Contacts of the strand formed by residues 292 - 299 (chain C) in PDB entry 5I4A
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 PRO 292 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C GLU 4.8 0.2 - - - +
291C GLN* 1.3 95.2 - - + +
293C LEU* 1.3 61.2 + - - +
294C LYS* 3.7 28.3 + - + +
332C PHE* 4.4 1.6 - - - -
333C SER* 3.5 13.0 - - - +
334C LYS* 3.7 29.4 - - + +
336C GLU* 6.0 0.2 - - + -
369C ASN* 4.9 5.4 - - - +
423C ILE* 4.2 12.0 - - - +
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Residues in contact with LEU 293 (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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291C GLN 3.8 1.0 + - - -
292C PRO* 1.3 69.1 - - - +
294C LYS* 1.3 63.3 + - - +
295C ALA* 5.4 2.8 - - + +
323C PHE* 4.2 19.5 - - + -
327C ALA* 4.4 10.5 - - + -
332C PHE* 3.8 37.9 - - + -
334C LYS 2.9 15.5 + - - +
335C VAL* 3.4 9.5 - - + +
336C GLU 2.9 24.8 + - - +
371C MET* 4.1 13.0 - - + -
416C VAL* 4.3 8.7 - - + -
419C MET* 3.9 42.4 - - + -
423C ILE* 4.3 7.6 - - + -
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Residues in contact with LYS 294 (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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292C PRO* 3.7 29.5 + - + +
293C LEU* 1.3 76.9 - - - +
295C ALA* 1.3 63.6 + - - +
334C LYS* 4.9 3.1 - - - +
336C GLU* 3.1 37.4 + - + +
338C LEU* 4.3 16.0 - - + +
367C GLU 5.8 0.4 - - - +
368C ASP* 4.5 18.7 + - + +
369C ASN 3.8 19.1 + - - +
370C VAL* 3.5 16.4 - - + -
371C MET* 2.8 28.1 + - - +
423C ILE* 6.0 0.2 - - - +
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Residues in contact with ALA 295 (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 LEU* 5.4 3.6 - - + +
294C LYS* 1.3 76.5 - - - +
296C ILE* 1.3 62.7 + - - +
323C PHE* 5.9 1.6 - - + -
336C GLU 3.0 6.5 + - - -
337C PHE* 3.2 32.2 - - + +
338C LEU* 3.1 24.5 + - - +
370C VAL* 4.1 3.3 - - - +
371C MET* 3.2 22.4 - - + +
373C ILE* 4.0 15.0 - - + -
419C MET* 5.4 2.9 - - + -
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Residues in contact with ILE 296 (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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295C ALA* 1.3 79.1 - - - +
297C PHE* 1.3 68.2 + - - +
298C PHE* 3.6 33.0 - - + -
338C LEU* 3.5 34.8 - - + +
346C SER* 3.7 9.6 - - - +
348C PHE* 4.1 13.7 - - + -
362C PHE* 4.2 9.9 - - + -
363C ILE* 5.0 3.1 - - + -
366C ILE* 3.8 22.7 - - + -
370C VAL* 4.5 5.6 - - + -
371C MET 2.9 14.3 + - - +
372C ALA* 3.7 1.7 - - - -
373C ILE* 2.9 29.5 + - - +
394C LEU* 4.1 9.2 - - + -
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Residues in contact with PHE 297 (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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296C ILE* 1.3 76.2 - - - +
298C PHE* 1.3 62.5 + - - +
299C PHE* 3.5 30.3 - + + -
312C LEU* 4.4 5.8 - - + -
316C PHE* 3.5 41.3 - + + -
337C PHE* 3.4 45.8 - + + -
346C SER* 3.0 24.8 + - - +
347C ALA* 3.5 2.9 - - + -
348C PHE* 2.8 32.5 + - - -
373C ILE* 3.4 35.0 - - + +
375C LEU* 4.8 1.6 - - + -
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Residues in contact with PHE 298 (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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296C ILE* 3.6 33.0 - - + -
297C PHE* 1.3 75.2 - - - +
299C PHE* 1.3 64.6 + - - +
348C PHE* 3.2 25.1 - - + -
349C LEU 4.0 9.0 - - - -
350C TYR* 3.8 14.6 - - + -
357C VAL* 3.5 40.4 - - + -
363C ILE* 4.4 8.5 - - + -
372C ALA* 3.8 15.0 - - + -
373C ILE 2.8 9.4 + - - +
374C VAL* 3.6 13.6 - - + -
375C LEU* 3.0 28.9 + - - +
390C PHE* 3.8 20.2 - + - -
394C LEU* 3.8 17.3 - - + -
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Residues in contact with PHE 299 (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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297C PHE* 3.5 30.7 - + + -
298C PHE* 1.3 73.9 - - - +
300C SER* 1.3 63.3 - - - +
301C SER 3.2 15.0 - - - +
304C GLN* 3.3 16.2 - - - +
305C PHE* 3.7 27.1 - + + -
308C VAL* 4.2 2.2 - - + -
312C LEU* 3.5 36.3 - - + -
347C ALA* 3.6 22.2 - - + -
348C PHE 2.7 18.3 + - - +
349C LEU* 3.2 12.4 - - + +
350C TYR* 2.9 25.5 + - - -
375C LEU* 3.6 28.3 - - + -
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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