Contacts of the strand formed by residues 322 - 330 (chain C) in PDB entry 5Y7K
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 TYR 322 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292C SER* 4.3 9.0 - - - -
293C MET* 3.7 9.1 - - + +
316C LEU* 3.2 15.7 - - - +
317C ARG* 3.3 69.2 + - - +
319C ILE 3.8 1.0 + - - +
320C GLN 3.6 1.0 - - - -
321C ASN* 1.3 85.6 + - - +
323C SER* 1.3 60.6 + - - +
324C VAL* 3.5 21.1 - - + +
344C GLN* 5.7 0.2 + - - -
346C ILE* 3.3 39.5 - - + +
347C GLU 4.1 1.6 - - - -
348C MET* 3.8 27.8 - - + +
354C VAL* 3.9 0.4 - - - +
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Residues in contact with SER 323 (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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293C MET* 4.0 0.2 - - - -
314C GLN* 3.8 11.4 + - - +
315C TRP 3.1 14.8 + - - -
316C LEU* 4.5 1.8 - - - -
322C TYR* 1.3 75.1 - - - +
324C VAL* 1.3 75.0 + - - +
346C ILE* 3.4 4.7 - - - +
347C GLU* 2.8 45.6 + - - +
354C VAL* 4.2 7.2 - - - -
359C PRO* 3.6 29.2 - - - +
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Residues in contact with VAL 324 (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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290C PRO* 3.9 19.7 - - + -
292C SER* 3.8 10.1 - - - +
293C MET* 3.6 13.7 - - + -
314C GLN* 3.4 0.7 - - - -
315C TRP* 2.8 37.1 + - - -
322C TYR* 3.5 25.6 - - + +
323C SER* 1.3 86.0 + - - +
325C MET* 1.3 64.1 + - - +
344C GLN* 3.5 37.5 - - + +
345C HIS 3.4 4.3 - - - +
346C ILE* 4.1 11.2 - - + -
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Residues in contact with MET 325 (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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312C SER* 4.6 8.3 - - - -
313C LEU 3.1 11.4 - - - +
314C GLN* 3.8 28.9 - - + +
324C VAL* 1.3 73.7 - - - +
326C ASP* 1.3 69.8 + - - +
327C ILE* 4.3 13.2 - - + -
344C GLN* 3.3 11.8 - - - +
345C HIS* 2.6 46.9 + - + +
362C PRO* 3.7 34.3 - - + -
364C PHE* 4.7 1.6 - - - -
371C PHE* 3.8 28.9 - - + -
373C LYS* 4.1 11.7 - - - +
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Residues in contact with ASP 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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287C ILE* 6.0 0.4 - - + -
288C THR 4.3 5.7 - - - +
290C PRO* 3.1 35.9 - - + +
311C ILE 4.0 0.5 - - - +
312C SER* 3.2 5.0 - - - -
313C LEU* 2.7 38.8 + - + +
315C TRP* 4.6 11.7 + - - +
324C VAL 4.0 1.2 + - - -
325C MET* 1.3 75.4 - - - +
327C ILE* 1.3 61.9 + - - +
328C CYS* 3.9 11.3 - - - -
339C CYS* 3.5 31.2 - - - +
340C LEU 4.4 2.4 - - - +
341C VAL* 5.8 0.2 - - - -
344C GLN* 4.1 15.6 - - - +
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Residues in contact with ILE 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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310C ARG* 3.6 34.3 - - + +
311C ILE 3.9 2.9 - - - +
312C SER* 4.5 5.2 - - - +
325C MET* 4.3 12.3 - - + -
326C ASP* 1.3 78.0 + - - +
328C CYS* 1.3 60.2 + - - +
329C ASP* 3.9 6.7 - - - +
338C ASN 3.9 0.9 - - - +
339C CYS* 3.5 13.2 - - - -
340C LEU* 4.0 5.6 + - - +
343C ARG* 3.4 39.7 + - + +
345C HIS* 4.1 12.8 - - + -
364C PHE* 4.3 9.2 - - + -
371C PHE* 4.1 10.3 - - + -
389C ILE* 3.7 34.1 - - + +
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Residues in contact with CYS 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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287C ILE* 3.6 32.3 - - + -
310C ARG* 3.3 3.1 - - - -
311C ILE* 2.9 42.0 + - + +
313C LEU* 5.2 4.7 - - - -
326C ASP* 4.1 12.3 - - - -
327C ILE* 1.3 71.6 - - - +
329C ASP* 1.3 64.0 + - - +
337C TRP* 3.8 7.4 - - + -
338C ASN 3.2 7.2 - - - +
339C CYS* 2.0 45.3 - - - -
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Residues in contact with ASP 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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309C GLU 3.3 5.6 - - - +
310C ARG* 2.9 36.4 + - - +
327C ILE* 3.9 6.8 - - - +
328C CYS* 1.3 78.5 - - - +
330C TYR* 1.3 64.8 + - - +
331C ASP 3.8 0.9 + - - -
337C TRP* 3.4 5.5 - - - -
338C ASN* 2.8 36.3 + - + +
340C LEU* 5.8 2.9 - - + +
343C ARG* 2.6 33.9 + - - +
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Residues in contact with TYR 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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222C PHE* 3.8 26.4 - + + -
272C ASN* 5.1 7.5 + - - +
285C ILE* 5.7 0.9 - - + -
309C GLU* 2.8 45.9 + - + +
329C ASP* 1.3 74.7 - - - +
331C ASP* 1.3 75.3 + - - +
332C GLU* 3.8 22.4 + - + +
335C GLY* 3.5 31.6 + - - -
336C ARG 3.7 7.9 - - - -
337C TRP* 3.4 42.8 - + + -
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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