Contacts of the strand formed by residues 39 - 44 (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 THR 39 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386 GLY* 1.4 74.8 + - - -
406 ILE* 1.3 74.3 + - - +
416 LEU* 6.1 0.2 - - + -
536 SER* 3.6 1.8 + - - -
546 ASP* 3.3 43.0 + - - +
1656 ALA* 5.8 0.4 - - + -
1666 GLY 3.6 15.3 - - - +
1676 GLY* 4.2 0.7 - - - -
1686 SER* 4.4 1.4 - - - -
1696 ALA* 3.3 39.7 + - + +
1706 SER* 4.2 7.4 - - - +
1736 LEU* 4.6 7.9 - - + -
2076 PHE* 4.3 15.2 - - + -
2166 TYR* 4.7 4.9 + - - +
2176 THR* 4.2 4.5 + - - +
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Residues in contact with ILE 40 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386 GLY 5.8 0.2 - - - -
396 THR* 1.3 79.4 - - - +
416 LEU* 1.4 67.5 + - - +
426 ALA* 6.1 0.7 - - + -
516 VAL* 5.0 11.4 - - + -
526 ALA 3.3 7.9 - - - +
536 SER* 3.5 25.6 - - - +
706 LYS* 5.1 15.3 - - + -
716 CYS* 5.4 1.3 - - + +
816 GLY* 4.5 12.8 - - - +
836 SER* 5.1 13.7 - - - -
1356 TYR 5.9 0.9 - - - +
1376 ILE* 3.5 34.5 - - + -
1646 LYS 5.3 1.6 - - - +
1656 ALA* 3.5 4.7 - - - +
1666 GLY* 3.1 47.4 + - - +
2076 PHE* 4.4 3.4 - - - -
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Residues in contact with LEU 41 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406 ILE* 1.4 76.5 - - - +
426 ALA* 1.3 64.2 + - - +
436 ILE* 3.8 18.4 - - + +
506 ILE 4.2 0.9 - - - +
516 VAL* 3.3 4.1 - - - +
526 ALA* 2.8 33.2 + - + +
1646 LYS 3.8 4.0 - - - -
1656 ALA* 3.8 24.7 - - + +
1736 LEU* 6.0 4.7 - - + -
1776 LEU* 3.6 49.1 - - + -
2036 VAL* 4.7 11.4 - - + -
2066 VAL* 4.4 15.3 - - + -
2076 PHE* 3.8 27.4 - - + -
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Residues in contact with ALA 42 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406 ILE* 6.1 1.3 - - + -
416 LEU* 1.3 74.6 - - - +
436 ILE* 1.3 65.0 + - - +
506 ILE 3.7 5.6 - - - -
516 VAL* 4.1 18.8 - - + -
1376 ILE* 3.7 24.7 - - + -
1496 VAL* 4.5 14.8 - - + -
1636 PHE* 3.8 4.6 - - - +
1646 LYS 2.9 37.8 + - - +
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Residues in contact with ILE 43 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416 LEU* 3.8 32.5 - - + +
426 ALA* 1.3 81.8 - - - +
446 ALA* 1.3 68.4 + - - +
456 GLY 4.1 0.2 - - - -
486 PHE* 5.4 2.2 - - + -
496 ALA* 3.1 8.0 - - - +
506 ILE* 3.0 44.3 + - + +
526 ALA* 6.4 0.2 - - + -
1496 VAL* 5.3 2.4 - - - +
1636 PHE* 4.7 5.2 - - + -
1776 LEU* 4.0 18.6 - - + -
1816 VAL* 4.5 22.4 - - + -
1946 LEU* 4.9 3.8 - - + -
1996 ALA* 4.4 21.8 - - + -
2036 VAL* 4.1 21.3 - - + -
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Residues in contact with ALA 44 (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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426 ALA 4.3 0.2 - - - -
436 ILE* 1.3 74.9 - - - +
456 GLY* 1.3 64.5 + - - +
486 PHE 4.4 0.4 - - - -
496 ALA* 4.4 5.4 - - - +
1476 GLY* 5.6 9.9 - - - +
1496 VAL* 4.3 17.9 - - + -
1606 ARG* 5.8 2.9 - - - +
1626 SER* 3.0 27.6 + - - +
1636 PHE* 4.0 7.9 - - + -
1946 LEU* 3.4 20.4 - - - +
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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