Contacts of the strand formed by residues 160 - 166 (chain 8) in PDB entry 1O18
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 160 (chain 8).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1538 LEU* 4.4 6.5 - - + -
1548 ASP 3.2 9.6 - - - +
1558 SER* 2.6 25.3 + - - +
1598 VAL* 1.4 71.4 - - - +
1618 HIS* 1.3 74.6 + - - +
1628 ASN* 5.0 3.1 - - - +
1778 ARG* 3.3 6.2 - - - +
1788 LEU* 2.9 46.5 + - + -
1808 LEU 3.1 16.3 + - - -
1818 ALA* 4.3 0.2 - - - +
2618 LEU* 5.1 0.3 - - - +
2748 ILE* 3.6 31.5 - - + +
2778 THR* 6.1 0.2 - - + -
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Residues in contact with HIS 161 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738 HIS 5.2 0.9 - - - -
1088 ALA* 4.9 7.0 - - + -
1098 PRO* 3.6 41.3 - - + +
1108 LEU* 5.2 3.4 + - - +
1528 VAL 4.1 0.2 - - - -
1538 LEU* 3.4 4.9 - - - -
1548 ASP* 2.7 40.5 + - + +
1598 VAL* 4.0 31.8 - - + +
1608 THR* 1.3 80.6 + - - +
1628 ASN* 1.3 67.5 + - - +
1638 VAL* 4.2 10.8 - - + -
1758 ILE* 4.0 9.1 - - + +
1768 MET 3.0 15.7 - - - -
1778 ARG* 3.7 28.9 + - + +
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Residues in contact with ASN 162 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1518 ILE* 4.5 6.5 - - + +
1528 VAL 3.2 7.2 + - - +
1538 LEU* 3.6 21.3 - - - +
1608 THR* 5.0 2.6 - - - +
1618 HIS* 1.3 74.2 - - - +
1638 VAL* 1.3 64.0 + - - +
1648 PRO* 3.5 2.0 - - - +
1758 ILE* 3.2 24.4 - - - +
1768 MET* 2.9 15.1 + - - +
1788 LEU 5.8 0.3 + - - -
2778 THR* 2.9 31.4 - - - +
2788 THR* 3.4 34.6 + - - +
2818 SER* 3.6 19.7 - - - +
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Residues in contact with VAL 163 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098 PRO* 3.5 32.5 - - + -
1368 ILE* 5.1 2.5 - - + -
1388 ALA* 3.4 22.2 - - + -
1398 VAL* 5.0 0.9 - - + -
1518 ILE* 3.7 1.0 - - - +
1528 VAL 2.9 28.8 + - - +
1548 ASP* 5.8 0.2 - - + -
1618 HIS* 4.2 9.6 - - + -
1628 ASN* 1.3 78.1 - - - +
1648 PRO* 1.3 63.8 - - - +
1658 ILE* 3.5 17.6 + - + +
1708 ALA* 3.6 30.7 - - + -
1758 ILE* 3.9 16.6 - - + -
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Residues in contact with PRO 164 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1508 GLY 3.7 6.1 - - - +
1518 ILE* 3.9 15.9 - - + -
1628 ASN 3.5 7.2 - - - +
1638 VAL* 1.3 83.9 - - - +
1658 ILE* 1.4 59.4 + - - +
1708 ALA* 3.6 0.2 - - - -
1718 LEU* 2.8 37.3 + - + +
1748 ALA* 3.7 15.5 - - + -
1758 ILE* 4.0 17.7 - - + +
2818 SER* 3.4 20.6 - - - +
2858 CYS* 3.8 21.3 - - - -
2938 LEU* 4.4 8.7 - - + -
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Residues in contact with ILE 165 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1388 ALA* 3.7 9.6 - - + +
1398 VAL* 3.5 40.2 - - + +
1428 LEU* 3.9 18.6 - - + -
1488 THR 3.4 16.8 - - - +
1498 THR* 3.1 24.1 - - - +
1508 GLY 2.9 13.0 + - - +
1528 VAL* 4.5 2.9 - - + -
1638 VAL* 3.5 21.1 + - + +
1648 PRO* 1.4 75.4 - - - +
1668 TYR* 1.3 62.1 + - - +
1688 GLY* 3.6 26.0 - - - +
1698 TYR 3.7 2.7 - - - -
1708 ALA* 3.6 16.2 - - + -
1718 LEU* 4.7 1.1 - - - -
2938 LEU* 4.3 1.9 - - - +
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Residues in contact with TYR 166 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1498 THR* 3.6 18.8 - - + -
1658 ILE* 1.3 73.2 - - - +
1678 GLU* 1.3 90.0 + - + +
1688 GLY 2.9 4.8 + - - -
1698 TYR* 3.1 26.8 + + + +
1718 LEU* 4.3 21.9 - - + +
2898 ILE* 3.7 36.3 - - + -
2928 ASP* 4.0 16.4 + - - -
44V MET* 5.9 1.3 - - + -
60V SER 4.8 9.5 + - - -
61V LYS* 6.1 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