Contacts of the strand formed by residues 368 - 374 (chain C) in PDB entry 2BYL
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 368 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360C LEU 4.5 6.1 - - - +
363C LEU* 3.7 35.4 - - + +
364C PRO 2.8 11.9 + - - +
365C SER* 3.5 19.7 - - - -
367C VAL* 1.3 72.5 - - + +
369C THR* 1.3 61.9 + - - +
370C ALA 3.8 19.3 - - - +
371C VAL* 4.2 13.9 - - + -
380C ILE* 4.1 26.0 - - + -
381C VAL 3.5 6.5 - - - +
382C ILE* 4.6 2.9 - - + +
436C ILE* 4.2 17.0 - - + -
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Residues in contact with THR 369 (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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383B LYS* 4.4 15.0 + - - +
365C SER* 4.0 14.2 + - - -
367C VAL 3.7 1.0 + - - -
368C VAL* 1.3 73.1 - - - +
370C ALA* 1.3 60.2 + - + +
381C VAL* 2.6 35.9 + - + -
382C ILE 4.5 7.6 - - - +
383C LYS* 4.4 21.9 + - - +
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Residues in contact with ALA 370 (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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368C VAL* 3.5 4.2 + - - +
369C THR* 1.3 83.3 - - + +
371C VAL* 1.3 67.8 + - - +
372C ARG* 5.2 7.6 - - - +
379C ALA 4.7 0.2 - - - -
380C ILE* 3.2 6.6 - - - +
381C VAL* 2.8 46.0 + - + -
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Residues in contact with VAL 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C ARG* 3.9 30.3 - - + +
360C LEU* 3.9 33.9 - - + +
361C MET* 3.6 48.9 - - + +
368C VAL* 4.2 10.1 - - + -
370C ALA* 1.3 80.1 - - - +
372C ARG* 1.3 67.7 + - - +
378C ASN* 5.9 0.4 - - + -
379C ALA 3.6 7.0 - - - +
380C ILE* 4.4 2.0 - - + -
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Residues in contact with ARG 372 (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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236C ALA 4.6 0.4 + - - -
237C GLY* 2.9 28.7 + - - -
238C VAL* 3.3 17.2 + - - +
239C VAL* 4.4 14.6 - - - +
240C VAL* 4.8 6.5 - - + +
357C ARG* 4.1 5.8 - - - +
370C ALA* 5.2 7.2 - - - +
371C VAL* 1.3 79.4 - - - +
373C GLY* 1.3 58.7 + - - +
378C ASN* 3.2 9.3 - - - +
379C ALA* 2.9 43.1 + - + +
381C VAL* 3.7 24.2 - - + +
411C ILE* 3.5 27.9 - - - +
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Residues in contact with GLY 373 (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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238C VAL* 3.9 3.6 - - - -
240C VAL* 3.8 19.4 - - - +
357C ARG* 3.6 15.9 + - - +
372C ARG* 1.3 78.5 - - - +
374C LYS* 1.3 67.9 + - - +
377C LEU 3.1 14.1 - - - -
378C ASN* 3.4 7.4 + - - -
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Residues in contact with LYS 374 (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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232C ILE* 3.9 27.2 - - + +
240C VAL* 4.2 20.2 - - + -
246C LEU* 6.0 2.8 - - - +
272C THR* 3.7 17.8 - - - +
277C ALA* 5.1 1.9 + - + -
280C TYR* 3.6 51.0 - - + +
281C GLU* 5.6 5.1 + - - +
357C ARG* 3.7 5.4 - - - +
373C GLY* 1.3 77.7 - - - +
375C GLY* 1.3 70.3 + - - +
376C LEU 3.2 0.2 + - - -
377C LEU* 3.1 19.7 + - - +
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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