Contacts of the strand formed by residues 160 - 166 (chain 2) 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 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1532 LEU* 4.4 6.3 - - + -
1542 ASP 3.2 9.9 - - - +
1552 SER* 2.6 25.7 + - - +
1592 VAL* 1.4 71.2 - - - +
1612 HIS* 1.3 74.8 + - - +
1622 ASN* 5.0 2.9 - - - +
1772 ARG* 3.3 6.2 - - - +
1782 LEU* 2.9 46.7 + - + -
1802 LEU 3.1 16.6 + - - -
1812 ALA* 4.3 0.2 - - - +
2612 LEU* 5.1 0.3 - - - +
2742 ILE* 3.6 31.3 - - + +
2772 THR* 6.1 0.2 - - + -
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Residues in contact with HIS 161 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732 HIS 5.2 0.9 - - - -
1082 ALA* 4.9 7.0 - - + -
1092 PRO* 3.6 41.5 - - + +
1102 LEU* 5.2 3.4 + - - +
1522 VAL 4.1 0.2 - - - -
1532 LEU* 3.4 4.9 - - - -
1542 ASP* 2.7 40.2 + - + +
1592 VAL* 4.0 31.6 - - + +
1602 THR* 1.3 80.1 + - - +
1622 ASN* 1.3 67.2 + - - +
1632 VAL* 4.2 11.0 - - + -
1752 ILE* 4.0 8.9 - - + +
1762 MET 3.0 16.4 - - - -
1772 ARG* 3.7 28.9 + - + +
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Residues in contact with ASN 162 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1512 ILE* 4.5 6.3 - - + +
1522 VAL 3.2 7.1 + - - +
1532 LEU* 3.6 20.9 - - - +
1602 THR* 5.0 2.4 - - - +
1612 HIS* 1.3 74.4 + - - +
1632 VAL* 1.3 64.0 + - - +
1642 PRO* 3.5 2.0 - - - +
1752 ILE* 3.2 24.3 - - - +
1762 MET* 2.9 15.1 + - - +
1782 LEU* 5.8 0.7 + - - +
2772 THR* 2.9 31.0 - - - +
2782 THR* 3.4 34.6 + - - +
2812 SER* 3.6 20.0 - - - +
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Residues in contact with VAL 163 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092 PRO* 3.5 32.5 - - + -
1362 ILE* 5.1 2.5 - - + -
1382 ALA* 3.4 21.5 - - + -
1392 VAL* 5.0 0.9 - - + -
1512 ILE* 3.7 1.0 - - - +
1522 VAL 2.9 28.5 + - - +
1542 ASP* 5.8 0.7 - - + -
1612 HIS* 4.2 9.6 - - + -
1622 ASN* 1.3 78.5 - - - +
1642 PRO* 1.3 63.2 - - - +
1652 ILE* 3.5 17.6 + - + +
1702 ALA* 3.6 30.7 - - + -
1752 ILE* 3.9 16.6 - - + -
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Residues in contact with PRO 164 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1502 GLY 3.7 6.3 - - - +
1512 ILE* 3.9 16.2 - - + -
1622 ASN 3.5 7.0 - - - +
1632 VAL* 1.3 83.4 - - - +
1652 ILE* 1.4 58.3 + - - +
1702 ALA* 3.6 0.2 - - - -
1712 LEU* 2.8 37.2 + - + +
1742 ALA* 3.7 15.3 - - + -
1752 ILE* 4.0 18.2 - - + +
2812 SER* 3.4 21.3 - - - +
2852 CYS* 3.8 21.3 - - - -
2932 LEU* 4.4 8.7 - - + -
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Residues in contact with ILE 165 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1382 ALA* 3.7 9.4 - - + +
1392 VAL* 3.5 40.4 - - + +
1422 LEU* 3.9 18.4 - - + -
1482 THR 3.4 16.4 - - - +
1492 THR* 3.1 23.9 - - - +
1502 GLY 2.9 12.8 + - - +
1522 VAL* 4.5 3.1 - - + -
1632 VAL* 3.5 21.1 + - + +
1642 PRO* 1.4 75.8 - - - +
1662 TYR* 1.3 61.2 + - - +
1682 GLY* 3.6 26.2 - - - +
1692 TYR 3.7 2.9 - - - -
1702 ALA* 3.6 16.2 - - + -
1712 LEU* 4.7 1.3 - - - -
2932 LEU* 4.3 1.9 - - - +
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Residues in contact with TYR 166 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1492 THR* 3.6 18.6 - - + -
1652 ILE* 1.3 72.8 - - - +
1672 GLU* 1.3 89.5 + - + +
1682 GLY 2.9 5.0 + - - -
1692 TYR* 3.1 26.1 + - + +
1712 LEU* 4.3 21.7 - - + +
2892 ILE* 3.7 36.3 - - + -
2922 ASP* 4.0 16.6 + - - -
444 MET* 4.9 10.0 - - - +
604 SER 5.3 1.2 + - - -
614 LYS* 5.0 14.9 - - - +
644 ILE* 4.3 34.1 - - + +
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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