Contacts of the strand formed by residues 292 - 297 (chain A) in PDB entry 5FFO
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 ASP 292 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A PHE* 4.6 0.7 - - - -
281A ALA 3.5 1.6 - - - +
282A ALA* 3.2 8.4 - - - -
283A THR 3.2 31.2 + - - +
284A ASP* 3.5 0.5 - - - +
285A ILE* 2.8 34.4 + - + +
286A ASN* 3.0 17.4 - - - +
288A ASP* 4.6 0.2 - - - +
290A TYR 2.9 16.0 - - - +
291A ALA* 1.3 73.5 - - - +
293A VAL* 1.3 61.8 + - - +
294A PHE* 3.5 14.8 - - + -
317A VAL* 5.9 0.2 - - + -
318A SER 3.5 11.4 - - - +
319A LEU* 3.8 6.6 - - + -
320A GLN* 3.1 25.7 + - - +
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Residues in contact with VAL 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A PHE* 3.4 34.1 - - + -
240A VAL* 4.5 17.5 - - + -
255A ILE* 4.4 5.8 - - + -
267A PHE* 4.0 29.8 - - + -
280A VAL* 5.5 1.1 - - + -
281A ALA 3.7 5.4 - - - +
282A ALA* 5.0 0.7 - - + +
292A ASP* 1.3 72.4 - - - +
294A PHE* 1.3 65.2 + - - +
295A ILE* 3.6 30.4 - - + +
316A SER 3.7 2.8 - - - +
318A SER* 3.2 33.7 + - - +
326A PHE* 4.3 5.6 - - + -
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Residues in contact with PHE 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A SER 3.9 0.3 - - - +
280A VAL* 3.1 9.7 - - - +
281A ALA* 3.0 37.0 + - + +
283A THR* 3.6 31.6 - - + -
285A ILE* 3.9 30.1 - - + -
292A ASP* 3.5 15.9 - - + -
293A VAL* 1.3 72.6 - - - +
295A ILE* 1.3 61.8 + - - +
315A VAL* 4.6 6.7 - - + -
316A SER 3.7 3.8 - - - +
317A VAL* 3.8 35.0 - - + -
344A ILE* 4.0 23.5 - - + +
358A ILE* 3.7 25.1 - - + -
360A ILE* 5.8 1.1 - - + -
383A LEU* 4.1 17.9 - - + -
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Residues in contact with ILE 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A VAL* 3.6 25.8 - - + -
267A PHE* 3.6 28.7 - - + -
276A PHE* 3.5 40.0 - - + -
277A GLY* 3.6 22.9 - - - +
279A SER 3.7 2.2 - - - -
280A VAL* 4.2 4.3 - - + -
293A VAL* 3.6 17.9 - - + -
294A PHE* 1.3 75.7 - - - +
296A GLY* 1.3 61.4 + - - +
314A GLN 3.8 0.9 - - - +
315A VAL* 3.2 7.7 - - - +
316A SER* 3.0 43.5 + - - +
318A SER* 5.3 1.3 - - - +
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Residues in contact with GLY 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A TYR 3.2 3.3 - - - +
277A GLY 3.0 23.4 + - - -
278A PHE 3.3 7.1 + - - -
279A SER* 2.8 20.3 + - - -
295A ILE* 1.3 71.1 - - - +
297A ALA* 1.3 59.5 + - - -
298A PRO* 3.7 5.2 - - - -
314A GLN 3.7 3.4 - - - -
315A VAL* 4.0 4.5 - - - -
341A GLY 3.7 17.0 - - - -
344A ILE* 3.7 8.1 - - - +
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A ALA* 3.3 14.4 - - + +
275A TYR 3.4 4.0 - - - -
276A PHE* 3.7 26.9 - - + +
295A ILE 5.3 0.4 - - - +
296A GLY* 1.3 71.7 - - - -
298A PRO* 1.3 60.2 - - - +
299A LEU 3.1 4.7 - - - -
300A PHE* 2.9 29.3 + - + -
314A GLN* 2.6 34.1 + - + +
315A VAL* 4.9 0.4 - - - +
340A PHE 4.4 0.2 - - - -
341A GLY* 4.5 0.6 + - - -
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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