Contacts of the strand formed by residues 195 - 200 (chain 3) 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 ILE 195 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2592 ILE* 3.6 1.0 - - - -
2602 THR* 3.1 52.7 + - + +
2622 LEU* 4.7 10.3 - - + -
473 ASP* 3.6 38.6 - - + +
483 ARG* 4.7 3.8 - - - +
503 TYR* 4.0 16.4 - - + +
1883 HIS* 4.5 7.2 - - + -
1893 ILE 3.2 17.0 - - - +
1903 ILE* 4.0 19.1 - - + -
1913 GLU 4.3 6.7 - - - +
1943 LYS* 1.3 83.2 - - - +
1963 THR* 1.3 69.3 + - - +
1973 THR* 4.7 1.8 - - - +
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Residues in contact with THR 196 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2492 LYS* 5.0 5.3 + - - +
2582 LYS 3.0 23.7 + - - +
2592 ILE* 4.9 2.5 - - + +
1873 VAL 4.0 0.2 - - - +
1883 HIS* 3.5 2.1 - - - -
1893 ILE* 2.8 46.8 + - + +
1913 GLU* 4.9 4.2 + - - -
1943 LYS* 4.5 14.0 - - - +
1953 ILE* 1.3 76.3 + - - +
1973 THR* 1.4 55.4 + - - +
1983 ARG* 3.6 41.7 - - + +
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Residues in contact with THR 197 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2562 THR* 4.0 0.9 - - - +
2572 GLU 3.6 1.0 - - - -
2582 LYS* 3.0 46.4 + - + +
2592 ILE* 5.1 0.8 - - - +
2602 THR* 4.9 6.5 + - - -
1863 ILE* 5.4 4.9 - - + -
1873 VAL 3.3 10.3 - - - +
1883 HIS* 3.3 37.4 + - + +
1953 ILE* 4.7 2.9 - - - +
1963 THR* 1.4 68.3 - - - +
1983 ARG* 1.3 71.6 + - - +
1993 THR* 4.4 3.1 + - - +
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Residues in contact with ARG 198 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2492 LYS* 3.5 46.1 + - - +
2542 VAL* 4.2 16.4 - - + +
2562 THR 3.3 10.1 - - - +
2572 GLU* 4.5 20.6 - - - +
1643 PHE* 3.8 29.3 - - + -
1863 ILE* 3.4 2.0 - - - -
1873 VAL* 2.7 48.3 + - + +
1893 ILE* 5.3 0.9 - - + -
1963 THR* 3.6 24.3 - - + +
1973 THR* 1.3 85.2 - - - +
1993 THR* 1.4 61.2 + - - +
2003 LEU* 3.6 16.2 - - + +
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Residues in contact with THR 199 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2542 VAL* 3.2 8.8 - - - +
2552 LEU* 3.3 21.5 + - + -
2562 THR* 3.0 52.6 + - - +
263 ARG* 5.9 3.8 + - - +
1843 GLY* 6.0 1.8 - - - -
1853 VAL 3.5 18.4 - - - +
1863 ILE* 4.1 12.3 - - + +
1973 THR* 4.3 3.4 + - - +
1983 ARG* 1.4 72.9 - - - +
2003 LEU* 1.4 63.3 + - - +
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Residues in contact with LEU 200 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2522 THR* 6.0 5.2 - - + -
2532 ALA 5.2 2.0 - - - +
2542 VAL* 4.3 4.9 - - + +
2552 LEU* 3.6 15.8 - - - +
1643 PHE* 3.7 28.9 - - + -
1683 SER* 4.3 20.2 - - - +
1713 MET* 4.2 14.6 - - + -
1723 LEU* 6.3 2.5 - - + -
1843 GLY* 5.7 2.4 - - - -
1853 VAL* 3.5 37.3 + - + +
1873 VAL* 3.8 20.4 - - + -
1983 ARG* 3.6 24.5 - - + +
1993 THR* 1.4 86.1 - - - +
2013 LYS* 1.4 63.7 + - - +
2023 ALA* 4.1 1.6 + - - +
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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