Contacts of the strand formed by residues 163 - 167 (chain 6) 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 PHE 163 (chain 6).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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426 ALA 3.8 9.4 - - - +
436 ILE* 4.7 3.6 - - + -
446 ALA* 4.0 25.4 - - + -
1496 VAL* 6.1 0.9 - - - -
1616 ASP* 4.3 6.7 - - - +
1626 SER* 1.3 108.1 + - - +
1646 LYS* 1.4 65.3 + - - +
1746 GLN* 5.9 2.1 + - - +
1776 LEU* 4.4 15.3 - - + -
1786 ASP* 4.0 22.0 - - - +
1816 VAL* 3.9 30.5 - - + -
1826 GLY* 3.6 28.7 - - - -
1846 LYS* 3.8 25.6 - - + -
1946 LEU* 4.3 7.6 - - + -
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Residues in contact with LYS 164 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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805 THR 6.1 1.3 - - - -
406 ILE* 5.3 1.2 - - - +
416 LEU* 3.8 3.6 - - - -
426 ALA* 2.9 39.5 + - + +
1356 TYR* 6.3 0.6 - - - -
1376 ILE* 3.9 16.3 - - + +
1496 VAL* 5.3 0.9 - - + +
1516 SER* 3.4 37.7 - - - +
1526 PHE 5.1 5.5 + - - -
1536 ASP* 5.3 4.2 + - - -
1596 GLN* 4.6 14.1 - - - +
1616 ASP* 4.1 12.4 + - + +
1636 PHE* 1.4 76.1 - - - +
1656 ALA* 1.3 76.1 + - - +
1666 GLY* 4.1 3.6 + - - +
1746 GLN* 6.1 3.4 - - + -
1776 LEU* 6.1 0.2 - - - -
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Residues in contact with ALA 165 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396 THR* 5.8 0.4 - - + -
406 ILE 3.5 11.9 - - - +
416 LEU* 3.8 18.0 - - + +
1646 LYS* 1.3 94.1 - - - +
1666 GLY* 1.4 58.2 + - - +
1706 SER* 3.7 32.1 + - - +
1736 LEU* 5.3 6.3 - - + -
1746 GLN* 4.6 19.5 - - + +
1776 LEU* 6.0 0.2 - - + -
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Residues in contact with GLY 166 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396 THR* 3.6 7.3 - - - +
406 ILE* 3.1 46.2 + - - +
836 SER* 5.3 1.3 - - - -
1356 TYR* 6.3 2.0 - - - -
1646 LYS* 4.1 4.9 + - - +
1656 ALA* 1.4 74.2 - - - +
1676 GLY* 1.3 63.1 + - - -
1706 SER* 3.7 4.5 - - - -
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Residues in contact with GLY 167 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356 PHE* 5.9 3.1 - - - -
376 GLY 5.8 0.2 - - - -
386 GLY 3.4 14.1 - - - -
396 THR* 4.2 0.7 - - - -
836 SER* 4.0 19.4 + - - -
1356 TYR* 5.8 5.9 - - - +
1666 GLY* 1.3 73.3 - - - -
1686 SER* 1.4 59.6 + - - +
1696 ALA 3.6 0.4 - - - -
1706 SER* 2.8 20.1 + - - -
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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