Contacts of the strand formed by residues 285 - 291 (chain D) in PDB entry 1SHZ
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 SER 285 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241D THR* 3.0 10.5 + - - +
242D ALA* 2.9 20.7 - - - +
243D ILE 2.7 32.2 + - - -
284D THR* 1.3 69.3 - - - +
286D ILE* 1.3 54.8 + - - +
287D ILE* 3.5 9.6 - - - +
339D LYS* 4.9 0.2 - - - +
342D TYR* 4.3 16.6 - - - -
364D VAL* 4.4 2.1 - - - +
365D ILE* 4.1 15.0 - - - +
368D ASN* 3.7 26.1 - - - +
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Residues in contact with ILE 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D ILE* 3.7 18.4 - - + +
245D PHE* 5.8 1.3 - - + -
272D PHE* 4.5 25.1 - - + -
275D ILE* 5.0 4.9 - - + +
276D CYS* 3.7 27.1 - - - +
281D PHE* 4.3 17.5 - - + -
284D THR* 3.1 11.2 + - - +
285D SER* 1.3 72.5 - - - +
287D ILE* 1.3 65.4 + - - +
288D LEU 4.1 0.8 + - - +
339D LYS* 3.3 34.9 - - + +
340D GLU 3.9 8.2 + - - +
341D ILE* 3.8 11.9 - - + -
342D TYR* 3.2 27.7 + - - -
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Residues in contact with ILE 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D ALA* 4.0 11.9 - - + -
243D ILE 2.7 18.3 + - - +
244D ILE* 3.3 6.3 - - + -
245D PHE* 2.7 33.5 + - - +
285D SER* 3.5 28.5 - - - +
286D ILE* 1.3 78.3 - - - +
288D LEU* 1.3 53.7 + - - +
289D PHE* 3.3 31.8 + - + -
342D TYR* 2.9 37.0 - - + +
344D HIS* 4.4 2.7 - - + -
361D VAL* 3.5 35.4 - - + -
364D VAL* 5.0 1.1 - - + -
365D ILE* 4.3 1.3 - - + -
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Residues in contact with LEU 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D PHE* 3.4 27.8 - - + +
247D VAL* 3.6 24.7 - - + -
272D PHE* 4.2 23.3 - - + -
286D ILE 4.1 1.2 + - - -
287D ILE* 1.3 71.7 - - - +
289D PHE* 1.3 62.9 + - - +
290D LEU* 4.0 15.5 - - + -
326D GLN* 5.4 0.9 - - - +
329D PHE* 3.8 32.5 - - + -
330D GLU* 5.2 2.2 - - + -
341D ILE* 4.4 13.9 - - + -
342D TYR 3.1 7.7 + - - +
343D THR* 3.5 18.7 - - + +
344D HIS 3.1 24.8 + - - +
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Residues in contact with PHE 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D PHE* 4.1 28.0 - + + -
244D ILE* 3.6 29.8 - - + -
245D PHE 2.8 15.4 + - - +
246D CYS* 3.6 15.9 - - - -
247D VAL* 3.0 31.2 + - - +
287D ILE* 3.3 24.9 + - + -
288D LEU* 1.3 79.7 - - - +
290D LEU* 1.3 62.5 + - - +
291D ASN* 4.7 1.3 - - + +
344D HIS* 3.5 9.0 - - + -
346D THR* 3.5 27.1 - - + +
357D VAL* 3.2 34.1 - - + -
358D PHE* 5.6 0.4 - + - -
361D VAL* 3.7 13.9 - - + -
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Residues in contact with LEU 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D VAL* 3.6 15.5 - - + -
249D LEU* 3.7 31.5 - - + +
288D LEU* 4.0 21.8 - - + -
289D PHE* 1.3 77.3 - - - +
291D ASN* 1.3 65.9 - - - +
322D ALA 4.7 0.2 - - - +
325D ILE* 5.0 6.5 - - + -
326D GLN* 4.1 22.9 - - + +
329D PHE* 5.2 4.7 - - + -
343D THR* 4.2 11.7 - - + -
344D HIS 2.8 16.2 + - - +
345D PHE* 3.5 38.7 - - + -
346D THR 3.2 19.1 + - - +
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Residues in contact with ASN 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D SER 2.9 22.3 + - - +
60D GLY* 3.6 6.9 - - - -
246D CYS* 5.2 6.3 - - + -
247D VAL 2.7 21.5 + - - +
249D LEU* 2.9 24.8 + - - +
289D PHE* 3.4 3.4 + - + +
290D LEU* 1.3 76.5 - - - +
292D LYS* 1.3 70.8 + - + +
293D LYS 3.4 0.2 - - - -
346D THR* 2.9 20.9 + - - +
347D CYS 3.5 0.7 + - - -
348D ALA* 2.9 27.0 + - - +
476D GDP 2.7 34.3 + - - +
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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