Contacts of the helix formed by residues 18 - 29 (chain I) in PDB entry 5T0J
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 LEU 18 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I PHE* 3.5 33.7 - - + -
13I SER* 4.6 0.4 - - - -
16I GLY 3.9 2.4 + - - +
17I ARG* 1.3 74.5 + - - +
19I TYR* 1.3 68.2 + - - +
21I VAL* 3.6 44.2 - - + -
22I GLU* 3.1 30.0 + - - +
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Residues in contact with TYR 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H GLU* 4.2 10.2 + - - -
5H GLY* 3.7 33.7 + - - -
4I ARG* 2.9 41.4 + - + -
6I ASP 3.2 17.4 + - - -
8I ARG* 4.9 7.9 - - + -
9I THR* 4.6 16.6 - - - -
11I ILE 4.7 3.6 - - - +
12I PHE* 4.0 10.3 - - - -
13I SER* 3.5 40.6 - - - +
14I PRO* 5.3 0.2 - - + -
17I ARG* 3.3 11.9 + - - +
18I LEU* 1.3 75.7 - - - +
20I GLN* 1.3 76.6 + - + +
22I GLU* 3.9 6.6 + - - +
23I TYR* 3.5 35.4 - + - -
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Residues in contact with GLN 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H ARG 4.3 0.2 + - - -
5H GLY* 2.9 42.5 + - - +
6H TYR* 3.0 37.4 + - - +
9I THR* 5.2 5.8 - - + +
19I TYR* 1.3 80.9 - - + +
21I VAL* 1.3 55.8 + - + +
22I GLU 3.1 2.9 - - - -
23I TYR* 2.8 22.8 + - - +
24I ALA* 2.6 37.9 + - + -
129I PRO* 3.5 27.8 - - + -
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Residues in contact with VAL 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I LEU* 3.6 46.0 + - + -
19I TYR 3.4 1.0 - - - -
20I GLN* 1.3 79.7 - - + +
22I GLU* 1.3 64.3 + - - +
24I ALA* 3.9 10.3 - - + -
25I MET* 3.0 38.7 + - + +
122I THR* 6.1 5.8 - - + -
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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
----------------------------------------------------------
17I ARG* 4.6 22.1 - - - +
18I LEU* 3.1 33.9 + - - +
19I TYR 4.1 4.5 - - - +
20I GLN 3.1 0.6 - - - -
21I VAL* 1.3 81.9 - - - +
23I TYR* 1.3 70.1 + - + +
25I MET* 3.7 15.5 + - - +
26I GLU* 3.4 23.7 + - - +
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Residues in contact with TYR 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H GLU* 2.8 56.7 + - + -
6H TYR* 3.2 16.8 + - + +
14H SER 5.9 1.1 - - - +
15H PRO 5.8 4.9 - - - +
4I ARG* 4.6 14.2 + - - -
17I ARG* 4.7 11.8 + - - -
19I TYR* 3.5 38.5 - + - -
20I GLN* 2.8 36.6 + - - +
22I GLU* 1.3 80.1 - - + +
24I ALA* 1.3 63.5 + - - +
26I GLU* 3.2 25.6 + - + +
27I ALA 3.4 2.6 + - - -
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Residues in contact with ALA 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H TYR* 4.1 6.7 - - + -
20I GLN* 2.6 31.0 + - + +
21I VAL* 3.2 14.3 + - + +
23I TYR* 1.3 73.3 - - - +
25I MET* 1.3 60.5 + - + +
27I ALA* 3.3 6.8 + - - +
28I ILE* 3.2 28.0 + - + +
129I PRO* 5.3 7.6 - - + -
130I PHE 5.0 10.3 - - - +
131I GLY* 4.9 5.5 - - - +
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Residues in contact with MET 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I VAL* 3.0 29.7 + - + +
22I GLU* 4.1 14.8 - - - +
24I ALA* 1.3 73.7 - - + +
26I GLU* 1.3 65.9 + - - +
28I ILE* 3.4 19.6 + - + +
29I GLY* 3.2 17.7 + - - -
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Residues in contact with GLU 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H PRO 5.3 8.7 - - - +
16H SER 5.4 1.1 - - - +
22I GLU 3.4 17.7 - - - +
23I TYR* 3.2 19.3 + - + +
24I ALA 3.2 0.2 - - - -
25I MET* 1.3 79.4 - - - +
27I ALA* 1.3 55.2 + - - +
29I GLY* 3.3 8.2 + - - -
30I HIS* 2.3 43.6 + - + -
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Residues in contact with ALA 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H TYR* 4.0 18.8 - - + +
16H SER 5.5 2.7 + - - +
23I TYR 3.4 2.0 + - - -
24I ALA* 3.3 9.9 + - - +
26I GLU* 1.3 76.3 - - - +
28I ILE* 1.3 64.1 + - - +
30I HIS* 3.3 26.2 + - - +
78I GLY* 5.4 4.9 - - - -
79I ILE* 5.1 12.9 - - + +
131I GLY* 4.5 18.0 - - - +
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Residues in contact with ILE 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I ALA* 3.2 23.8 + - + +
25I MET* 3.6 23.8 - - + +
26I GLU 3.2 0.4 - - - -
27I ALA* 1.3 79.0 - - - +
29I GLY* 1.3 57.6 + - - +
30I HIS 3.1 8.6 + - - +
32I GLY* 4.1 13.9 - - - -
77I ALA* 5.5 9.7 - - + +
78I GLY* 5.9 2.0 - - - -
130I PHE 5.7 1.6 - - - +
131I GLY* 3.8 19.7 - - - +
132I VAL 5.5 0.2 - - - -
133I SER* 3.2 38.4 - - - +
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Residues in contact with GLY 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I MET 3.2 12.6 + - - -
26I GLU* 3.3 7.1 + - - -
27I ALA 3.3 0.4 - - - -
28I ILE* 1.3 75.9 - - - +
30I HIS* 1.3 60.0 + - - +
31I ALA 3.8 2.7 + - - -
32I GLY 4.6 2.1 + - - -
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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