Contacts of the strand formed by residues 338 - 344 (chain L) in PDB entry 6AHU
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 338 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112H LEU* 3.7 48.9 - - + +
113H ALA* 4.2 9.9 - - + +
36L HIS* 6.1 0.2 - - - -
241L PHE* 3.8 20.2 - - + -
313L SER* 5.2 1.3 - - - -
314L VAL 3.5 15.7 - - - +
315L GLN* 3.7 28.7 - - + +
316L GLY 4.8 0.4 - - - +
324L TRP* 4.1 4.8 - - - -
336L GLU* 5.1 1.1 - - + +
337L HIS* 1.3 78.0 - - - +
339L TYR* 1.3 88.8 + - - +
340L ASN* 4.7 0.7 - - + -
353L MET* 3.3 3.5 - - - +
354L ALA* 2.5 44.9 + - + +
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Residues in contact with TYR 339 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32L LEU* 4.8 7.9 - - + -
33L VAL* 4.0 23.3 - - + +
36L HIS* 3.4 41.3 - + + +
39L ASN* 3.9 6.2 + - - -
290L ILE* 3.7 14.2 - - + +
313L SER* 3.9 0.3 - - - -
314L VAL* 3.3 68.4 + - + +
324L TRP* 4.7 8.5 - + + -
338L LEU* 1.3 85.5 - - - +
340L ASN* 1.3 61.1 + - - +
341L PHE* 3.5 36.1 - + - -
351L LEU* 4.7 4.5 - - + -
352L GLN 3.3 6.7 - - - -
353L MET* 4.1 17.9 - - + -
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Residues in contact with ASN 340 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112H LEU* 4.5 0.9 - - - +
240L LEU* 4.8 1.4 - - - +
241L PHE* 4.0 13.1 - - + -
244L LEU* 3.5 23.8 - - - +
311L THR* 4.4 0.3 - - - +
312L LEU 3.0 7.6 + - - +
313L SER* 2.6 23.3 + - - -
338L LEU* 4.7 1.1 - - + -
339L TYR* 1.3 79.4 - - - +
341L PHE* 1.3 92.2 + - - +
342L VAL* 4.3 11.0 - - - +
350L TRP 3.1 12.7 - - - +
351L LEU* 3.5 8.0 - - - +
352L GLN* 3.0 50.1 + - + +
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Residues in contact with PHE 341 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L PHE* 5.2 0.2 - + - -
29L HIS* 4.5 9.4 - - + -
32L LEU* 5.4 1.8 - - + -
33L VAL* 3.7 23.8 - - + -
290L ILE* 6.0 0.7 - - + -
294L LEU* 4.2 23.1 - - + -
311L THR* 3.7 3.6 - - - -
312L LEU* 2.6 68.0 + - + +
339L TYR* 3.5 32.3 - + - -
340L ASN* 1.3 80.5 + - - +
342L VAL* 1.3 64.0 + - - +
343L ILE* 3.6 13.7 + - + +
349L TYR* 3.8 32.8 - + + -
350L TRP 3.3 2.2 - - - -
351L LEU* 3.9 21.3 - - + -
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Residues in contact with VAL 342 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222L LEU* 4.1 17.9 - - + -
240L LEU* 4.0 23.3 - - + -
244L LEU* 5.8 0.9 - - + -
309L TRP* 3.7 30.7 - - + -
310L VAL 3.7 3.1 - - - -
311L THR* 5.8 1.8 - - + -
340L ASN* 4.3 13.7 - - - +
341L PHE* 1.3 72.6 - - - +
343L ILE* 1.3 60.7 + - - +
344L PHE* 3.5 17.1 - - + -
349L TYR* 3.3 4.3 - - - -
350L TRP* 3.2 49.4 + - + +
352L GLN* 4.9 3.8 - - - +
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Residues in contact with ILE 343 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L PHE* 3.8 30.5 - - + -
294L LEU* 3.9 24.5 - - + +
297L LEU* 3.9 48.5 - - + +
298L CYS* 4.8 2.7 - - - -
301L PHE* 4.0 6.8 - - + -
309L TRP* 3.4 4.6 - - - +
310L VAL* 3.1 41.3 + - + +
312L LEU* 4.8 2.2 - - + -
341L PHE* 3.6 17.2 - - + +
342L VAL* 1.3 71.9 - - - +
344L PHE* 1.3 73.3 - - - +
348L ASP 3.6 3.6 - - - -
349L TYR* 4.3 2.0 - - + +
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Residues in contact with PHE 344 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222L LEU* 3.8 37.2 - - + -
224L SER* 3.5 28.5 - - - -
301L PHE* 3.6 10.3 - - - -
308L PRO 4.2 6.5 - - - -
309L TRP* 3.8 16.6 - + + -
342L VAL* 3.5 17.3 - - + -
343L ILE* 1.3 86.8 - - - +
345L ASN* 1.3 67.1 + - - +
346L ASN* 3.3 15.9 + - - +
347L GLN* 3.8 7.4 + - - -
348L ASP 2.7 29.8 + - - +
350L TRP* 3.6 44.9 - + - -
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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