Contacts of the helix formed by residues 286 - 297 (chain C) in PDB entry 3EXG
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 286 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C ARG* 2.8 33.3 + - - -
260C TYR* 3.0 20.8 + - - +
282C ARG* 3.2 25.9 + - + +
285C SER* 1.3 73.9 - - - +
287C PRO* 1.3 72.4 - - - +
288C ILE* 3.0 29.6 + - - +
289C MET* 3.1 27.9 + - + +
290C LEU* 3.0 26.3 + - - +
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Residues in contact with PRO 287 (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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39C MET* 3.5 12.7 - - - +
43C ARG* 4.1 4.5 - - - +
67C GLY 3.8 17.5 - - - +
69C GLU* 3.4 24.7 - - + +
70C ALA* 3.6 23.1 - - + +
228C MET* 3.4 32.7 - - + +
230C ILE* 5.2 2.8 - - - +
260C TYR* 3.9 6.5 - - - +
285C SER 3.6 0.6 - - - -
286C ASP* 1.3 92.9 - - - +
288C ILE* 1.3 63.2 + - + +
290C LEU* 3.9 2.6 - - + +
291C LEU* 3.3 17.3 + - - +
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Residues in contact with ILE 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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36C TYR* 3.5 32.7 - - + +
39C MET* 3.6 56.5 - - + +
40C GLN* 3.8 24.7 - - - +
43C ARG* 3.8 23.8 - - + +
69C GLU* 4.6 2.7 - - - -
286C ASP* 3.0 12.3 + - - +
287C PRO* 1.3 78.7 - - + +
289C MET* 1.3 54.6 + - + +
291C LEU* 3.3 4.2 + - - +
292C LYS* 2.8 37.3 + - + +
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Residues in contact with MET 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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282C ARG* 4.6 11.9 - - - +
283C SER* 5.0 13.5 - - - +
286C ASP* 3.1 32.1 + - + +
288C ILE* 1.3 77.1 - - + +
290C LEU* 1.3 54.0 + - + +
292C LYS* 3.2 19.2 + - + +
293C ASP* 2.8 61.6 + - - +
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Residues in contact with LEU 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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226C ASP* 5.9 1.1 - - - +
228C MET* 4.2 24.5 - - + +
229C ASP* 5.0 12.3 - - + +
284C LYS 4.3 7.4 - - - +
285C SER* 3.9 33.7 - - - +
286C ASP 3.0 19.7 + - - +
287C PRO* 3.9 4.0 - - + +
289C MET* 1.3 74.8 - - + +
291C LEU* 1.3 65.9 + - - +
293C ASP* 3.1 9.3 + - + +
294C ARG* 3.1 36.3 + - - +
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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
----------------------------------------------------------
27C LEU* 4.5 13.9 - - + -
32C GLY* 3.9 6.7 - - - +
35C TYR* 4.2 6.3 - - + -
36C TYR* 3.6 40.6 - - + +
39C MET* 3.6 23.1 - - + -
230C ILE* 4.6 18.1 - - + +
231C LEU* 5.8 4.3 - - + -
287C PRO 3.3 12.5 + - - +
288C ILE 3.5 6.7 - - - +
290C LEU* 1.3 77.1 - - - +
292C LYS* 1.3 58.0 + - - +
294C ARG* 3.2 11.7 + - + +
295C MET* 2.8 55.5 + - + +
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Residues in contact with LYS 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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36C TYR* 4.1 19.3 - - + +
288C ILE* 2.8 19.6 + - + +
289C MET* 3.3 23.8 - - + +
291C LEU* 1.3 74.9 - - - +
293C ASP* 1.3 70.7 + - - +
295C MET* 4.0 0.4 - - - +
296C VAL* 3.0 32.4 + - + +
303C VAL* 4.2 25.9 - - + +
306C LEU* 3.8 35.2 - - + -
307C LYS* 5.9 3.8 - - - +
310C ASP* 5.2 4.7 - - - -
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Residues in contact with ASP 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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289C MET* 2.8 45.1 + - - +
290C LEU* 3.1 9.7 + - + +
292C LYS* 1.3 85.3 + - - +
294C ARG* 1.3 58.9 + - + +
296C VAL* 4.7 2.5 - - - +
297C ASN* 2.9 47.3 + - - +
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Residues in contact with ARG 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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7C PHE* 3.5 39.6 - - + +
8C GLU 3.1 26.9 + - - -
9C ILE* 4.4 0.8 - - - +
27C LEU* 6.2 0.7 - - + -
229C ASP* 3.0 39.8 + - - -
230C ILE* 5.4 3.0 - - - +
231C LEU* 3.2 28.3 - - + +
290C LEU* 3.1 25.3 + - - +
291C LEU* 3.6 12.4 - - + +
292C LYS 3.0 0.8 - - - -
293C ASP* 1.3 79.5 - - + +
295C MET* 1.3 62.0 + - - +
296C VAL 3.1 1.1 + - - -
297C ASN* 5.2 0.9 - - - -
298C SER* 2.7 34.3 + - - -
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Residues in contact with MET 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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27C LEU* 3.6 27.1 - - - +
29C ARG 4.2 5.6 - - - +
32C GLY 2.9 35.7 - - - +
33C LEU* 3.5 26.2 - - + +
36C TYR* 5.0 1.6 - - + -
291C LEU* 2.8 37.0 + - + +
292C LYS* 4.0 4.5 - - - +
294C ARG* 1.3 75.6 - - - +
296C VAL* 1.3 62.1 + - - +
299C ASN 3.4 0.7 + - - -
300C LEU* 2.8 41.8 + - + +
301C ALA* 3.4 20.7 + - + +
306C LEU* 4.7 14.6 - - + -
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Residues in contact with VAL 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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292C LYS* 3.0 22.3 + - + +
293C ASP* 4.8 1.1 - - - +
295C MET* 1.3 74.1 - - - +
297C ASN* 1.3 69.8 + - - +
298C SER 2.4 20.1 + - - -
299C ASN* 2.6 17.0 + - - -
301C ALA 3.5 20.2 - - - +
302C SER 4.2 1.8 - - - -
303C VAL* 3.9 30.3 - - + +
306C LEU* 4.8 9.0 - - + -
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Residues in contact with ASN 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 ASP* 2.9 34.0 + - - +
294C ARG* 4.0 2.5 - - - -
296C VAL* 1.3 84.5 - - - +
298C SER* 1.3 59.2 + - - +
299C ASN 3.8 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