Contacts of the helix formed by residues 291 - 302 (chain C) in PDB entry 5UH8
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 291 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278C TYR* 3.5 18.0 - - - -
286C PRO 3.7 4.9 + - - -
288C THR* 2.9 37.3 + - - -
290C GLU* 1.3 77.5 - - - +
292C ALA* 1.3 61.0 + - - +
293C GLN 3.5 0.4 - - - -
294C THR* 4.0 6.3 - - - -
295C LEU* 3.4 29.5 + - - +
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Residues in contact with ALA 292 (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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274C LEU* 3.5 40.9 - - + +
275C LEU* 4.3 4.9 - - + +
278C TYR* 3.8 21.5 - - + -
287C PRO 6.0 0.2 - - - -
288C THR 3.2 13.5 + - - +
289C LYS* 4.9 2.9 - - - +
291C SER* 1.3 77.5 - - - +
293C GLN* 1.3 63.0 + - - +
294C THR 3.3 0.4 - - - -
295C LEU* 4.5 2.2 - - - -
296C LEU* 3.2 29.2 + - - +
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Residues in contact with GLN 293 (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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240C ALA 5.2 3.7 + - - +
241C LEU 5.8 2.0 + - - -
270C THR* 5.6 1.9 - - - +
274C LEU* 3.3 28.1 - - + +
289C LYS 3.6 18.9 + - - +
290C GLU* 4.1 13.4 - - - +
291C SER 3.5 0.2 - - - -
292C ALA* 1.3 80.3 - - - +
294C THR* 1.3 61.2 + - - +
296C LEU* 4.1 2.1 + - - +
297C GLU* 3.2 43.1 + - - +
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Residues in contact with THR 294 (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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290C GLU* 2.5 27.0 + - - -
291C SER* 4.3 6.5 - - - -
292C ALA 3.3 0.4 - - - -
293C GLN* 1.3 78.0 - - - +
295C LEU* 1.3 64.5 + - - +
297C GLU* 3.2 14.3 + - - +
298C ASN* 3.1 36.6 + - - +
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Residues in contact with LEU 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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278C TYR* 3.5 28.7 - - + -
281C LEU* 3.7 27.4 - - + -
282C ARG* 4.4 22.0 - - + +
285C GLU* 5.7 0.2 - - - +
291C SER 3.4 20.5 + - - +
292C ALA 4.4 2.0 - - - +
294C THR* 1.3 75.6 - - + +
296C LEU* 1.3 83.8 + - + +
297C GLU 3.1 1.3 - - - -
298C ASN* 4.1 11.0 - - + +
299C LEU* 2.8 42.6 + - + +
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Residues in contact with LEU 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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237C LEU* 4.6 9.9 - - + -
240C ALA* 4.2 7.9 - - + +
241C LEU* 5.8 5.2 - - + -
274C LEU* 3.6 28.5 - - + +
277C ILE* 3.9 42.8 - - + -
278C TYR 5.2 0.9 - - - +
281C LEU* 5.3 0.9 - - + -
292C ALA* 3.2 23.7 + - + +
293C GLN 4.3 4.9 - - - +
294C THR 3.3 0.4 - - - -
295C LEU* 1.3 98.4 - - + +
297C GLU* 1.3 60.3 + - + +
299C LEU* 4.2 5.2 + - - -
300C PHE* 4.3 10.0 + - + -
301C PHE* 3.5 20.9 - - - -
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Residues in contact with GLU 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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293C GLN* 3.2 41.2 + - - +
294C THR* 3.3 11.1 - - - +
295C LEU 3.1 0.6 - - - -
296C LEU* 1.3 78.5 - - + +
298C ASN* 1.3 62.4 + - - +
301C PHE* 3.0 45.4 + - + +
302C LYS* 4.2 4.2 - - + +
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Residues in contact with ASN 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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294C THR* 3.1 34.0 + - - +
295C LEU* 3.1 10.5 + - + +
297C GLU* 1.3 82.2 - - - +
299C LEU* 1.3 63.8 + - + +
300C PHE 3.2 1.2 + - - -
302C LYS* 3.8 31.0 + - + +
305C ARG* 3.3 35.1 - - + +
306C TYR 4.4 0.7 + - - -
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Residues in contact with LEU 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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210C ALA* 3.7 22.8 + - + +
226C ILE* 5.0 4.5 - - + -
227C ASP* 6.6 0.2 - - + -
281C LEU* 3.7 37.5 - - + -
282C ARG* 4.9 5.6 - - - +
295C LEU* 2.8 29.6 + - + +
296C LEU* 4.2 1.3 + - - +
297C GLU 3.4 0.2 - - - -
298C ASN* 1.3 74.3 - - + +
300C PHE* 1.3 86.7 + - + +
305C ARG* 3.6 36.2 - - - +
306C TYR* 3.3 19.0 + - - +
11H G 4.6 8.3 - - - +
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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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210C ALA* 4.3 8.5 - - + -
211C TRP 3.3 28.9 - - - -
212C LEU* 3.6 35.7 - - + -
226C ILE* 3.6 29.4 - - + -
281C LEU* 6.2 0.4 - - + -
296C LEU* 4.3 11.8 + - + -
297C GLU 3.7 1.2 + - - -
298C ASN 3.2 0.6 + - - -
299C LEU* 1.3 109.9 - - + +
301C PHE* 1.3 80.4 + + + +
302C LYS 3.7 1.6 - - - -
306C TYR* 3.5 29.0 - + - -
333C LEU* 3.3 35.2 + - + +
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Residues in contact with PHE 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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241C LEU* 4.6 13.7 - - + -
296C LEU* 3.5 25.4 - - + -
297C GLU* 3.0 17.6 + - + +
300C PHE* 1.3 93.5 - + + +
302C LYS* 1.3 64.5 - - - +
303C GLU 4.4 0.2 + - - -
332C THR* 3.4 17.4 - - - +
333C LEU* 3.2 21.9 - - + +
334C THR* 3.4 32.3 - - - -
335C GLU* 3.5 17.5 - - + -
338C VAL* 4.3 17.0 - - + -
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Residues in contact with LYS 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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297C GLU* 3.7 8.0 + - + +
298C ASN* 3.8 33.5 + - + +
300C PHE 3.7 0.2 - - - -
301C PHE* 1.3 85.6 - - + +
303C GLU* 1.3 58.8 + - - +
304C LYS* 3.1 48.0 + - + +
305C ARG* 4.7 2.9 - - + +
306C TYR* 2.7 38.4 + - - +
332C THR* 3.7 4.0 - - - +
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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