Contacts of the strand formed by residues 167 - 171 (chain 2) in PDB entry 5LN3
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 TYR 167 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631 ARG* 3.3 37.7 + - - -
482 GLY 3.4 12.8 - - - +
492 VAL* 4.5 13.7 - - + -
1532 LEU* 4.4 0.9 - - - -
1652 LEU* 3.2 9.7 - - - +
1662 PRO* 1.4 85.5 - - + +
1682 VAL* 1.3 69.8 + - - +
1692 THR* 6.5 0.4 - - + -
1782 MET* 4.6 2.2 - - - -
1812 PHE* 3.9 35.0 - + + -
1822 GLU* 2.7 40.5 + - - -
1852 PHE* 3.5 52.4 - + + +
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Residues in contact with VAL 168 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631 ARG* 5.5 2.2 - - - +
472 ALA* 3.3 4.0 - - - +
482 GLY 3.0 30.9 + - - +
1422 VAL* 4.0 26.2 - - + -
1532 LEU* 4.1 18.2 - - + +
1542 TYR 4.5 2.2 - - - +
1552 SER* 3.5 28.9 - - - +
1632 ASP* 5.0 6.1 - - - +
1652 LEU* 3.8 31.9 - - + +
1672 TYR* 1.3 82.2 - - - +
1692 THR* 1.4 63.1 + - - +
1812 PHE* 5.1 2.6 - - - -
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Residues in contact with THR 169 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452 THR* 3.4 18.9 - - - +
462 ILE 3.0 18.1 + - - -
472 ALA* 3.7 9.9 - - - +
1422 VAL* 5.4 1.6 - - - -
1672 TYR* 6.5 0.7 - - + -
1682 VAL* 1.4 77.2 - - - +
1702 MET* 1.4 77.2 + - - +
1742 SER* 3.4 29.7 + - - +
1772 ALA* 4.2 12.0 - - + +
1782 MET* 4.4 14.4 - - + +
1812 PHE* 4.1 13.5 - - + -
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Residues in contact with MET 170 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452 THR* 3.4 3.3 - - - +
462 ILE* 2.9 46.0 + - + +
892 ALA* 5.3 0.7 - - + -
1402 ALA* 4.1 32.5 - - + -
1412 LEU 5.4 1.1 - - - +
1422 VAL* 4.9 5.4 - - + -
1552 SER* 4.9 14.8 - - - +
1562 ILE 5.6 1.8 - - - +
1572 TYR* 4.0 40.2 - - + -
1692 THR* 1.4 87.2 + - - +
1712 GLY* 1.4 64.5 + - - +
1742 SER* 3.7 17.5 - - - +
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Residues in contact with GLY 171 (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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442 THR* 3.3 20.0 - - - -
452 THR* 3.7 4.9 - - - -
892 ALA* 5.1 8.0 - - - +
1402 ALA* 5.8 0.6 - - - +
1702 MET* 1.4 82.5 - - - +
1722 SER* 1.4 63.3 + - - +
1732 GLY 3.1 3.1 - - - -
1742 SER* 3.3 15.9 + - - -
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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