Contacts of the strand formed by residues 324 - 330 (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 THR 324 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A ALA* 5.9 1.6 - - + -
257C GLU* 5.7 0.5 + - - -
284C LEU* 5.9 0.4 - - + -
319C LYS* 3.7 2.6 - - - +
320C LEU* 2.9 49.8 + - + +
322C ASN* 2.9 25.7 + - - -
323C THR* 1.3 79.7 - - - +
325C VAL* 1.3 69.7 + - - +
326C LEU* 4.1 11.7 - - + -
340C ILE* 4.2 11.5 - - + +
341C LEU 3.6 9.8 + - - +
342C ARG* 3.5 23.3 + - - +
343C GLU* 5.4 0.2 - - - +
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Residues in contact with VAL 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C ILE* 4.1 12.6 - - + -
318C ILE 3.4 7.6 - - - +
319C LYS* 4.4 5.8 - - + -
324C THR* 1.3 77.2 - - - +
326C LEU* 1.3 81.0 + - - +
327C TYR* 4.6 0.9 - - + -
341C LEU* 2.7 49.7 + - + +
343C GLU* 3.1 44.4 - - - +
346C PHE* 4.0 31.0 - - + -
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Residues in contact with LEU 326 (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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238A PHE* 4.9 5.2 - - + -
284C LEU* 3.5 35.9 - - + -
285C CYS* 5.0 7.2 - - - -
288C MET* 3.8 31.7 - - + +
317C ILE* 3.4 4.9 - - - -
318C ILE* 2.8 52.6 + - + +
320C LEU* 4.9 4.7 - - + -
324C THR* 4.1 9.9 - - + -
325C VAL* 1.3 82.7 - - - +
327C TYR* 1.3 60.6 + - - +
338C VAL* 5.1 1.6 - - + -
339C CYS 3.2 2.2 - - - +
340C ILE* 3.5 37.9 - - + -
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Residues in contact with TYR 327 (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* 5.9 0.2 - - + -
288C MET* 4.2 1.3 - - - +
315C MET* 3.5 24.8 - - + +
316C ALA 3.4 13.0 - - - -
317C ILE* 3.8 12.1 - - + -
325C VAL* 4.6 4.3 - - + -
326C LEU* 1.3 75.3 - - - +
328C LEU* 1.3 59.5 - - - +
329C LYS* 3.2 30.8 + - + +
337C LEU 3.8 1.2 - - - +
338C VAL* 3.5 2.6 - - - +
339C CYS* 2.8 57.1 + - + +
341C LEU* 4.3 11.2 - - + -
346C PHE* 4.1 17.9 - + - -
349C LYS* 3.2 19.3 + - + -
352C ILE* 4.1 20.6 - - + -
353C ASP* 2.5 31.0 + - - -
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Residues in contact with LEU 328 (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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264C VAL* 6.1 0.9 - - + -
288C MET* 3.8 20.1 - - + +
289C ILE* 4.1 19.7 - - + -
292C VAL* 4.3 25.1 - - + -
310C TYR* 4.9 7.6 - - + -
314C SER* 4.0 18.6 - - - +
315C MET* 3.5 5.3 - - - +
316C ALA* 3.2 35.6 + - + +
327C TYR* 1.3 71.9 - - - +
329C LYS* 1.3 75.4 + - - +
330C GLU 4.5 0.7 - - - +
336C ALA* 4.4 13.9 - - + -
337C LEU 3.2 10.3 - - - +
338C VAL* 3.9 19.3 - - + +
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Residues in contact with LYS 329 (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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314C SER 4.0 5.1 + - - -
315C MET* 4.4 18.4 - - + +
327C TYR* 3.2 42.7 + - + +
328C LEU* 1.3 83.8 - - - +
330C GLU* 1.3 62.0 + - - +
331C VAL* 3.7 1.0 - - - +
336C ALA* 3.4 2.4 - - - -
337C LEU* 2.7 38.8 + - + +
352C ILE* 6.1 0.2 - - + -
353C ASP* 4.0 12.0 + - - +
356C PHE* 3.4 49.4 - - + -
357C HIS* 5.5 6.8 - - - -
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Residues in contact with GLU 330 (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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310C TYR* 3.2 33.7 - - + +
311C ASP 3.5 22.7 - - - +
312C LYS* 4.0 27.1 + - - +
314C SER 3.3 16.0 + - - +
328C LEU* 4.5 1.4 - - - +
329C LYS* 1.3 73.6 - - - +
331C VAL* 1.3 64.0 + - - +
332C THR* 2.9 23.4 - - - -
333C LYS* 3.4 4.7 + - - -
356C PHE* 3.3 17.3 - - - -
360C ARG* 3.1 30.9 + - - -
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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