Contacts of the strand formed by residues 302 - 314 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319F HIS* 3.1 22.5 + - - -
320F LYS* 3.3 30.2 + - - +
227H GLU* 3.7 12.1 - - - +
269H VAL* 3.9 22.0 - - + -
300H ARG* 2.9 43.4 + - + +
301H ASN* 1.3 75.6 - - - +
303H TYR* 1.3 81.6 + - - +
347H THR* 4.1 0.2 - - - -
348H VAL* 3.0 23.5 + - - +
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Residues in contact with TYR 303 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F HIS* 2.5 44.5 + + + +
106F ASN* 3.0 14.4 + - - -
319F HIS* 3.6 15.7 - - - +
320F LYS* 4.2 26.4 + - + +
227H GLU* 3.2 27.6 + - + +
269H VAL* 4.1 0.3 - - - +
302H ASP* 1.3 90.1 + - - +
304H VAL* 1.3 66.1 + - - +
305H HIS* 3.8 22.0 - + + -
345H TYR* 3.6 27.1 - + + -
346H LEU 3.2 6.7 - - - +
347H THR* 3.9 26.9 - - + -
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Residues in contact with VAL 304 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225H ALA* 3.9 27.6 - - + -
226H ILE 3.3 9.4 - - - +
269H VAL* 4.0 26.2 - - + -
298H ILE* 5.2 0.2 - - + -
303H TYR* 1.3 78.0 - - - +
305H HIS* 1.3 63.6 + - - +
306H ALA 4.0 9.9 - - - +
307H LEU* 5.1 1.6 - - + -
342H LEU* 4.1 16.2 - - + +
345H TYR* 3.3 4.8 - - - -
346H LEU* 2.9 51.1 + - + -
348H VAL* 4.2 12.6 - - + -
354H ILE* 4.6 6.5 - - + -
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Residues in contact with HIS 305 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226H ILE 2.9 5.1 + - - -
227H GLU* 3.9 8.1 - - + +
228H ASP* 3.3 33.8 + - + +
229H ARG* 3.1 42.4 - - + +
232H LYS* 4.1 25.5 - - + +
303H TYR* 3.8 26.2 + + + -
304H VAL* 1.3 75.3 - - - +
306H ALA* 1.3 61.2 + - + +
341H TYR* 4.0 4.1 - - + -
342H LEU* 3.0 33.0 + - - +
345H TYR* 3.7 31.6 - + + +
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Residues in contact with ALA 306 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225H ALA* 3.5 5.0 - - - +
226H ILE* 2.9 40.1 + - + +
228H ASP* 5.4 0.2 - - + -
304H VAL* 3.6 4.0 - - - +
305H HIS* 1.3 82.7 - - + +
307H LEU* 1.3 61.9 + - - +
339H VAL* 3.8 25.4 - - + -
340H PHE 3.2 18.2 - - - +
341H TYR* 3.9 11.2 - - + -
342H LEU* 4.2 3.8 - - - -
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Residues in contact with LEU 307 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223H VAL* 4.7 15.0 - - + -
224H VAL 3.4 4.0 - - - +
225H ALA* 3.9 23.3 - - + -
294H PHE* 4.0 18.8 - - + -
296H LEU* 4.1 14.4 - - + -
304H VAL* 5.1 4.3 - - + -
306H ALA* 1.3 75.1 - - - +
308H VAL* 1.3 62.1 + - - +
340H PHE* 2.6 52.7 + - + +
342H LEU* 4.7 7.6 - - + -
354H ILE* 5.1 2.5 - - + -
358H ILE* 6.4 1.3 - - + -
374H VAL* 3.8 32.8 - - + -
376H LEU* 4.3 18.8 - - + -
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Residues in contact with VAL 308 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223H VAL* 3.4 4.0 - - - -
224H VAL* 2.8 43.1 + - + +
226H ILE* 3.7 39.3 - - + -
263H VAL* 4.1 8.3 - - + -
