Contacts of the strand formed by residues 302 - 314 (chain J) in PDB entry 5DST
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 302 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319H HIS* 3.1 22.2 + - - -
320H LYS* 2.9 30.8 + - - +
227J GLU* 3.7 10.2 - - - +
269J VAL* 3.6 23.3 - - + +
300J ARG* 2.8 45.3 + - - +
301J ASN* 1.3 75.6 - - - +
303J TYR* 1.3 80.3 + - - +
347J THR 4.1 0.3 - - - -
348J VAL* 3.0 21.0 + - - +
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Residues in contact with TYR 303 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105H HIS* 2.7 46.1 + + + +
106H ASN* 3.3 13.3 + - - -
319H HIS* 3.7 10.7 - - - +
320H LYS* 4.1 35.2 + - + +
227J GLU* 3.0 31.3 + - + +
269J VAL* 4.2 0.3 - - - +
302J ASP* 1.3 85.8 + - - +
304J VAL* 1.3 65.8 + - - +
305J HIS* 3.9 20.4 - + + +
345J TYR* 3.7 26.0 - + + -
346J LEU 3.3 4.9 - - - +
347J THR* 3.6 29.6 - - + -
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Residues in contact with VAL 304 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225J ALA* 3.9 26.2 - - + -
226J ILE 3.3 11.0 - - - +
269J VAL* 3.9 26.2 - - + -
303J TYR* 1.3 77.4 - - - +
305J HIS* 1.3 63.1 + - - +
306J ALA 3.9 9.6 - - - +
307J LEU* 5.1 1.3 - - + -
342J LEU* 4.1 15.7 - - + +
345J TYR* 3.1 5.2 - - - -
346J LEU* 2.7 55.0 + - + +
348J VAL* 4.1 14.4 - - + -
354J ILE* 4.6 6.7 - - + -
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Residues in contact with HIS 305 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226J ILE 2.9 5.3 + - - -
227J GLU* 3.7 10.0 - - + -
228J ASP* 3.2 34.0 + - + +
229J ARG* 3.1 41.4 - - + +
232J LYS* 4.2 22.9 - - + +
303J TYR* 3.9 25.8 + + + -
304J VAL* 1.3 72.3 - - - +
306J ALA* 1.3 61.7 + - + +
341J TYR* 3.9 5.1 - - + -
342J LEU* 3.0 31.1 + - - +
345J TYR* 3.6 33.3 - + + +
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Residues in contact with ALA 306 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225J ALA* 3.4 5.0 - - - +
226J ILE* 2.9 38.4 + - + +
304J VAL* 3.7 4.0 - - - +
305J HIS* 1.3 82.2 - - + +
307J LEU* 1.3 67.5 + - - +
339J VAL* 3.7 26.7 - - + -
340J PHE 3.4 16.2 - - - +
341J TYR* 3.9 10.3 - - + -
342J LEU* 4.1 4.3 - - - -
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Residues in contact with LEU 307 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223J VAL* 4.6 15.5 - - + -
224J VAL 3.3 7.6 - - - +
225J ALA* 4.0 18.8 - - + -
294J PHE* 4.1 18.2 - - + -
296J LEU* 4.2 11.0 - - + -
304J VAL* 5.1 4.0 - - + -
306J ALA* 1.3 81.4 - - - +
308J VAL* 1.3 64.2 - - - +
339J VAL* 3.5 0.2 - - - -
340J PHE* 2.8 45.4 + - + +
342J LEU* 4.6 9.4 - - + -
354J ILE* 5.1 2.2 - - + -
358J ILE* 6.4 1.3 - - + -
374J VAL* 3.8 32.3 - - + -
376J LEU* 4.3 19.7 - - + -
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Residues in contact with VAL 308 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222J TYR 4.5 0.2 - - - -
223J VAL* 3.3 3.5 - - - -
224J VAL* 2.9 42.8 + - + +
226J ILE* 3.6 40.4 - - + -
263J VAL* 4.1 7.9 - - + -
307J LEU* 1.3 79.3 - - - +
