Contacts of the strand formed by residues 160 - 166 (chain 9) 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 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1539 LEU* 4.4 6.3 - - + -
1549 ASP 3.2 10.1 - - - +
1559 SER* 2.6 26.0 + - - +
1599 VAL* 1.4 70.6 - - - +
1619 HIS* 1.3 74.8 + - - +
1629 ASN* 5.0 2.7 - - - +
1779 ARG* 3.3 6.8 - - - +
1789 LEU* 2.9 45.9 + - + -
1809 LEU 3.1 17.0 + - - -
1819 ALA* 4.3 0.2 - - - +
2619 LEU* 5.1 0.2 - - - +
2749 ILE* 3.6 31.2 - - + +
2779 THR* 6.1 0.2 - - + -
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Residues in contact with HIS 161 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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739 HIS 5.2 0.9 - - - -
1089 ALA* 4.9 7.2 - - + -
1099 PRO* 3.6 41.5 - - + +
1109 LEU* 5.2 3.2 + - - +
1529 VAL 4.1 0.2 - - - -
1539 LEU* 3.4 4.9 - - - -
1549 ASP* 2.7 41.7 + - + +
1599 VAL* 4.0 31.6 - - + +
1609 THR* 1.3 80.0 + - - +
1629 ASN* 1.3 66.4 + - - +
1639 VAL* 4.2 11.0 - - + -
1759 ILE* 4.0 8.4 - - + +
1769 MET 3.0 17.0 - - - -
1779 ARG* 3.7 28.7 + - + +
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Residues in contact with ASN 162 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1519 ILE* 4.5 6.1 - - + +
1529 VAL 3.2 6.9 + - - +
1539 LEU* 3.6 21.4 - - - +
1609 THR* 5.0 2.3 - - - +
1619 HIS* 1.3 75.1 - - - +
1639 VAL* 1.3 63.7 + - - +
1649 PRO* 3.5 2.0 - - - +
1759 ILE* 3.2 24.3 - - - +
1769 MET* 2.9 14.9 + - + +
1789 LEU 5.8 0.3 + - - -
2779 THR* 2.9 31.1 - - - +
2789 THR* 3.4 34.2 + - - +
2819 SER* 3.6 20.2 - - - +
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Residues in contact with VAL 163 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099 PRO* 3.5 34.3 - - + -
1369 ILE* 5.1 2.5 - - + -
1389 ALA* 3.4 21.1 - - + -
1399 VAL* 5.0 1.1 - - + -
1519 ILE* 3.7 1.5 - - - +
1529 VAL 2.9 29.1 + - - +
1619 HIS* 4.2 9.4 - - + -
1629 ASN* 1.3 77.9 - - - +
1649 PRO* 1.3 63.7 - - - +
1659 ILE* 3.5 18.3 + - + +
1709 ALA* 3.6 30.5 - - + -
1759 ILE* 3.9 15.3 - - + -
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Residues in contact with PRO 164 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1509 GLY 3.8 7.4 - - - +
1519 ILE* 3.9 16.2 - - + -
1629 ASN 3.5 7.2 - - - +
1639 VAL* 1.3 82.8 - - - +
1659 ILE* 1.4 60.2 + - - +
1709 ALA* 3.6 0.3 - - - -
1719 LEU* 2.8 35.4 + - + +
1749 ALA* 3.7 15.5 - - + -
1759 ILE* 4.0 17.5 - - + +
2819 SER* 3.4 20.4 - - - +
2859 CYS* 3.8 22.9 - - - -
2939 LEU* 4.4 8.5 - - + -
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Residues in contact with ILE 165 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1389 ALA* 3.7 9.0 - - + +
1399 VAL* 3.5 41.3 - - + +
1429 LEU* 3.9 19.3 - - + -
1489 THR 3.4 17.3 - - - +
1499 THR* 3.1 24.4 - - - +
1509 GLY 2.9 13.9 + - - +
1529 VAL* 4.5 2.5 - - + -
1639 VAL* 3.5 21.3 + - + +
1649 PRO* 1.4 75.0 - - - +
1669 TYR* 1.3 62.2 + - - +
1689 GLY* 3.6 25.1 - - - +
1699 TYR 3.7 3.4 - - - +
1709 ALA* 3.6 15.9 - - + -
1719 LEU* 4.5 1.5 - - - +
2939 LEU* 4.3 1.8 - - - +
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Residues in contact with TYR 166 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1499 THR* 3.6 18.6 - - + -
1659 ILE* 1.3 72.8 - - - +
1679 GLU* 1.3 90.8 + - + +
1689 GLY 2.9 4.5 + - - -
1699 TYR* 3.1 25.9 + - + +
1719 LEU* 4.3 21.5 - - + +
2899 ILE* 3.7 36.3 - - + -
2929 ASP* 4.0 17.5 + - - -
44W MET* 5.9 1.8 - - + -
60W SER 4.8 9.9 + - - -
61W LYS* 6.1 2.2 - - + +
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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
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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