307H LEU* 1.3 81.1 - - - +
309H THR* 1.3 67.3 + - - +
310H TYR* 4.2 3.5 + - + -
328H PRO* 4.8 8.3 - - + -
337H GLN* 3.6 30.7 - - + -
338H THR 3.2 10.8 - - - +
339H VAL* 4.1 13.9 - - + -
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Residues in contact with THR 309 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190H CYS* 3.1 30.6 - - - +
221H LEU* 4.1 7.4 - - + -
222H TYR 3.1 13.9 - - - +
223H VAL* 3.7 17.3 - - + -
275H ILE* 4.7 8.7 - - + -
308H VAL* 1.3 79.0 - - - +
310H TYR* 1.3 61.5 - - - +
337H GLN* 3.8 3.8 - - - +
338H THR* 2.9 41.0 + - - -
340H PHE* 3.7 20.6 - - + -
358H ILE* 4.9 4.9 - - + -
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Residues in contact with TYR 310 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190H CYS* 6.4 0.2 - - - +
221H LEU* 3.6 4.3 - - - +
222H TYR* 2.8 63.5 + + + +
224H VAL* 4.2 22.4 - - + -
272H ALA* 3.3 21.1 - - - +
308H VAL* 4.9 6.5 - - + -
309H THR* 1.3 74.8 - - - +
311H PHE* 1.3 66.5 + - - +
312H ASN* 3.8 19.5 - - - -
326H THR* 3.5 25.4 - - - +
327H ALA* 3.6 28.0 - - + -
328H PRO* 3.9 17.9 - - + -
329H ASP* 5.6 1.8 - - - -
336H LYS 5.3 0.4 - - - -
337H GLN* 4.4 2.7 - - + -
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Residues in contact with PHE 311 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187H MET* 4.2 7.6 - - + -
188H GLY 3.7 8.1 - - - -
190H CYS* 4.4 7.0 - - - -
191H LEU* 3.5 49.4 - - + -
220H ALA 3.1 19.5 - - - +
221H LEU* 4.0 8.5 - - + -
310H TYR* 1.3 79.0 - - - +
312H ASN* 1.3 62.7 + - - +
313H ILE* 3.8 26.5 - - + -
324H PHE* 4.4 2.6 - + - +
326H THR* 2.9 52.5 + - + +
335H TRP* 3.7 42.4 - + + -
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Residues in contact with ASN 312 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218H ARG* 5.8 3.9 + - - +
219H ALA* 3.4 4.5 - - - +
220H ALA* 2.9 34.9 + - + +
222H TYR* 3.3 28.0 + - + -
310H TYR* 3.8 11.1 - - - -
311H PHE* 1.3 78.7 + - - +
313H ILE* 1.3 68.3 + - - +
324H PHE 3.4 6.7 - - - +
325H SER* 2.6 37.7 + - - +
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Residues in contact with ILE 313 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186H TRP* 4.9 0.9 - - + -
187H MET* 3.9 29.2 - - + -
216H PRO* 3.5 32.5 - - + -
218H ARG 3.8 2.7 - - - +
219H ALA* 3.7 21.3 - - + -
311H PHE* 3.8 18.8 - - + -
312H ASN* 1.3 83.7 - - - +
314H GLU* 1.3 65.2 + - - +
315H PHE* 4.0 12.6 - - + -
321H LYS* 4.6 3.1 + - - -
323H GLY* 3.1 20.9 - - - -
324H PHE* 2.8 42.4 + - + +
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Residues in contact with GLU 314 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216H PRO* 3.3 2.8 - - - +
217H ASP* 3.2 8.1 + - - +
218H ARG* 2.8 73.9 + - + +
313H ILE* 1.3 77.5 - - - +
315H PHE* 1.3 69.7 + - - +
316H THR* 3.8 21.5 - - + +
321H LYS* 4.0 30.2 + - + +
322H MET 3.6 11.7 - - - +
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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