Contacts of the helix formed by residues 287 - 298 (chain C) in PDB entry 5YGP
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 THR 287 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282C GLU 4.3 2.5 - - - +
283C ASN* 3.9 18.8 - - - +
284C TYR* 2.8 26.0 + - - +
285C LEU 2.8 6.1 + - - -
286C LEU* 1.3 76.9 - - - +
288C ASP* 1.3 60.8 + - - +
289C GLU* 3.3 24.5 - - - +
290C GLY 2.6 27.7 + - - -
291C LEU* 3.0 31.0 + - - +
305C LEU* 3.4 7.7 - - - +
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Residues in contact with ASP 288 (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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287C THR* 1.3 74.7 - - - +
289C GLU* 1.3 65.9 + - - +
292C GLU* 3.3 25.6 + - - +
305C LEU* 3.4 2.5 - - - +
307C SER* 2.7 33.5 + - - -
308C TYR* 3.2 34.3 + - + +
311C GLU* 6.2 1.3 - - - -
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Residues in contact with GLU 289 (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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27C LYS* 6.5 2.2 - - + -
283C ASN 5.4 0.7 - - - +
284C TYR 5.1 1.1 - - - +
287C THR* 3.3 26.3 - - + +
288C ASP* 1.3 84.5 + - - +
290C GLY* 1.3 59.7 + - - +
292C GLU* 4.1 8.1 - - - +
293C ALA* 3.6 18.5 + - - +
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Residues in contact with GLY 290 (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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24C VAL* 3.5 24.6 - - - +
284C TYR 3.4 13.2 - - - -
285C LEU* 3.6 6.3 - - - -
287C THR* 2.6 23.5 + - - -
289C GLU* 1.3 72.8 - - - +
291C LEU* 1.3 62.9 + - - +
292C GLU 3.2 1.1 - - - -
293C ALA 3.3 9.2 + - - -
294C VAL* 3.5 11.1 + - - +
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Residues in contact with LEU 291 (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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109C ILE* 4.3 23.1 - - + +
285C LEU* 3.3 31.6 + - + +
286C LEU* 4.4 11.0 - - + -
287C THR 3.0 15.7 + - - +
290C GLY* 1.3 75.1 - - - +
292C GLU* 1.3 58.2 + - - +
294C VAL* 3.4 3.5 + - - +
295C ASN* 2.9 29.5 + - - +
300C LEU* 4.1 12.5 - - + +
303C VAL* 3.8 23.3 - - + -
305C LEU* 3.6 32.1 - - + +
308C TYR* 3.5 20.4 - - + -
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Residues in contact with GLU 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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288C ASP 3.3 20.4 + - - +
289C GLU* 4.2 7.3 - - - +
290C GLY 3.2 0.8 - - - -
291C LEU* 1.3 76.4 - - - +
293C ALA* 1.3 59.4 + - - +
295C ASN* 4.0 1.1 - - - +
296C LYS* 2.9 32.7 + - + +
308C TYR* 3.3 29.6 + - + +
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Residues in contact with ALA 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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20C GLY* 3.3 30.1 - - - +
23C GLU* 4.0 22.4 - - + +
24C VAL* 3.8 9.6 - - + -
289C GLU 3.6 11.1 + - - +
290C GLY 3.3 11.0 + - - +
292C GLU* 1.3 81.7 - - - +
294C VAL* 1.3 60.0 + - - +
296C LYS* 3.9 5.6 + - - +
297C ASP* 3.8 9.0 + - - +
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Residues in contact with VAL 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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16C LYS* 6.0 0.2 - - + -
17C GLY* 3.4 24.2 - - - +
20C GLY* 3.9 7.0 - - - +
21C LEU* 3.7 39.0 - - + +
24C VAL* 4.4 0.9 - - + -
285C LEU* 4.1 9.0 - - + -
290C GLY 3.5 13.0 + - - +
291C LEU 3.4 5.7 + - - +
293C ALA* 1.3 74.7 - - - +
295C ASN* 1.3 63.9 + - - +
296C LYS 3.2 0.4 - - - -
297C ASP* 3.1 4.2 + - - +
298C LYS 2.9 25.1 + - - +
300C LEU* 4.0 29.6 - - + -
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Residues in contact with ASN 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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291C LEU 2.9 19.1 + - - +
292C GLU 4.0 1.3 - - - +
294C VAL* 1.3 76.4 - - - +
296C LYS* 1.3 62.6 + - - +
298C LYS 3.6 6.1 - - - -
299C PRO* 3.4 28.4 - - - +
300C LEU* 3.0 32.2 + - + +
301C GLY 4.4 3.5 + - - +
303C VAL* 5.1 0.9 - - - +
308C TYR* 3.9 20.9 + - + +
312C LEU* 4.3 25.1 - - - +
317C ARG* 6.2 0.2 - - - +
318C ILE* 6.3 0.4 - - - +
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Residues in contact with LYS 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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23C GLU* 5.9 3.4 - - - +
234C SER* 4.4 3.3 + - - -
292C GLU* 2.9 21.7 + - + +
293C ALA* 4.2 6.5 - - - +
294C VAL 3.2 0.2 - - - -
295C ASN* 1.3 77.0 - - - +
297C ASP* 1.3 66.5 + - - +
299C PRO* 5.7 0.2 - - - +
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Residues in contact with ASP 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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16C LYS 4.7 0.2 - - - +
17C GLY* 3.2 15.2 - - - -
18C TYR* 3.6 1.0 + - - -
19C ASN* 3.1 38.0 + - - +
20C GLY* 3.1 17.6 + - - +
234C SER* 2.7 28.8 + - - -
293C ALA 3.8 3.2 + - - +
294C VAL 3.1 9.3 + - - +
295C ASN 4.2 0.2 - - - -
296C LYS* 1.3 79.6 - - - +
298C LYS* 1.3 67.7 + - - +
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Residues in contact with LYS 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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14C GLY 4.5 7.0 - - - -
15C ASP* 3.3 27.6 - - - +
16C LYS* 3.5 17.3 - - - +
17C GLY* 3.8 11.0 + - - +
18C TYR* 5.4 4.0 - - - -
231C TRP* 3.9 22.1 + - + +
234C SER* 4.0 6.2 + - - -
235C ASN* 3.6 31.3 + - - +
294C VAL* 2.9 16.6 + - - +
295C ASN* 3.5 4.6 - - - -
297C ASP* 1.3 94.8 + - - +
299C PRO* 1.3 71.3 - - - +
300C LEU* 3.5 6.4 + - - +
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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