Contacts of the strand formed by residues 338 - 343 (chain B) in PDB entry 4L1O
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 VAL 338 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B LYS* 2.9 18.6 + - - +
293B VAL* 3.8 28.7 - - + +
296B LEU* 5.2 2.7 - - + +
297B ILE* 3.9 29.6 - - + -
315B ILE* 4.7 2.5 - - + -
318B THR* 3.4 10.1 - - + +
320B LEU* 3.7 32.1 - - + -
329B VAL* 4.1 13.5 - - + -
334B ILE* 3.5 14.7 - - + +
336B GLY 2.9 8.1 + - - -
337B PRO* 1.3 77.7 - - - +
339B LEU* 1.3 59.7 + - - +
340B PRO* 3.3 8.0 - - - +
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Residues in contact with LEU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ILE* 4.3 7.0 - - + -
235B LYS* 4.0 13.9 - - + +
236B PHE* 4.1 20.2 - - + -
246B PRO 4.1 12.6 - - - +
247B ASP 3.8 16.8 - - - +
248B TYR* 4.1 4.7 - - - -
249B ILE* 3.9 29.4 - - + -
263B LEU* 3.6 37.9 - - + -
318B THR 2.7 16.7 + - - +
319B ILE* 3.4 9.9 - - + +
320B LEU* 2.9 23.1 + - - -
338B VAL* 1.3 73.3 - - - +
340B PRO* 1.3 63.8 - - - +
341B ILE* 5.3 0.2 - - + -
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Residues in contact with PRO 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ASP 3.4 14.8 - - - +
248B TYR* 3.6 13.1 - - + +
249B ILE* 3.1 25.3 + - - +
320B LEU* 3.7 9.2 - - + +
323B VAL* 3.7 27.8 - - + -
329B VAL* 4.0 12.6 - - + -
330B MET* 3.8 11.9 - - - -
334B ILE* 3.5 17.5 - - + -
338B VAL 3.3 11.7 - - - +
339B LEU* 1.3 87.9 - - - +
341B ILE* 1.3 61.6 + - - +
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Residues in contact with ILE 341 (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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249B ILE* 3.7 21.5 - - + +
251B CYS* 3.6 30.1 - - - -
256B GLN* 3.8 24.0 - - + +
259B ILE* 4.3 16.8 - - + -
260B VAL* 3.8 29.8 - - + -
263B LEU* 4.9 0.7 - - + -
319B ILE* 3.9 16.2 - - + -
320B LEU 2.9 17.1 + - - +
321B THR* 4.5 0.9 - - + -
322B ASP* 3.4 6.6 + - - -
323B VAL* 3.1 24.1 + - - +
339B LEU 4.4 1.1 - - - +
340B PRO* 1.3 75.0 - - - +
342B VAL* 1.3 67.7 + - - +
343B CYS* 4.1 0.8 + - - -
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Residues in contact with VAL 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B TYR* 4.5 1.8 - - + -
249B ILE 2.9 11.4 + - - +
250B LEU* 3.4 22.0 - - + +
251B CYS 3.3 22.2 + - - +
323B VAL* 4.0 16.6 - - + +
325B PRO* 3.9 26.7 - - + -
330B MET* 3.9 43.5 - - + -
340B PRO 5.1 0.4 - - - -
341B ILE* 1.3 79.5 - - - +
343B CYS* 1.3 72.4 + - - +
344B VAL* 5.1 0.2 - - + -
353B PHE* 4.3 8.7 - - + -
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Residues in contact with CYS 343 (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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251B CYS 3.4 6.1 - - - +
253B PRO* 4.0 30.1 - - + -
256B GLN* 3.4 34.3 - - - -
322B ASP* 3.7 16.7 - - - +
323B VAL 5.1 1.8 + - - +
341B ILE* 4.1 2.2 + - - -
342B VAL* 1.3 82.4 - - - +
344B VAL* 1.3 66.2 + - - +
349B GLU* 4.6 4.0 - - - +
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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
------------------------------------------------------------
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