309J THR* 1.3 67.3 + - - +
310J TYR* 4.4 2.4 + - + -
328J PRO* 4.8 8.5 - - + -
337J GLN* 3.6 34.8 - - + -
338J THR 3.2 6.1 - - - +
339J VAL* 4.0 13.7 - - + -
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Residues in contact with THR 309 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190J CYS* 3.4 25.6 - - - +
221J LEU* 4.1 10.8 - - + -
222J TYR 3.0 16.8 - - - +
223J VAL* 3.6 21.1 - - + -
275J ILE* 4.6 9.2 - - + -
308J VAL* 1.3 75.2 - - - +
310J TYR* 1.3 60.7 + - - +
337J GLN* 4.0 4.0 - - - -
338J THR* 3.0 38.2 + - - -
340J PHE* 3.8 20.6 - - + -
358J ILE* 4.9 4.9 - - + -
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Residues in contact with TYR 310 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190J CYS* 6.4 0.2 - - - +
221J LEU* 3.4 7.4 - - - +
222J TYR* 2.9 61.9 + + + +
224J VAL* 4.3 22.0 - - + -
272J ALA* 3.2 22.9 - - - +
308J VAL* 5.0 4.9 - - + -
309J THR* 1.3 77.0 - - - +
311J PHE* 1.3 65.8 + - - +
312J ASN* 3.8 18.6 - - - -
325J SER* 4.4 0.2 - - - -
326J THR* 3.5 15.5 - - - +
327J ALA* 3.5 37.9 - - + -
328J PRO* 3.9 19.5 - - + -
329J ASP* 5.7 1.3 - - - -
336J LYS 5.4 0.7 - - - -
337J GLN* 4.4 2.9 - - + -
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Residues in contact with PHE 311 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187J MET* 4.2 8.5 - - + -
188J GLY 3.8 5.2 - - - -
190J CYS* 4.4 5.6 - - - -
191J LEU* 3.5 48.5 - - + -
220J ALA 3.0 17.0 - - - +
221J LEU* 4.0 9.0 - - + -
310J TYR* 1.3 78.3 - - - +
312J ASN* 1.3 64.6 + - - +
313J ILE* 3.7 29.2 - - + -
324J PHE* 4.5 2.6 - + - +
326J THR* 2.9 52.5 + - + +
335J TRP* 3.6 44.0 - + + -
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Residues in contact with ASN 312 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218J ARG* 5.8 4.2 + - - +
219J ALA* 3.3 5.9 - - - +
220J ALA* 2.8 35.2 + - + +
222J TYR* 3.2 28.8 + - + -
310J TYR* 3.8 11.8 - - - -
311J PHE* 1.3 77.8 + - - +
313J ILE* 1.3 68.0 + - - +
324J PHE 3.5 7.6 - - - +
325J SER* 2.8 35.6 + - - -
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Residues in contact with ILE 313 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186J TRP* 4.9 1.1 - - + -
187J MET* 3.8 30.3 - - + -
191J LEU* 4.3 0.2 - - + -
216J PRO* 3.5 31.4 - - + -
218J ARG* 3.6 3.8 - - - +
219J ALA* 3.7 20.6 - - + -
280J ILE* 6.2 0.2 - - + -
311J PHE* 3.7 22.7 - - + -
312J ASN* 1.3 82.5 - - - +
314J GLU* 1.3 63.6 + - - +
315J PHE* 4.1 12.3 - - + -
321J LYS* 4.7 2.6 + - - -
323J GLY* 3.0 22.2 - - - -
324J PHE* 3.0 37.6 + - + +
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Residues in contact with GLU 314 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216J PRO* 3.3 3.3 - - - +
217J ASP* 3.3 6.8 + - - +
218J ARG* 2.9 68.2 + - + +
313J ILE* 1.3 75.5 - - - +
315J PHE* 1.3 73.6 - - - +
316J THR* 3.8 16.5 - - + +
321J LYS* 3.9 31.3 + - - +
322J MET 3.5 13.5 - - - +
323J GLY* 4.1 0.4 - - - -
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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