Contacts of the strand formed by residues 302 - 314 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227C GLU* 3.7 10.5 - - - +
269C VAL* 3.9 22.7 - - + -
300C ARG* 2.9 43.2 + - - +
301C ASN* 1.3 74.9 - - - +
303C TYR* 1.3 78.6 + - - +
348C VAL* 3.0 22.9 + - - +
319E HIS* 3.0 23.9 + - - -
320E LYS* 2.9 35.7 + - - +
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Residues in contact with TYR 303 (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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227C GLU* 3.1 28.3 + - + +
269C VAL* 4.0 2.4 - - - +
302C ASP* 1.3 89.6 + - - +
304C VAL* 1.3 66.1 + - - +
305C HIS* 3.8 22.0 - + + -
345C TYR* 3.7 24.7 - + + -
346C LEU 3.3 5.2 - - - +
347C THR* 3.8 28.9 - - + -
105E HIS* 2.6 46.8 + + + +
106E ASN* 2.6 19.3 + - - -
319E HIS* 3.5 11.6 + - - +
320E LYS* 4.0 31.3 + - + +
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Residues in contact with VAL 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C ALA* 3.9 25.8 - - + -
226C ILE 3.5 8.1 - - - +
269C VAL* 3.9 31.0 - - + -
298C ILE* 5.2 0.2 - - + -
303C TYR* 1.3 77.3 - - - +
305C HIS* 1.3 62.8 + - - +
306C ALA 4.0 8.7 - - - +
307C LEU* 5.1 1.3 - - + -
342C LEU* 4.1 15.3 - - + +
345C TYR* 3.2 3.7 - - - -
346C LEU* 2.8 55.3 + - + +
348C VAL* 4.1 13.5 - - + -
354C ILE* 4.7 6.7 - - + -
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Residues in contact with HIS 305 (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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226C ILE 2.9 4.9 + - - -
227C GLU* 3.8 9.8 - - + -
228C ASP* 3.2 34.8 + - + +
229C ARG* 3.1 40.6 - - + +
232C LYS* 4.2 22.2 + - + +
303C TYR* 3.8 26.4 + + + -
304C VAL* 1.3 75.5 - - - +
306C ALA* 1.3 61.3 - - + +
341C TYR* 3.9 3.8 - - + -
342C LEU* 2.9 34.0 + - - +
345C TYR* 3.6 32.9 - + + +
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Residues in contact with ALA 306 (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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225C ALA* 3.4 4.7 - - - +
226C ILE* 2.8 38.3 + - + +
304C VAL* 3.7 3.6 - - - +
305C HIS* 1.3 81.2 - - + +
307C LEU* 1.3 65.8 + - - +
339C VAL* 3.7 25.1 - - + -
340C PHE 3.1 17.5 - - - +
341C TYR* 3.8 10.5 - - + -
342C LEU* 4.1 5.2 - - - -
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Residues in contact with LEU 307 (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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223C VAL* 4.6 15.7 - - + -
224C VAL 3.4 7.6 - - - +
225C ALA* 3.9 23.6 - - + -
294C PHE* 4.2 17.5 - - + -
296C LEU* 4.2 11.4 - - + -
304C VAL* 5.1 4.0 - - + -
306C ALA* 1.3 76.8 - - - +
308C VAL* 1.3 59.7 + - - +
339C VAL* 3.5 2.3 - - - -
340C PHE* 2.7 47.0 + - + +
342C LEU* 4.7 9.0 - - + -
354C ILE* 5.2 2.0 - - + -
358C ILE* 6.3 1.1 - - + -
374C VAL* 3.8 33.2 - - + -
376C LEU* 4.3 20.4 - - + -
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Residues in contact with VAL 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C VAL* 3.4 3.0 - - - -
224C VAL* 2.9 37.3 + - + +
226C ILE* 3.6 44.2 - - + -
263C VAL* 4.1 8.3 - - + -
307C LEU* 1.3 80.0 - - - +
309C THR* 1.3 67.7 + - - +
310C TYR* 4.4 2.5 + - + -
328C PRO* 4.8 9.4 - - + -
337C GLN* 3.7 33.4 - - + -
