Contacts of the strand formed by residues 244 - 251 (chain C) in PDB entry 1FZA
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 244 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152C ASP* 3.0 34.0 + - - +
192C THR* 4.8 0.2 - - + -
236C ILE* 3.2 34.4 - - + +
237C SER* 4.1 9.4 - - - -
239C GLN* 3.1 13.5 + - + -
242C ILE* 3.5 39.8 + - + +
243C PRO* 1.3 74.6 - - - +
245C ALA* 1.3 58.8 + - - +
264C MET* 3.0 12.7 + - - +
265C PHE* 2.7 48.8 + - + +
386C ILE* 4.1 14.8 - - + -
387C ILE* 3.3 29.6 - - - -
388C PRO* 3.6 25.6 - - + +
389C PHE* 4.0 3.3 - - - +
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Residues in contact with ALA 245 (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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191C TRP* 6.0 0.4 - - + -
244C TYR* 1.3 76.5 - - - +
246C LEU* 1.3 62.9 + - - +
247C ARG 4.2 0.7 - - - +
261C ASP* 5.8 3.8 - - + -
262C TYR 3.6 10.8 - - - +
263C ALA* 4.5 3.4 - - - -
265C PHE* 3.8 3.6 - - - -
386C ILE* 3.1 29.5 - - - +
387C ILE* 2.8 24.6 + - + +
389C PHE* 3.9 26.9 - - + -
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Residues in contact with LEU 246 (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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194C PHE* 4.1 12.3 - - + -
245C ALA* 1.3 76.4 - - - +
247C ARG* 1.3 78.2 + - - +
248C VAL* 3.5 22.0 - - + -
260C ALA 3.3 1.7 - - - +
261C ASP* 3.1 7.4 - - - -
262C TYR* 3.0 44.6 + - + +
265C PHE* 3.2 38.8 - - + -
290C PHE* 4.1 13.7 - - + -
384C MET* 4.0 15.3 - - + -
385C LYS 3.4 19.5 - - - +
386C ILE* 4.2 1.1 - - + -
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Residues in contact with ARG 247 (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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191C TRP* 3.5 43.7 - - + -
245C ALA 4.2 0.2 - - - -
246C LEU* 1.3 90.0 - - - +
248C VAL* 1.3 60.9 + - - +
249C GLU* 3.9 14.1 + - + +
259C THR* 2.8 55.0 + - - +
261C ASP* 2.9 37.8 + - - +
283C GLY 4.0 2.0 + - - -
383C THR 3.8 0.6 - - - +
385C LYS* 3.1 38.1 + - - +
392C LEU* 4.7 15.6 - - - +
394C ILE 4.9 11.5 + - - -
395C GLY* 5.1 4.9 - - - -
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Residues in contact with VAL 248 (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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246C LEU* 3.5 30.7 - - + -
247C ARG* 1.3 83.4 - - - +
249C GLU* 1.3 60.9 + - - +
250C LEU* 3.7 14.6 + - + +
258C SER 3.4 14.0 - - - +
259C THR* 3.4 9.4 - - - -
260C ALA* 3.3 23.9 + - + +
262C TYR* 4.6 6.3 - - + -
286C ALA* 5.2 0.3 - - - +
290C PHE* 5.6 2.0 - - + -
344C LEU* 3.9 26.2 - - + -
369C TRP* 4.8 17.3 - - + -
383C THR 3.5 5.6 - - - +
384C MET* 4.7 6.1 - - + -
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Residues in contact with GLU 249 (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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183C GLU* 4.1 10.4 - - - +
247C ARG* 3.9 20.3 + - + +
248C VAL* 1.3 72.3 - - - +
250C LEU* 1.3 61.8 - - - +
257C THR* 6.2 2.2 - - - -
258C SER 4.1 3.6 - - - -
259C THR* 4.5 8.7 - - + -
382C THR* 3.4 2.8 - - - -
383C THR* 2.8 58.8 + - + +
385C LYS* 2.9 36.4 + - - -
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Residues in contact with LEU 250 (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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248C VAL* 4.6 10.1 - - + +
249C GLU* 1.3 77.6 - - - +
251C GLU* 1.3 61.5 + - - +
257C THR* 3.2 28.4 - - - +
258C SER* 3.5 19.2 + - - +
286C ALA* 4.9 1.6 - - + -
344C LEU* 3.6 15.3 - - + -
369C TRP* 3.4 47.6 - - + +
372C TRP* 4.3 9.4 - - + -
379C MET* 3.3 30.5 - - + -
381C LYS* 3.8 2.7 - - - +
382C THR* 3.1 26.5 - - - +
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Residues in contact with GLU 251 (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 LEU* 1.3 78.4 - - - +
252C ASP* 1.3 74.1 + - - +
255C GLY* 4.2 15.7 + - - -
256C ARG 3.7 5.6 - - - +
257C THR* 3.5 22.5 - - + +
372C TRP* 4.3 4.0 - - - -
379C MET* 3.7 2.8 - - - -
380C LYS* 2.6 49.7 + - - +
381C LYS* 3.3 53.7 + - + +
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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