Contacts of the helix formed by residues 294 - 305 (chain C) in PDB entry 1DS5
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 294 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130C ASP* 5.2 0.7 - - - -
134C ARG* 4.0 19.7 + - - -
292C LEU 3.6 3.7 + - - -
293C VAL* 1.3 79.1 - - - +
295C PRO* 1.3 81.5 - - - +
296C GLU* 2.5 13.0 + - - +
297C ALA* 2.8 32.0 + - - +
298C ILE* 2.9 12.4 + - - +
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Residues in contact with PRO 295 (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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294C SER* 1.3 85.9 - - - +
296C GLU* 1.3 74.7 + - - +
298C ILE* 3.5 9.5 + - + +
299C ASP* 3.2 19.1 + - - +
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Residues in contact with GLU 296 (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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134C ARG* 5.1 4.6 + - - +
294C SER* 2.5 11.6 + - - +
295C PRO* 1.3 88.4 - - - +
297C ALA* 1.3 69.4 + - - +
298C ILE 2.8 1.6 - - - -
299C ASP* 2.6 16.5 + - - +
300C PHE* 2.7 13.3 + - - +
321C HIS* 3.7 13.8 - - + -
322C PRO* 3.7 34.5 - - + +
323C TYR* 4.0 14.4 - - + -
325C GLN* 5.5 2.1 - - - +
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Residues in contact with ALA 297 (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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222C PHE* 3.5 16.8 - - + -
226C ILE* 4.6 7.9 - - + -
292C LEU 3.7 15.0 - - - +
293C VAL* 4.6 2.5 - - - -
294C SER* 2.8 28.0 + - - +
296C GLU* 1.3 72.3 - - - +
298C ILE* 1.3 59.0 + - + +
300C PHE* 3.4 0.6 + - - -
301C LEU* 2.8 30.5 + - - +
323C TYR* 3.4 29.1 - - + +
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Residues in contact with ILE 298 (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* 5.2 2.7 - - + -
227C PHE* 3.8 20.4 - - + -
281C TRP* 3.6 48.9 - - + -
282C LEU* 4.4 18.6 - - + -
293C VAL* 3.9 18.2 - - + -
294C SER 2.9 15.9 + - - +
295C PRO* 3.6 9.6 - - + +
296C GLU 2.7 2.0 + - - -
297C ALA* 1.3 75.2 - - - +
299C ASP* 1.3 65.9 + - - +
301C LEU* 4.4 4.3 - - + +
302C ASP* 2.8 26.7 + - + +
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Residues in contact with ASP 299 (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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295C PRO 3.2 12.7 + - - +
296C GLU* 2.6 12.2 + - - +
298C ILE* 1.3 76.2 - - - +
300C PHE* 1.3 62.3 + - - +
302C ASP* 3.0 7.0 + - - +
303C LYS* 2.6 65.5 + - - +
321C HIS* 2.7 27.1 + - + +
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Residues in contact with PHE 300 (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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137C ILE* 4.3 8.7 - - + -
141C LEU* 4.3 11.0 - - + -
218C LEU* 4.4 1.1 - - + -
222C PHE* 3.5 30.5 - + - -
296C GLU 2.7 14.0 + - - +
297C ALA 3.6 2.9 - - - +
299C ASP* 1.3 74.2 - - - +
301C LEU* 1.3 68.3 + - - +
303C LYS* 2.9 14.0 + - - +
304C LEU* 3.3 32.0 + - + +
313C LEU* 3.7 14.6 - - + -
318C ALA* 3.3 31.9 - - + -
321C HIS* 3.3 29.1 + + + +
323C TYR* 4.4 6.1 - + + -
324C PHE* 3.7 33.2 - + - -
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Residues in contact with LEU 301 (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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219C GLY* 3.7 13.0 - - - +
222C PHE* 3.8 15.3 - - + -
223C ALA* 3.5 37.5 - - + +
226C ILE* 4.3 2.9 - - + -
227C PHE* 3.6 31.4 - - + -
281C TRP* 3.7 21.8 - - + -
297C ALA 2.8 20.7 + - - +
298C ILE* 3.8 5.2 - - - +
300C PHE* 1.3 72.9 - - - +
302C ASP* 1.3 57.2 + - - +
304C LEU* 2.6 30.4 + - - +
305C LEU* 3.0 31.7 + - + -
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Residues in contact with ASP 302 (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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278C ARG* 3.4 18.9 + - - -
281C TRP* 2.7 40.0 + - + +
298C ILE* 2.8 23.5 + - + +
299C ASP* 3.3 7.1 - - - +
301C LEU* 1.3 74.5 - - - +
303C LYS* 1.3 65.6 + - - +
304C LEU 3.4 0.5 + - - -
305C LEU 3.7 10.7 + - - +
306C ARG* 3.2 36.4 + - - -
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Residues in contact with LYS 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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299C ASP* 2.6 51.6 + - - +
300C PHE 2.9 7.3 + - - +
301C LEU 2.8 0.2 + - - -
302C ASP* 1.3 82.6 + - - +
304C LEU* 1.3 57.6 + - - +
306C ARG* 3.9 21.8 - - - +
311C GLU 4.1 0.9 - - - +
312C ARG* 3.4 9.4 - - - -
313C LEU* 3.1 54.8 + - + +
321C HIS* 4.3 9.4 - - + -
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Residues in contact with LEU 304 (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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215C MET* 3.6 38.3 - - + +
216C TRP* 4.1 7.3 - - - -
218C LEU* 4.1 24.0 - - + -
219C GLY* 3.8 19.1 - - - -
222C PHE* 4.5 4.5 - - + -
300C PHE* 3.4 51.8 - - + +
301C LEU* 2.6 17.9 + - - +
303C LYS* 1.3 74.9 - - - +
305C LEU* 1.3 60.1 + - - +
306C ARG 3.1 7.0 + - - -
312C ARG* 3.3 21.9 - - - -
313C LEU* 4.8 8.1 - - + -
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Residues in contact with LEU 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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216C TRP* 3.3 44.2 - - + +
219C GLY* 4.1 7.0 - - - -
220C CYS 4.0 14.4 - - - +
223C ALA* 4.1 12.6 - - + -
232C PHE* 4.7 0.2 - - + -
233C PHE* 4.2 15.5 - - + -
249C LEU* 3.2 16.7 - - + +
281C TRP* 3.7 33.7 - - + -
301C LEU* 3.0 34.6 + - + +
302C ASP* 3.7 7.0 + - - +
303C LYS 3.6 0.2 - - - -
304C LEU* 1.3 78.6 - - - +
306C ARG* 1.3 60.1 + - - +
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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