Contacts of the strand formed by residues 46 - 52 (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 VAL 46 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391 ALA* 3.7 20.4 - - + -
401 VAL 3.5 12.8 - - - +
411 GLN* 4.6 3.6 - - + -
421 PHE* 3.4 5.5 - - - -
451 GLY* 1.3 76.8 - - - +
471 VAL* 1.3 77.1 + - - +
481 LEU* 4.2 0.7 - - + -
1351 ALA* 3.8 21.3 - - + -
1361 GLY 3.8 22.9 - - - +
1371 TRP 4.8 0.2 - - - +
1431 GLY* 5.2 0.4 - - - -
1441 GLN 4.4 5.4 - - - +
1451 VAL* 4.7 7.4 - - + -
2131 ILE* 2.9 53.6 + - + +
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Residues in contact with VAL 47 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391 ALA* 3.3 2.9 - - - -
401 VAL* 2.8 45.6 + - + +
421 PHE* 4.1 15.3 - - + -
461 VAL* 1.3 79.6 - - - +
481 LEU* 1.4 69.8 + - - +
1831 LYS* 5.7 5.6 - - + +
1861 CYS* 4.1 26.0 - - + -
1871 LEU* 6.1 2.2 - - + +
1901 THR* 5.9 2.5 - - - +
2101 LEU* 4.4 17.7 - - + -
2111 ALA 3.4 17.9 - - - +
2121 ALA* 3.9 12.3 - - + +
2211 GLN* 4.8 2.0 - - - +
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Residues in contact with LEU 48 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381 MET 3.8 5.4 - - - +
391 ALA* 4.3 3.8 - - + +
461 VAL* 4.2 1.3 - - + +
471 VAL* 1.4 80.8 - - - +
491 GLY* 1.4 55.3 + - - +
681 LEU* 4.5 17.3 - - + -
761 PHE* 3.8 33.9 - - + -
771 CYS* 4.5 4.0 - - - +
781 CYS* 4.2 23.1 - - - -
1331 ILE* 5.5 0.7 - - + +
1351 ALA* 4.0 28.5 - - + +
1901 THR* 5.6 0.4 - - - -
2101 LEU* 3.2 10.4 - - - +
2111 ALA* 3.0 43.8 + - + +
2131 ILE* 4.0 21.8 - - + -
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Residues in contact with GLY 49 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371 ILE* 3.6 2.0 - - - +
381 MET* 3.0 31.5 + - - +
481 LEU* 1.4 71.8 - - - +
501 ALA* 1.3 63.1 + - - +
681 LEU* 4.9 2.5 - - - -
781 CYS* 4.4 3.4 - - - -
1901 THR* 4.2 24.5 - - - +
1941 LEU* 4.8 1.1 - - - -
2081 ILE* 5.1 0.4 - - - -
2091 ARG 3.5 11.4 - - - -
2101 LEU* 4.4 2.9 - - - -
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Residues in contact with ALA 50 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361 THR 3.7 9.2 - - - -
371 ILE* 3.6 17.0 - - + -
491 GLY* 1.3 77.3 - - - +
511 ASP* 1.3 69.0 + - - +
671 LYS* 5.8 4.9 - - + -
681 LEU* 3.7 22.4 - - + -
781 CYS* 4.6 5.2 - - + -
1941 LEU* 3.5 8.9 - - - +
2081 ILE* 3.4 7.1 - - - +
2091 ARG 3.2 26.8 + - - -
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Residues in contact with ASP 51 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341 GLY 4.8 0.3 - - - +
351 THR* 4.4 9.0 - - - +
361 THR* 3.4 30.8 + - + +
371 ILE* 4.6 4.7 - - - +
501 ALA* 1.3 86.7 - - - +
521 SER* 1.4 75.2 + - - +
531 ARG 3.5 10.4 - - - +
651 THR 4.9 1.0 - - - +
671 LYS* 5.6 5.9 + - - +
681 LEU* 5.5 0.7 - - - +
1941 LEU* 3.6 5.3 - - + +
1981 MET* 4.1 23.1 - - + -
2041 SER* 3.6 14.6 - - - -
2051 GLY 4.2 5.6 - - - +
2071 VAL 3.8 5.4 - - - +
2081 ILE* 4.6 4.3 - - + +
2091 ARG* 5.6 0.9 - - - +
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Residues in contact with SER 52 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511 ASP* 1.4 79.0 + - - +
531 ARG* 1.3 74.6 + - - +
641 VAL* 3.6 22.0 - - - -
651 THR 3.4 20.5 + - - -
671 LYS* 6.4 0.9 - - - -
2051 GLY 3.0 15.9 + - - +
2071 VAL* 3.0 27.9 + - - +
2091 ARG* 3.8 19.4 + - - +
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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