Contacts of the helix formed by residues 144 - 158 (chain 0) in PDB entry 5IY8
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 SER 144 (chain 0).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090 THR* 3.2 12.4 - - - -
1120 LYS 3.5 21.8 + - - -
1130 ARG* 3.6 25.6 + - - -
1140 ALA 4.0 0.7 - - - -
1430 PRO* 1.4 71.5 - - - +
1450 LEU* 1.3 57.6 + - - +
1460 TYR 3.6 0.4 - - - -
1470 ASN* 3.8 9.9 + - - +
1480 SER* 2.8 30.8 + - - -
1760 THR* 3.5 3.6 - - - -
1780 ASP* 2.6 25.3 + - - -
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Residues in contact with LEU 145 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640 VAL* 5.0 6.3 - - + -
660 ASP* 6.6 0.4 - - + -
1090 THR* 4.4 14.1 - - + +
1430 PRO* 4.2 9.6 - - + -
1440 SER* 1.3 70.7 - - - +
1460 TYR* 1.4 49.9 + - - +
1480 SER* 3.1 8.2 + - - -
1490 LEU* 2.8 47.1 + - + +
1690 ILE* 4.7 27.6 - - + -
1710 PHE* 4.2 27.4 - - + -
1750 THR 4.6 1.1 - - - +
1760 THR* 3.0 33.2 + - + +
1780 ASP* 4.1 0.2 - - - +
1820 ILE* 5.2 4.3 - - + -
2070 VAL* 6.3 0.2 - - + -
2080 CYS* 4.4 13.0 - - - -
2110 LEU* 5.9 6.5 - - + -
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Residues in contact with TYR 146 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1450 LEU* 1.4 71.5 - - - +
1470 ASN* 1.3 64.8 + - + +
1490 LEU* 3.3 4.4 + - - -
1500 SER* 2.9 45.6 + - - -
1760 THR* 5.7 0.7 - - + -
1780 ASP* 3.1 24.4 + - + +
1800 SER* 3.2 47.4 - - - -
1810 ASN 3.5 18.1 + - - -
1820 ILE* 3.8 28.8 - - + +
1840 ASP* 5.5 2.9 + - - -
1850 LEU* 3.8 24.8 + - + +
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Residues in contact with ASN 147 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1130 ARG* 5.9 5.0 - - - +
1140 ALA* 3.3 26.7 + - - +
1440 SER* 3.8 19.3 - - - +
1450 LEU 3.5 0.2 - - - -
1460 TYR* 1.3 82.0 - - + +
1480 SER* 1.3 60.8 + - - +
1500 SER* 3.6 7.7 - - - -
1510 ILE* 3.0 41.0 + - - +
1780 ASP* 3.4 5.1 + - - +
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Residues in contact with SER 148 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640 VAL* 4.5 13.7 - - - -
1070 ILE* 3.7 25.6 - - - +
1090 THR* 3.0 18.9 - - - +
1140 ALA* 3.2 15.9 - - - +
1440 SER 2.8 18.9 + - - -
1450 LEU* 3.1 11.1 + - - -
1470 ASN* 1.3 76.7 - - - +
1490 LEU* 1.4 57.6 + - - +
1510 ILE* 3.5 0.8 + - - -
1520 ALA* 3.0 30.0 + - - +
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Residues in contact with LEU 149 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640 VAL* 5.6 1.3 - - + -
1450 LEU* 2.8 32.5 + - + +
1460 TYR 3.9 1.6 - - - +
1480 SER* 1.4 72.2 - - - +
1500 SER* 1.3 50.5 + - - +
1520 ALA* 3.7 3.6 - - + +
1530 MET* 2.8 36.4 + - - +
1670 VAL* 4.0 29.8 - - + -
1690 ILE* 4.2 12.8 - - + -
1820 ILE* 4.3 4.0 - - + -
1850 LEU* 3.6 33.7 - - + -
1890 LEU* 4.6 9.3 - - + +
1960 VAL* 4.2 17.0 - - + -
2110 LEU* 3.9 28.3 - - + -
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Residues in contact with SER 150 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1460 TYR* 2.9 35.0 + - - -
1470 ASN* 3.6 12.6 - - - -
1490 LEU* 1.3 66.9 - - - +
1510 ILE* 1.4 60.3 + - - +
1530 MET* 3.3 13.5 + - - +
1540 GLN* 2.9 30.5 + - - +
1850 LEU* 3.2 16.9 - - - +
