Contacts of the helix formed by residues 281 - 289 (chain C) in PDB entry 1JIQ
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 GLY 281 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C MET* 4.2 5.4 - - - -
164C PRO* 4.7 1.1 - - - -
276C LEU* 3.3 23.2 + - - -
278C SER 2.9 9.8 + - - -
280C ILE* 1.3 75.7 - - - +
282C LEU* 1.3 64.3 + - - +
283C SER* 3.2 3.4 - - - -
284C ILE* 2.8 31.3 + - - +
285C ALA 3.2 8.3 + - - -
293C PHE* 3.9 5.7 - - - -
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Residues in contact with LEU 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C MET* 3.8 36.3 - - + +
132C PHE* 3.9 28.9 - - + -
133C CYS* 3.9 21.1 - - - -
207C ILE* 4.5 7.6 - - + -
244C VAL* 4.5 4.0 - - + -
246C LEU* 3.9 24.2 - - + -
264C PHE* 4.0 16.4 - - + -
279C ALA 2.8 17.3 + - - +
280C ILE 3.2 2.0 - - - -
281C GLY* 1.3 75.2 - - - +
283C SER* 1.3 57.0 + - - +
285C ALA* 3.1 3.9 + - - +
286C LEU* 2.8 38.0 + - + +
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Residues in contact with SER 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C VAL* 4.6 7.0 - - - -
154C ASN* 3.9 13.9 + - - -
164C PRO* 3.4 18.2 - - - +
168C THR* 4.1 0.2 - - - +
181C VAL* 3.8 5.9 - - - +
183C TYR* 2.8 30.9 + - - -
207C ILE* 4.0 23.5 - - - +
280C ILE 4.5 1.5 + - - -
282C LEU* 1.3 77.7 - - - +
284C ILE* 1.3 63.7 + - - +
286C LEU* 3.7 6.3 - - - +
287C HIS* 3.0 24.9 + - - +
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Residues in contact with ILE 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C PRO* 3.9 33.2 - - + +
167C VAL* 3.8 40.4 - - + -
168C THR* 3.8 10.8 - - + -
171C LEU* 5.2 1.1 - - + -
276C LEU* 4.2 17.7 - - + +
281C GLY* 2.8 28.6 + - - +
283C SER* 1.3 72.9 + - - +
285C ALA* 1.3 62.0 + - - +
287C HIS* 3.1 2.3 + - - +
288C VAL* 3.0 39.0 + - + +
293C PHE* 3.9 19.3 - - + -
296C LEU* 4.4 4.0 - - + -
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Residues in contact with ALA 285 (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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129C MET* 4.8 3.8 - - + -
133C CYS* 3.4 22.9 - - - -
137C ARG* 4.0 1.0 - - - -
281C GLY 3.2 4.1 + - - +
282C LEU* 3.1 9.5 + - - +
284C ILE* 1.3 78.3 - - - +
286C LEU* 1.3 56.5 + - - +
289C GLY* 2.7 41.7 + - - -
290C PHE* 3.6 12.8 + - + -
293C PHE* 3.9 27.1 - - + -
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Residues in contact with LEU 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C PHE* 4.1 13.5 - - + -
133C CYS* 3.9 25.6 - - - +
136C VAL* 3.7 37.9 - - + -
137C ARG* 3.0 24.4 + - + +
152C VAL* 4.0 22.0 - - + -
179C PRO* 3.3 16.0 - - + +
181C VAL* 5.4 0.4 - - + -
205C LEU* 4.5 2.7 - - + -
207C ILE* 3.6 31.4 - - + -
282C LEU* 2.8 25.9 + - + +
283C SER* 3.7 5.6 - - - +
285C ALA* 1.3 77.5 - - - +
287C HIS* 1.3 56.9 + - - +
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Residues in contact with HIS 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ARG* 3.1 11.1 + - - -
168C THR* 3.8 17.4 + - + +
172C LYS* 3.1 47.2 + - + +
175C SER* 3.3 48.7 + - - +
178C GLY* 3.6 3.3 - - - -
179C PRO 2.9 30.9 + - - -
180C ARG* 4.7 2.6 - - - -
181C VAL* 3.7 26.5 + - + +
283C SER 3.0 18.4 + - - +
284C ILE 3.1 2.9 + - - +
286C LEU* 1.3 78.4 - - - +
288C VAL* 1.3 65.1 + - + +
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Residues in contact with VAL 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ARG* 3.6 8.1 + - - -
168C THR* 5.5 2.7 - - - -
171C LEU* 3.6 39.0 - - + +
174C TYR* 3.3 24.5 - - + +
284C ILE* 3.0 33.8 + - + +
287C HIS* 1.3 90.4 - - + +
289C GLY* 1.3 63.8 + - - +
292C ASN* 3.1 40.0 + - + +
293C PHE 4.4 3.1 - - - +
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Residues in contact with GLY 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ARG* 3.2 25.6 - - - +
285C ALA 2.7 23.8 + - - +
288C VAL* 1.3 77.1 - - - +
290C PHE* 1.3 65.6 + - - -
291C ASP* 3.3 3.4 - - - -
292C ASN* 3.3 3.6 + - - +
293C PHE* 3.1 19.8 + - - +
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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
------------------------------------------------------------
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