Contacts of the strand formed by residues 37 - 41 (chain 1) 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 37 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351 THR* 5.6 0.7 - - - -
361 THR* 1.4 80.4 + - - +
381 MET* 1.3 65.9 + - - +
491 GLY 3.6 6.3 - - - +
501 ALA* 3.6 23.3 - - + -
511 ASP* 4.6 3.6 - - - +
781 CYS* 4.5 16.6 - - + -
791 ARG 5.5 1.1 - - - +
801 SER* 3.6 30.3 - - - +
1311 GLY* 4.7 8.3 - - - +
1331 ILE* 3.8 24.2 - - + -
1611 ILE* 3.4 3.7 - - - +
1621 GLY* 2.7 45.0 + - - +
1631 GLY* 3.9 12.1 - - - +
1941 LEU* 5.2 0.7 - - - -
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Residues in contact with MET 38 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361 THR* 5.0 0.2 - - - +
371 ILE* 1.3 79.8 - - - +
391 ALA* 1.4 60.5 + - - +
401 VAL* 4.2 15.3 - - + -
481 LEU* 3.8 1.9 - - - +
491 GLY 3.0 29.7 + - - +
781 CYS* 4.9 2.8 - - - -
1331 ILE* 3.9 8.1 - - - -
1601 ALA 3.2 16.2 - - - +
1611 ILE* 3.8 32.1 - - + -
1691 ILE* 4.4 7.2 - - + -
1891 PHE* 4.6 8.3 - - + -
1901 THR* 3.5 42.0 - - + +
1931 ALA* 4.2 17.0 - - + -
1941 LEU* 3.8 20.9 - - + -
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Residues in contact with ALA 39 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381 MET* 1.4 74.6 - - - +
401 VAL* 1.4 63.1 + - - +
411 GLN 4.3 0.2 - - - -
461 VAL* 3.7 20.9 - - + -
471 VAL 3.3 7.0 - - - +
481 LEU* 4.3 4.7 - - + +
781 CYS* 6.2 0.4 - - - -
1331 ILE* 3.8 25.5 - - + +
1351 ALA* 4.2 8.3 - - + -
1451 VAL* 4.2 10.3 - - + -
1591 PHE* 3.4 2.8 - - - +
1601 ALA 2.9 29.9 + - - +
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Residues in contact with VAL 40 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381 MET* 4.2 19.3 - - + -
391 ALA* 1.4 78.5 - - - +
411 GLN* 1.4 74.9 + - - +
461 VAL* 3.5 3.1 - - - -
471 VAL* 2.8 41.2 + - + +
1451 VAL* 5.5 0.2 - - - -
1591 PHE* 3.7 16.2 - - + -
1611 ILE* 5.2 0.9 - - + -
1811 MET* 4.2 14.1 - - + -
1861 CYS* 4.4 15.5 - - + -
1891 PHE* 3.5 38.4 - - + -
1901 THR* 4.8 4.3 - - - +
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Residues in contact with GLN 41 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401 VAL* 1.4 87.9 - - - +
421 PHE* 1.3 85.0 + - - +
431 ASP* 5.2 1.6 + - - +
451 GLY* 3.5 12.5 + - - +
461 VAL* 4.4 2.7 - - + +
1431 GLY 4.6 14.2 + - - +
1451 VAL* 4.5 12.8 - - + +
1561 ARG* 4.3 21.8 - - - +
1581 SER 3.2 21.3 - - - +
1591 PHE* 3.9 6.4 - - - +
1811 MET* 3.7 14.9 - - - +
2381 PRO* 5.8 2.8 - - - +
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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
------------------------------------------------------------
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