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Residues in contact with ILE 151 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620 TYR* 5.1 4.3 - - + +
1070 ILE* 3.9 18.8 - - + -
1140 ALA* 5.2 9.6 - - + +
1160 LYS* 4.5 27.8 - - + -
1470 ASN* 3.0 37.9 + - - +
1480 SER 4.2 2.0 - - - +
1500 SER* 1.4 72.1 - - - +
1520 ALA* 1.3 63.7 + - - +
1540 GLN* 3.2 12.5 + - - +
1550 THR* 3.2 29.9 + - - +
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Residues in contact with ALA 152 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620 TYR* 4.1 36.8 - - + -
640 VAL* 5.6 1.6 - - + -
1070 ILE* 4.2 2.4 - - + +
1480 SER 3.0 19.2 + - - +
1490 LEU* 3.7 7.0 - - - +
1510 ILE* 1.3 76.2 - - - +
1530 MET* 1.3 56.9 + - - +
1550 THR* 3.4 1.3 + - - -
1560 LEU* 3.0 36.8 + - - +
1670 VAL* 4.1 18.6 - - + -
1940 ILE* 5.9 0.4 - - - -
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Residues in contact with MET 153 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1490 LEU 2.8 23.1 + - - +
1500 SER* 3.5 10.8 - - - +
1520 ALA* 1.3 70.6 - - - +
1540 GLN* 1.4 59.7 + - - +
1570 LYS* 2.8 65.6 + - + +
1850 LEU* 4.2 24.9 - - + -
1880 THR* 3.5 35.2 - - + +
1890 LEU* 4.2 16.4 - - + +
1920 ALA* 5.0 1.1 - - - -
1940 ILE* 3.8 18.3 - - + +
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Residues in contact with GLN 154 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1500 SER 2.9 17.1 + - - +
1510 ILE* 3.2 12.7 + - - +
1530 MET* 1.4 80.3 - - - +
1550 THR* 1.3 60.1 + - - +
1570 LYS* 4.0 8.3 + - - +
1580 HIS* 3.8 27.1 + - + +
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Residues in contact with THR 155 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620 TYR* 2.9 43.2 + - + +
1200 LEU* 3.9 19.7 - - + -
1510 ILE* 3.2 16.4 + - - +
1520 ALA 4.0 1.6 - - - -
1540 GLN* 1.3 76.1 - - - +
1560 LEU* 1.3 64.5 + - + +
1580 HIS* 3.6 23.2 - - + +
1590 MET* 3.6 15.9 - - + +
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Residues in contact with LEU 156 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600 HIS* 4.4 22.2 - - + +
620 TYR* 3.4 32.8 - - + -
1200 LEU* 5.0 2.5 - - + -
1520 ALA 3.0 15.5 + - - +
1530 MET 3.4 0.2 + - - -
1550 THR* 1.3 75.8 - - + +
1570 LYS* 1.4 61.6 + - - +
1590 MET* 3.0 22.6 + - + +
1650 ARG* 3.4 27.4 + - + -
1660 GLU 3.5 38.8 - - - +
1670 VAL* 4.1 6.3 - - + -
1940 ILE* 3.8 31.4 - - + -
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Residues in contact with LYS 157 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1530 MET* 2.8 55.8 + - + +
1540 GLN* 4.4 7.0 - - - +
1550 THR 3.4 0.2 - - - -
1560 LEU* 1.4 68.3 - - - +
1580 HIS* 1.3 63.5 + - + +
1590 MET 3.8 1.2 - - - +
1650 ARG* 3.3 23.1 + - - +
1880 THR* 5.7 3.3 - - + +
1920 ALA* 4.4 12.1 - - + -
1940 ILE* 4.3 8.5 - - + -
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Residues in contact with HIS 158 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1540 GLN* 3.8 23.4 + - + +
1550 THR* 3.6 16.3 + - + +
1560 LEU 3.2 1.0 + - - -
1570 LYS* 1.3 79.7 - - - +
1590 MET* 1.4 67.7 + - + +
1600 PRO* 4.0 1.6 - - - +
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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