Contacts of the strand formed by residues 537 - 540 (chain B) in PDB entry 1LDK
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 537 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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514B SER* 4.6 2.9 - - - +
517B LEU* 4.9 5.7 - - + +
518B ASN* 3.7 7.1 + - - +
535B PHE* 3.4 27.0 - - + -
536B SER* 1.3 77.1 - - - +
538B GLN* 1.3 87.3 + - - +
539B VAL* 4.2 12.4 + - + +
566B PHE* 3.7 23.8 - - + -
581B TRP* 3.7 27.1 - - + -
1029C ALA* 3.0 10.3 - - + -
1030C VAL* 3.1 39.9 - - - +
1031C ALA* 3.7 12.8 - - + -
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Residues in contact with GLN 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475B VAL 4.7 8.5 - - - +
477B GLN* 6.2 1.6 - - - +
511B ILE* 3.0 42.8 + - + +
514B SER* 3.2 19.6 + - - -
515B LYS* 4.3 9.5 - - - +
518B ASN* 3.7 14.6 + - - +
536B SER* 4.6 4.9 - - - +
537B ILE* 1.3 92.2 - - - +
539B VAL* 1.3 66.6 + - - +
540B LEU* 2.9 19.1 + - + +
1029C ALA 2.7 11.5 + - - +
1030C VAL* 3.5 26.1 - - + -
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Residues in contact with VAL 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510B ASP* 2.9 22.9 - - - +
511B ILE* 5.7 0.2 - - - -
513B VAL* 5.4 3.2 - - + +
514B SER* 4.1 8.6 - - - -
517B LEU* 3.5 29.8 - - + -
537B ILE* 4.0 12.7 + - + +
538B GLN* 1.3 68.6 - - - +
540B LEU* 1.3 60.9 + - - +
566B PHE* 5.4 3.6 - - + -
570B TYR* 4.8 18.6 - - + +
1031C ALA* 3.5 16.8 - - + +
1033C TRP* 3.4 34.1 - - + +
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Residues in contact with LEU 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475B VAL* 3.6 15.0 - - + -
510B ASP* 3.2 7.9 - - - -
511B ILE* 4.7 3.4 - - + -
538B GLN* 2.9 35.2 + - + +
539B VAL* 1.3 72.8 - - - +
541B SER* 1.3 61.7 + - - +
542B SER 3.3 5.4 + - - -
545B TRP* 3.3 58.1 - - + +
547B PHE* 3.7 4.3 - - + -
582B LEU* 3.3 33.2 - - + -
1030C VAL* 4.3 2.5 - - + -
1031C ALA 2.9 7.9 + - - +
1032C LEU* 3.5 9.9 - - + -
1033C TRP* 3.3 28.6 + - - -
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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