Contacts of the strand formed by residues 363 - 368 (chain B) in PDB entry 1LK9
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 TYR 363 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B GLY* 3.4 27.5 - - - -
206B ASN 5.6 0.4 - - - -
207B ASN* 3.9 7.0 - - + -
208B PRO 3.5 25.0 + - - +
228B TYR* 2.7 37.8 + + - -
251B LYS* 4.4 0.5 - - - -
342B GLN* 2.9 22.3 + - - -
361B PRO* 3.2 10.1 - - - +
362B SER* 1.3 100.8 + - - +
364B ALA* 1.3 61.3 + - - +
401B ARG* 3.3 58.5 + - + -
402B LEU 3.2 7.2 - - - +
403B SER* 3.7 18.6 - - - -
404B LEU* 3.8 7.2 - - - -
850B DHA 3.6 3.3 + - - +
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Residues in contact with ALA 364 (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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326B TRP* 3.9 16.6 - - + -
329B ILE* 4.1 19.7 - - + -
333B LEU* 5.3 2.7 - - + -
341B TYR* 5.3 1.3 - - + -
342B GLN* 3.8 4.5 - - - +
363B TYR* 1.3 73.6 - - - +
365B TRP* 1.3 60.4 - - - +
366B VAL* 3.5 20.4 + - + -
400B VAL 3.7 0.2 - - - +
401B ARG* 3.6 1.2 - - - -
402B LEU* 2.8 46.2 + - + +
404B LEU* 3.8 5.4 - - + +
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Residues in contact with TRP 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B PRO* 4.1 13.9 - - + +
208B PRO* 3.3 38.7 - - + +
209B GLU* 3.9 24.0 - - + -
341B TYR* 3.4 4.3 - - - -
342B GLN* 2.8 48.3 + - + +
363B TYR 3.8 0.4 - - - -
364B ALA* 1.3 69.8 - - - +
366B VAL* 1.3 60.6 + - - +
367B LYS 4.1 0.5 + - - -
390B GLY* 3.7 14.4 - - - -
393B PHE* 4.0 12.1 - + + -
395B ALA* 3.5 30.3 - - + -
399B TYR* 3.5 40.0 - + + -
400B VAL 3.5 23.3 - - - -
401B ARG* 3.8 16.8 - - + +
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Residues in contact with VAL 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LEU* 4.2 15.5 - - + -
339B PHE* 3.8 31.9 - - + -
340B SER 3.2 12.3 - - - +
341B TYR* 4.7 1.6 - - + -
364B ALA* 3.9 24.2 - - + +
365B TRP* 1.3 77.8 - - - +
367B LYS* 1.3 65.9 + - - +
368B CYS 4.1 0.2 + - - -
376B CYS* 4.4 0.2 - - - -
380B PHE* 4.1 13.7 - - + -
398B ARG 3.7 0.5 - - - +
399B TYR* 3.2 7.1 - - - -
400B VAL* 2.9 44.0 + - + +
402B LEU* 3.9 15.7 - - + -
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Residues in contact with LYS 367 (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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339B PHE* 3.3 5.5 - - - -
340B SER* 2.9 45.2 + - - +
365B TRP 4.1 0.8 + - - -
366B VAL* 1.3 77.7 - - - +
368B CYS* 1.3 72.6 - - - +
369B GLU* 3.3 23.2 + - - +
398B ARG* 3.2 39.3 - - + +
399B TYR* 3.6 27.3 - - + +
909B SO4 2.6 30.0 + - - -
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Residues in contact with CYS 368 (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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338B ARG 3.9 4.7 - - - -
339B PHE* 3.8 22.9 - - + -
367B LYS* 1.3 82.0 - - - +
369B GLU* 1.3 61.5 + - - +
370B TRP 3.5 3.8 + - - +
373B ASP* 3.5 32.5 - - + +
376B CYS* 2.1 50.0 - - + -
379B THR* 4.0 7.0 - - - -
380B PHE* 4.1 0.4 - - - -
398B ARG* 2.8 26.0 + - - +
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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