - - +
22I GLU* 3.3 12.3 + - - +
24I GLY* 1.3 71.7 - - - +
26I LYS* 1.3 58.6 + - - +
28I GLU* 3.2 11.5 + - - +
29I LYS* 2.9 31.1 + - - +
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Residues in contact with LYS 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I GLU 3.1 12.8 + - - +
23I VAL* 3.3 12.1 + - + +
25I LYS* 1.3 75.4 - - - +
27I PHE* 1.3 59.5 + - - +
29I LYS* 3.5 9.5 - - + +
30I ASP* 3.4 30.0 + - - +
283I TYR* 3.7 9.1 - - + -
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Residues in contact with PHE 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I LEU* 4.2 18.2 - - + -
23I VAL 3.0 12.3 + - - +
24I GLY 3.1 9.4 + - - +
26I LYS* 1.3 74.3 - - - +
28I GLU* 1.3 59.9 + - - +
30I ASP* 3.2 1.7 + - - +
31I THR* 2.8 47.5 + - - -
33I ILE* 4.0 22.7 - - + -
35I VAL* 3.7 19.5 - - + -
275I LEU* 3.9 24.7 - - + -
278I GLU* 4.4 7.9 - - + -
279I PHE* 3.7 33.2 - + + -
283I TYR* 3.5 35.6 - + + -
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Residues in contact with GLU 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I GLY 2.9 15.8 + - - +
25I LYS* 3.5 12.7 - - - +
27I PHE* 1.3 73.1 - - - +
29I LYS* 1.3 57.3 + - - +
32I GLY* 2.8 32.1 + - - -
33I ILE 3.3 30.4 + - - +
34I LYS* 3.3 22.8 - - - +
35I VAL* 3.9 6.0 + - + +
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Residues in contact with LYS 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I LYS 2.9 14.4 + - - +
26I LYS* 3.5 14.1 - - + +
27I PHE 3.2 0.4 - - - -
28I GLU* 1.3 79.0 - - - +
30I ASP* 1.3 78.3 + - - +
32I GLY* 4.4 1.2 + - - -
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Residues in contact with ASP 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I LYS* 3.4 12.4 + - - +
27I PHE 3.2 2.7 + - - +
29I LYS* 1.3 96.0 - - - +
31I THR* 1.3 62.3 + - - +
283I TYR* 3.1 30.6 + - - +
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Residues in contact with THR 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I PHE* 2.8 42.2 + - - -
30I ASP* 1.3 75.0 - - - +
32I GLY* 1.3 61.9 + - - +
33I ILE* 3.7 7.1 + - - +
283I TYR* 5.2 2.9 - - - -
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Residues in contact with GLY 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I GLU* 2.8 27.8 + - - -
29I LYS 4.4 1.3 + - - -
30I ASP 3.5 2.0 + - - -
31I THR* 1.3 73.9 - - - +
33I ILE* 1.3 57.8 + - - +
34I LYS 4.4 0.2 + - - -
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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