Contacts of the strand formed by residues 415 - 420 (chain A) in PDB entry 1SLL
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 LYS 415 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410A LYS 3.5 0.7 - - - +
411A GLU* 3.3 4.8 - - - +
412A VAL 2.9 33.0 + - - +
413A ASN 3.2 4.5 - - - +
414A GLY* 1.3 78.5 - - - +
416A LYS* 1.3 78.0 + - - +
417A TYR* 3.5 23.2 - - + +
436A GLU* 3.4 27.4 - - - +
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Residues in contact with LYS 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A SER* 5.8 1.8 - - - +
409A PHE* 4.2 23.8 - - + -
410A LYS 3.4 5.2 - - - +
411A GLU* 3.6 30.5 - - + +
415A LYS* 1.3 88.3 + - - +
417A TYR* 1.3 67.2 - - - +
528A SER* 3.4 36.4 + - - +
529A PHE* 4.8 7.1 + - - +
530A LYS 5.2 3.6 + - - -
532A GLU* 5.1 16.7 + - - +
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Residues in contact with TYR 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A PHE* 3.2 9.4 - - - -
410A LYS* 2.8 32.8 + - - +
412A VAL* 3.5 35.1 + - + -
413A ASN* 5.2 6.3 + - - +
415A LYS* 3.5 37.9 - - + +
416A LYS* 1.3 77.2 - - - +
418A LEU* 1.3 63.9 + - - +
433A THR* 3.7 16.6 - - + -
434A ILE 3.3 22.2 - - - +
435A ARG* 3.6 38.5 - - + -
436A GLU* 3.0 36.4 + - - -
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Residues in contact with LEU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A GLY 3.7 10.3 - - - +
409A PHE* 3.6 21.1 - - + -
417A TYR* 1.3 71.1 - - - +
419A LYS* 1.3 64.7 + - - +
420A LEU* 5.9 0.2 - - + -
433A THR* 3.2 5.2 - - - -
434A ILE* 3.0 46.8 + - + +
457A TYR* 3.6 36.6 - - + +
493A ILE* 4.4 4.3 - - + -
494A PHE* 5.1 4.0 - - + -
502A ALA* 5.1 4.7 - - + -
507A TYR* 3.4 37.2 - - + +
525A ILE* 3.6 20.4 - - + -
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Residues in contact with LYS 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A GLY* 3.0 16.1 + - - +
409A PHE 3.4 35.9 + - - +
410A LYS* 3.5 25.8 - - + +
418A LEU* 1.3 74.8 - - - +
420A LEU* 1.3 71.2 + - - +
430A TYR* 4.0 32.0 - - + +
432A TYR 3.5 8.1 - - - +
433A THR* 4.5 0.7 - - - -
502A ALA* 3.8 14.2 - - - +
503A PHE* 4.0 33.4 + - + -
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Residues in contact with LEU 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A LEU* 4.6 0.9 - - + +
419A LYS* 1.3 84.2 - - - +
421A ARG* 1.3 59.2 + - - +
422A TRP 4.2 0.2 - - - -
430A TYR* 3.3 12.8 - - - -
431A ASP 3.3 0.5 + - - -
432A TYR* 2.9 36.8 + - + +
434A ILE* 3.5 32.5 - - + +
440A ILE* 3.7 29.8 - - + -
493A ILE* 4.0 27.8 - - + -
500A PHE* 4.0 23.1 - - + +
501A LYS 3.3 21.8 - - - +
502A ALA* 3.8 5.2 - - + +
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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