Contacts of the strand formed by residues 424 - 429 (chain K) in PDB entry 5LS6
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 424 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82K PHE* 5.3 0.2 - - - -
101K PHE* 4.3 6.7 - - + -
111K LEU* 3.7 20.6 - - + -
126K CYS* 3.6 25.4 - - + -
417K SER 4.2 0.2 - - - +
418K PHE* 3.7 3.8 - - - -
419K SER* 3.2 30.0 + - - +
422K SER 3.3 6.4 - - - +
423K SER* 1.3 87.5 + - - +
425K LEU* 1.3 69.2 + - - +
426K ILE* 4.2 9.9 - - + -
436K ARG* 3.4 49.8 - - + +
437K TRP 3.6 3.4 - - - -
438K ASP* 3.7 17.5 - - - +
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Residues in contact with LEU 425 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82K PHE* 4.0 20.0 - - + -
378K ALA* 4.2 2.0 - - + -
386K LEU* 4.0 30.1 - - + -
388K VAL* 4.2 19.3 - - + -
404K LEU* 5.3 1.8 - - + -
416K THR* 4.0 18.4 - - + -
417K SER 3.6 16.4 - - - +
418K PHE* 3.8 25.8 - - + -
424K ILE* 1.3 74.9 - - - +
426K ILE* 1.3 72.1 + - - +
435K TRP 3.9 0.3 - - - +
436K ARG* 3.6 2.6 - - - -
437K TRP* 2.8 50.6 + - + +
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Residues in contact with ILE 426 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99K VAL* 4.1 17.4 - - + +
101K PHE* 3.4 32.5 - - + -
113K PHE* 3.8 32.5 - - + -
126K CYS* 4.8 0.4 - - - -
132K ILE* 4.3 6.5 - - + -
416K THR* 3.5 3.6 - - - -
417K SER 3.0 32.2 + - - +
424K ILE* 4.2 2.5 - - + -
425K LEU* 1.3 79.1 - - - +
427K ALA* 1.3 64.1 + - - +
428K VAL* 4.2 1.8 - - + -
434K ILE* 3.6 21.3 - - + -
435K TRP 3.4 12.6 - - - +
436K ARG* 3.6 27.8 - - + -
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Residues in contact with ALA 427 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99K VAL* 5.2 0.2 - - - -
386K LEU* 3.7 33.2 - - + -
413K ILE* 3.8 21.5 - - + -
415K GLN 3.7 6.5 - - - +
416K THR* 4.7 1.1 - - + -
425K LEU 4.4 0.2 + - - -
426K ILE* 1.3 76.7 - - - +
428K VAL* 1.3 62.9 + - - +
434K ILE* 3.6 0.7 - - - -
435K TRP* 3.0 43.8 + - + +
437K TRP* 5.0 0.2 - - - +
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Residues in contact with VAL 428 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96K LEU* 3.6 45.8 - - + +
98K GLY 4.2 9.9 - - - +
99K VAL* 3.8 40.8 - - + -
115K THR* 4.0 9.6 - - + -
413K ILE* 3.6 5.9 - - - +
414K ARG* 3.2 22.3 + - - +
415K GLN 3.5 12.0 + - - +
426K ILE* 4.2 4.3 - - + -
427K ALA* 1.3 76.7 - - - +
429K CYS* 1.3 61.9 + - - +
433K SER 3.6 3.1 - - - -
434K ILE* 4.0 9.2 - - + -
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Residues in contact with CYS 429 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96K LEU* 3.2 21.7 + - - +
409K CYS* 4.5 2.7 - - - -
410K GLY 6.0 0.2 - - - -
411K ALA 3.7 15.3 - - - +
412K ALA 3.3 5.4 - - - +
413K ILE* 3.5 32.1 - - - -
414K ARG 4.7 0.2 - - - +
427K ALA 4.8 0.2 - - - -
428K VAL* 1.3 76.5 - - - +
430K ASP* 1.3 60.5 + - - +
431K ASP* 3.2 19.7 - - - +
432K ALA* 3.1 17.9 + - - -
433K SER* 2.9 12.6 + - - +
435K TRP* 3.6 25.4 - - - -
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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