Contacts of the strand formed by residues 260 - 264 (chain H) 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 LEU 260 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252H MET* 4.3 6.7 - - + -
253H SER 3.3 9.9 - - - +
254H CYS* 3.8 11.0 - - + -
258H HIS 5.2 1.6 - - - +
259H SER* 1.3 77.0 - - - +
261H LYS* 1.3 61.5 + - - +
299H PHE* 4.5 1.6 - - - -
300H SER* 3.3 5.0 - - - -
301H THR* 3.0 33.8 + - + +
304H ILE* 4.0 12.6 - - + -
305H HIS* 3.7 29.4 - - + -
309H VAL* 4.2 2.7 - - + -
312H VAL* 3.4 33.7 - - + -
321H SER* 3.9 9.4 - - - +
331H TRP* 3.6 38.1 - - + -
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Residues in contact with LYS 261 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233H GLU* 2.7 40.7 + - - +
234H GLY 3.6 16.6 + - - -
235H HIS* 3.9 21.5 - - + +
252H MET* 3.5 4.2 - - - -
253H SER* 3.0 42.7 + - - +
257H ASP* 4.4 2.5 - - - -
259H SER* 4.0 16.1 + - - +
260H LEU* 1.3 77.7 - - - +
262H LEU* 1.3 60.4 + - - +
263H TRP* 3.1 24.5 + - + +
297H PRO* 4.1 7.8 - - + +
299H PHE 3.3 4.9 - - - +
300H SER* 3.7 26.1 + - - +
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Residues in contact with LEU 262 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250H LYS* 3.8 28.3 - - + -
251H ILE 3.4 11.9 - - - +
252H MET* 3.4 18.0 - - + -
261H LYS* 1.3 72.6 - - - +
263H TRP* 1.3 69.2 + - - +
264H ARG* 3.9 31.2 - - + +
297H PRO* 3.2 11.1 - - - +
298H ASP* 2.9 32.1 + - + -
299H PHE* 2.9 32.5 + - + -
314H TRP* 3.8 15.3 - - + -
340H ILE* 4.3 17.7 - - + -
343H ILE* 5.3 0.7 - - + -
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Residues in contact with TRP 263 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215H LEU* 4.4 5.6 - - + +
229H PHE* 3.6 61.0 - + + -
230H GLY 4.1 2.0 - - - -
233H GLU 4.5 4.7 - - - -
234H GLY* 4.1 16.8 - - - -
235H HIS* 4.3 8.1 - + - -
251H ILE* 2.7 54.5 + - + +
253H SER* 2.8 26.1 + - - -
261H LYS* 3.1 41.5 + - + -
262H LEU* 1.3 74.2 - - - +
264H ARG* 1.3 64.7 + - - +
265H ILE* 3.4 2.3 + - - +
294H ILE* 3.8 36.6 - - + -
296H PHE 4.3 2.2 - - - -
297H PRO* 4.1 20.2 - - + -
298H ASP* 4.1 3.6 - - - -
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Residues in contact with ARG 264 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229H PHE* 5.6 0.7 - - - -
250H LYS* 4.1 17.5 - - + +
262H LEU* 3.9 23.8 - - + +
263H TRP* 1.3 70.6 - - - +
265H ILE* 1.3 61.6 + - - +
266H ASN* 3.5 22.7 - - - +
267H SER* 4.0 18.5 + - - +
270H MET* 4.0 6.4 - - - +
298H ASP* 3.1 41.0 + - + +
340H ILE 2.9 29.0 + - - -
341H ASP* 3.6 25.6 + - - +
343H ILE* 3.3 33.1 + - - +
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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