Contacts of the strand formed by residues 342 - 349 (chain C) in PDB entry 3B60
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 342 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340C GLY 3.2 3.2 + - - +
341C ASP* 1.3 69.8 - - - +
343C GLU* 1.3 75.2 + - - +
344C PHE* 4.4 14.4 - - + -
364C LEU 4.4 6.3 - - - +
366C ILE* 2.8 80.1 + - + +
389C ILE* 4.0 35.9 - - + -
400C ILE* 6.0 4.3 - - + -
401C LEU 4.1 2.5 - - - -
402C MET* 4.7 4.0 - - - +
501C ILE* 4.7 23.8 - - + +
503C ILE* 5.8 0.7 - - + -
531C THR* 5.0 2.5 - - + -
533C LEU* 5.0 5.6 - - + -
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Residues in contact with GLU 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C ASP* 2.8 31.8 - - - +
342C LEU* 1.3 85.4 - - - +
344C PHE* 1.3 57.2 + - - +
345C ARG* 3.2 26.7 + - - +
364C LEU 3.6 7.0 - - - -
365C LYS* 3.1 31.9 + - + +
400C ILE* 4.4 1.4 - - - +
401C LEU* 2.6 48.5 + - + +
404C GLY* 3.2 29.5 + - - -
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Residues in contact with PHE 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342C LEU* 4.4 11.4 - - + -
343C GLU* 1.3 76.7 - - - +
345C ARG* 1.3 62.6 + - - +
347C VAL* 3.7 14.6 - - + -
359C LEU* 6.3 1.1 - - + -
362C ILE* 3.6 15.8 - - + +
363C ASN* 3.3 2.4 - - - -
364C LEU* 2.7 77.8 + - + -
385C ILE* 3.1 42.4 - - + -
388C LEU* 6.0 2.9 - - + -
389C ILE* 5.5 5.2 - - + -
399C HIS 3.0 17.3 - - - +
400C ILE* 3.2 41.3 - - + -
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Residues in contact with ARG 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343C GLU* 3.2 34.6 + - - +
344C PHE* 1.3 92.3 + - - +
346C ASN* 1.3 76.0 + - - +
347C VAL* 2.7 25.1 + - - +
362C ILE 3.6 0.4 - - - -
363C ASN* 3.6 13.0 - - + +
364C LEU 4.5 2.8 + - - +
365C LYS* 3.8 21.0 - - - +
399C HIS* 2.8 20.4 + - + +
401C LEU* 4.2 19.5 - - - +
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Residues in contact with ASN 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345C ARG* 1.3 82.7 - - - +
347C VAL* 1.3 62.5 + - - +
348C THR* 3.4 4.0 + - - -
361C ASN* 3.5 25.7 - - + +
362C ILE 3.2 12.4 + - - +
363C ASN* 2.4 31.7 + - - +
397C GLU* 3.4 11.8 - - - +
398C GLY* 3.6 11.8 - - - -
399C HIS* 4.2 2.8 + - - +
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Residues in contact with VAL 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344C PHE* 3.7 17.3 - - + -
345C ARG 2.7 19.4 + - - +
346C ASN* 1.3 72.9 - - - +
348C THR* 1.3 58.0 + - - +
349C PHE* 5.2 3.6 - - + -
359C LEU* 4.4 3.3 - - + +
360C ARG 2.4 25.1 - - - +
362C ILE* 3.1 14.6 + - + +
388C LEU* 5.2 3.8 - - + -
395C ILE* 3.2 33.2 - - + -
397C GLU 3.6 4.3 - - - -
398C GLY* 3.9 0.7 - - - -
399C HIS 3.3 25.1 - - - +
400C ILE* 3.6 22.2 - - + -
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Residues in contact with THR 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346C ASN 3.9 2.1 + - - -
347C VAL* 1.3 77.9 - - - +
349C PHE* 1.3 67.9 + - - +
357C PRO* 4.2 19.3 - - + -
359C LEU 3.2 12.8 - - - +
360C ARG* 3.6 8.7 - - + -
361C ASN* 3.6 27.7 + - - -
396C ASP* 2.8 23.2 + - - +
397C GLU* 2.8 31.9 + - - -
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Residues in contact with PHE 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347C VAL* 5.2 3.6 - - + +
348C THR* 1.3 75.8 - - - +
350C THR* 1.3 95.4 + - - +
351C TYR* 3.8 29.6 - + - -
357C PRO* 3.3 3.0 - - - +
358C ALA* 2.8 23.5 + - + -
359C LEU* 2.5 33.3 + - + +
384C THR* 4.4 6.5 - - + -
388C LEU* 3.4 32.1 - - + -
393C TYR* 3.3 53.8 - + + -
395C ILE* 3.6 7.9 - - - -
396C ASP* 3.1 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