338C THR 3.2 6.7 - - - +
339C VAL* 4.0 13.5 - - + -
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Residues in contact with THR 309 (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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190C CYS* 3.4 19.1 - - - +
221C LEU* 4.2 10.5 - - + -
222C TYR 3.1 17.0 - - - +
223C VAL* 3.7 20.2 - - + -
275C ILE* 4.7 9.4 - - + -
308C VAL* 1.3 75.6 - - - +
310C TYR* 1.3 60.3 + - - +
337C GLN* 3.9 4.2 - - - +
338C THR* 2.9 49.0 + - - -
340C PHE* 3.8 19.0 - - + -
358C ILE* 4.9 5.2 - - + -
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Residues in contact with TYR 310 (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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190C CYS* 6.4 0.2 - - - +
221C LEU* 3.4 7.3 - - - +
222C TYR* 3.0 61.3 + + + -
224C VAL* 4.3 21.5 - - + -
272C ALA* 3.4 20.5 - - + +
308C VAL* 5.1 4.7 - - + -
309C THR* 1.3 77.5 - - - +
311C PHE* 1.3 66.8 + - - +
312C ASN* 3.7 18.2 - - - -
325C SER* 4.2 0.2 - - - -
326C THR* 3.5 24.5 - - - +
327C ALA* 3.5 28.7 - - + -
328C PRO* 3.9 19.3 - - + -
329C ASP* 5.6 1.3 - - - -
336C LYS 5.4 0.9 - - - -
337C GLN* 4.4 2.9 - - + -
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Residues in contact with PHE 311 (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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187C MET* 4.2 8.1 - - + -
188C GLY 3.5 8.3 - - - -
190C CYS* 4.3 6.3 - - - -
191C LEU* 3.5 48.9 - - + -
220C ALA 3.1 18.6 - - - +
221C LEU* 4.1 9.0 - - + -
222C TYR* 4.9 0.2 - - - -
310C TYR* 1.3 77.5 - - - +
312C ASN* 1.3 63.4 + - - +
313C ILE* 3.8 29.2 - - + -
324C PHE* 4.6 3.1 - + - -
326C THR* 2.8 52.6 + - + +
335C TRP* 3.6 42.8 - + + -
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Residues in contact with ASN 312 (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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218C ARG* 6.1 4.0 - - - +
219C ALA* 3.4 4.5 - - - +
220C ALA* 3.0 33.9 + - + +
222C TYR* 3.2 29.6 + - + -
310C TYR* 3.7 10.2 - - - -
311C PHE* 1.3 79.0 + - - +
313C ILE* 1.3 67.7 + - - +
324C PHE 3.4 7.9 - - - +
325C SER* 2.7 36.8 + - - -
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Residues in contact with ILE 313 (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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186C TRP* 4.9 0.7 - - + -
187C MET* 3.9 28.9 - - + -
216C PRO* 3.5 31.4 - - + -
218C ARG* 3.6 3.4 - - - +
219C ALA* 3.6 21.5 - - + -
311C PHE* 3.8 22.2 - - + -
312C ASN* 1.3 83.2 - - - +
314C GLU* 1.3 66.0 + - - +
315C PHE* 4.1 12.8 - - + -
321C LYS* 4.8 2.3 + - - -
323C GLY* 3.0 22.9 - - - -
324C PHE* 2.9 38.0 + - + +
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Residues in contact with GLU 314 (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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216C PRO* 3.2 10.1 - - - +
217C ASP* 3.3 1.4 + - - +
218C ARG* 2.8 75.4 + - + +
313C ILE* 1.3 76.9 - - - +
315C PHE* 1.3 69.0 + - - +
316C THR* 3.7 22.4 - - + +
321C LYS* 4.0 28.7 + - + +
322C MET 3.5 12.8 - - - +
323C GLY* 4.2 0.2 - - - -
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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