Contacts of the strand formed by residues 335 - 342 (chain C) in PDB entry 6S6A
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 335 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C PHE* 4.2 19.1 - - + -
261C LEU* 4.5 12.8 - - + -
262C PHE 2.9 22.7 - - - +
263C ASP* 3.8 6.7 - - + +
270C ILE* 3.7 33.9 - - + -
310C TYR* 2.8 10.7 + - - -
331C VAL* 3.0 19.6 + - + -
332C THR* 2.8 39.5 + - - +
334C PHE* 1.3 83.8 - - + +
336C ALA* 1.3 54.8 - - - +
363C ILE* 4.8 4.9 - - + -
367C PHE* 3.8 24.2 - - + -
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Residues in contact with ALA 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C PHE 3.6 0.7 - - - +
261C LEU* 3.8 2.3 - - - -
262C PHE* 2.9 37.4 + - + +
264C VAL* 3.6 17.0 - - + -
289C ILE* 5.7 0.7 - - + -
310C TYR* 3.5 17.3 - - + +
328C LEU* 4.4 20.2 - - + -
329C LYS 3.4 10.8 - - - +
331C VAL* 3.9 2.0 - - - -
335C LEU* 1.3 73.7 - - - +
337C LEU* 1.3 61.5 + - - +
338C VAL* 5.1 1.1 - - + -
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Residues in contact with LEU 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C LEU* 3.5 30.5 - - + -
250C PHE* 3.3 35.2 - - + -
259C ALA* 4.1 6.7 - - + -
260C PHE 3.6 14.6 - - - +
261C LEU* 4.5 2.9 - - + -
327C TYR 3.8 0.9 - - - +
328C LEU* 3.2 4.9 - - - +
329C LYS* 2.7 35.6 + - + +
331C VAL* 3.3 16.6 - - + +
336C ALA* 1.3 72.8 - - - +
338C VAL* 1.3 60.9 + - - +
339C CYS* 3.8 13.5 - - - -
356C PHE* 3.6 24.7 - - + -
359C PHE* 4.1 11.9 - - + -
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Residues in contact with VAL 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C LYS 4.2 0.2 - - - +
259C ALA* 3.4 1.8 - - - -
260C PHE* 2.9 39.6 + - - +
262C PHE* 3.8 29.2 - - + -
285C CYS* 3.6 30.0 - - + +
288C MET* 4.2 19.5 - - - -
289C ILE* 4.4 8.1 - - + -
326C LEU* 5.1 1.6 - - + -
327C TYR 3.5 5.4 - - - +
328C LEU* 3.9 25.4 - - + -
336C ALA* 4.7 2.2 - - + +
337C LEU* 1.3 78.4 - - - +
339C CYS* 1.3 69.1 + - - +
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Residues in contact with CYS 339 (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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250C PHE* 3.9 4.7 - - - -
256C ILE* 3.8 33.7 - - + -
258C LYS 3.5 4.0 - - - -
259C ALA* 4.2 8.5 - - - -
325C VAL 3.7 1.2 - - - +
326C LEU* 3.2 8.7 - - - +
327C TYR* 2.8 55.1 + - + +
337C LEU* 3.8 30.5 - - - -
338C VAL* 1.3 75.3 - - - +
340C ILE* 1.3 63.9 + - - +
341C LEU* 4.0 5.1 - - + +
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Residues in contact with ILE 340 (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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256C ILE* 3.4 1.6 - - - +
257C GLU* 3.1 35.1 + - + +
258C LYS* 2.9 37.5 + - + +
260C PHE* 4.2 2.5 - - + -
281C SER* 3.8 33.4 - - - +
284C LEU* 6.1 2.0 - - + -
285C CYS* 3.9 21.8 - - - -
324C THR* 4.2 14.6 - - + +
325C VAL 3.7 2.2 - - - -
326C LEU* 3.5 25.6 - - + -
338C VAL 5.3 0.9 - - - +
339C CYS* 1.3 74.4 - - - +
341C LEU* 1.3 66.8 + - - +
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Residues in contact with LEU 341 (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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255C GLY 4.1 13.5 - - - +
256C ILE* 4.1 14.8 - - + -
257C GLU* 4.5 10.5 - - - +
324C THR* 3.6 7.2 - - - +
325C VAL* 2.7 56.3 + - + +
327C TYR* 4.3 9.6 - - + -
339C CYS* 4.0 19.3 - - + +
340C ILE* 1.3 79.9 - - - +
342C ARG* 1.3 62.5 + - - +
345C SER* 4.0 6.5 - - - -
346C PHE* 3.8 28.9 - - + +
352C ILE* 3.9 23.1 - - + -
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Residues in contact with ARG 342 (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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257C GLU* 3.7 28.5 + - - +
322C ASN* 2.8 48.0 + - - +
323C THR* 3.3 17.3 + - - +
324C THR* 3.5 12.4 + - - -
325C VAL* 4.2 2.9 - - - -
341C LEU* 1.3 76.9 - - - +
343C GLU* 1.3 57.1 + - - +
344C GLU* 4.1 11.4 - - + +
345C SER* 2.9 30.2 + - - +
346C PHE* 3.2 10.2 + - - +
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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