Contacts of the strand formed by residues 284 - 290 (chain A) in PDB entry 5F85
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 284 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LYS* 3.9 4.2 - - - +
223A ARG* 3.1 44.6 + - + -
225A LEU* 3.9 28.3 - - + +
227A PHE* 3.5 58.1 - + + -
252A GLU* 4.2 14.6 - - + +
276A VAL* 6.1 0.7 - - + -
280A ASP 3.9 14.8 - - - -
281A HIS 3.1 15.2 + - - +
282A CYS 3.2 0.7 - - - +
283A LYS* 1.3 91.8 - - + +
285A LYS* 1.3 55.7 + - - +
286A TYR 3.6 0.4 + - - +
287A LEU* 3.9 4.9 - - + +
307A SER* 2.6 32.1 + - - -
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Residues in contact with LYS 285 (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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219A TRP* 3.0 55.5 + - + +
220A SER* 4.6 6.3 - - - +
222A LYS* 3.3 31.8 - - + +
223A ARG 2.8 19.3 + - - +
224A SER* 3.2 30.5 - - - +
284A TYR* 1.3 73.7 - - - +
286A TYR* 1.3 82.7 + - + +
307A SER* 3.8 2.9 - - - -
308A LEU* 2.6 37.9 + - - +
353A ASP* 3.2 13.1 + - - -
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Residues in contact with TYR 286 (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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219A TRP* 4.3 12.1 - + - -
224A SER* 3.8 19.8 + - - -
225A LEU* 3.5 25.6 + - - +
226A GLY* 3.3 2.2 - - - -
227A PHE* 2.8 31.9 + - - +
284A TYR 3.3 0.4 - - - -
285A LYS* 1.3 104.9 - - + +
287A LEU* 1.3 59.4 + - - +
288A PHE* 4.0 1.2 + - + -
308A LEU* 3.5 8.5 - - + -
310A PHE* 3.6 27.8 - + + -
346A LEU* 3.8 24.7 - - + -
349A PHE* 4.0 18.0 + - + -
350A LYS* 3.3 47.6 + - + +
353A ASP* 4.6 6.1 + - - -
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Residues in contact with LEU 287 (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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227A PHE* 3.8 21.3 - - + +
281A HIS* 3.4 31.0 - - + +
284A TYR* 3.9 17.7 - - + -
286A TYR* 1.3 72.7 - - - +
288A PHE* 1.3 62.8 + - - +
289A ASN 4.0 0.3 + - - -
302A LEU* 3.7 45.1 - - + +
305A CYS* 3.9 9.9 - - + -
307A SER* 3.6 31.0 - - - +
308A LEU 2.8 13.7 + - - +
309A VAL* 3.4 7.0 - - + +
310A PHE* 2.8 26.3 + - - -
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Residues in contact with PHE 288 (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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226A GLY* 3.8 22.0 - - - -
227A PHE 3.1 24.9 + - - +
228A PHE* 3.3 19.9 - - + -
240A LEU* 3.6 36.3 - - + -
286A TYR* 4.1 2.7 - - + -
287A LEU* 1.3 74.6 - - - +
289A ASN* 1.3 60.0 + - - +
290A PHE* 3.9 6.7 - + + -
298A ARG* 3.8 4.2 - - - -
302A LEU* 3.7 10.2 - - - +
310A PHE* 3.5 34.1 - + + -
312A VAL* 4.5 5.4 - - + -
333A LEU* 3.9 7.9 - - + -
342A TYR* 3.5 38.4 - + - -
345A ILE* 5.3 0.7 - - + -
346A LEU* 3.9 26.0 - - + -
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Residues in contact with ASN 289 (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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287A LEU 4.0 0.2 + - - -
288A PHE* 1.3 75.5 - - - +
290A PHE* 1.3 72.5 + - - +
296A SER* 4.1 10.1 + - - +
298A ARG* 3.5 14.9 - - - +
299A LEU* 3.2 46.7 + - + +
302A LEU* 3.7 13.2 - - + -
309A VAL* 4.8 0.4 - - + -
310A PHE 2.9 10.4 + - - +
311A HIS* 3.0 33.4 + - - +
312A VAL* 3.0 32.6 + - - +
321A TYR* 4.9 1.6 + - - -
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Residues in contact with PHE 290 (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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228A PHE* 3.6 31.1 - + - -
236A GLU* 3.4 28.0 - - + -
237A ARG* 3.2 37.7 + - + +
240A LEU* 3.7 34.3 - - + -
288A PHE* 3.9 8.5 - - + -
289A ASN* 1.3 83.6 + - - +
291A ARG* 1.3 73.0 + - - +
296A SER* 3.4 14.7 - - - -
298A ARG* 5.3 0.4 - - - +
312A VAL* 3.7 32.8 - - + -
342A TYR* 3.2 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