Contacts of the helix formed by residues 272 - 284 (chain C) in PDB entry 5JLH
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 272 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177C LEU* 5.1 0.2 - - - -
260C LEU 3.3 13.7 - - - -
261C PHE* 4.2 7.4 + - - -
263C PRO* 3.7 16.5 - - - +
271C CYS* 1.3 77.9 - - - +
273C ILE* 1.3 66.5 + - - -
275C GLU* 3.0 21.5 + - - +
276C THR* 3.0 18.9 + - - +
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Residues in contact with ILE 273 (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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152C MET* 3.6 31.9 - - + +
159C THR* 4.7 3.1 - - + +
177C LEU* 3.7 18.8 - - + -
179C LEU* 4.3 4.7 - - + -
260C LEU* 3.1 39.4 + - + +
261C PHE* 3.7 25.4 - - + -
272C GLY* 1.3 70.4 - - - -
274C HIS* 1.3 61.2 + - - +
276C THR* 2.3 26.6 + - - -
277C THR* 2.9 18.2 + - - -
298C LEU* 6.4 0.2 - - + -
303C THR* 6.4 1.3 - - + -
308C ILE* 5.1 4.7 - - + -
312C MET* 3.5 27.8 - - + -
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Residues in contact with HIS 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C PHE* 3.5 29.6 - + + -
262C GLN* 5.5 2.2 - - - -
273C ILE* 1.3 79.7 + - - +
275C GLU* 1.3 103.5 + - - +
277C THR* 3.1 6.0 + - - -
278C PHE* 3.0 25.2 + - - +
312C MET* 3.9 18.6 - - - -
315C GLU* 2.9 52.0 + - + +
316C ILE* 4.1 16.6 - - + +
319C LEU* 4.0 15.2 - - + +
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Residues in contact with GLU 275 (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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261C PHE 4.8 2.1 - - - +
262C GLN* 5.9 0.3 + - - -
271C CYS* 3.6 22.4 - - + -
272C GLY* 3.0 20.5 - - - +
274C HIS* 1.3 120.0 + - + +
276C THR* 1.3 56.1 + - - +
278C PHE* 3.4 8.9 + - + +
279C ASN* 2.9 25.3 + - - +
319C LEU* 4.3 11.9 - - + +
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Residues in contact with THR 276 (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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152C MET* 4.9 2.4 - - - +
159C THR* 5.7 0.5 - - - +
161C THR* 4.5 10.7 + - - -
175C LEU* 3.5 24.3 - - + +
177C LEU* 3.8 26.0 - - + +
271C CYS* 3.6 21.3 - - + +
272C GLY 3.0 12.3 + - - +
273C ILE* 2.3 31.4 + - - +
275C GLU* 1.3 72.6 - - - +
277C THR* 1.3 61.4 + - - +
279C ASN* 3.2 5.5 + - - +
280C SER* 2.9 30.1 + - - -
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Residues in contact with THR 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C ILE* 4.0 18.2 - - + -
152C MET* 4.3 13.4 - - + +
161C THR* 4.7 5.0 - - - +
273C ILE 2.9 14.4 + - - -
274C HIS 3.1 8.7 + - - -
276C THR* 1.3 77.5 + - - +
278C PHE* 1.3 57.6 + - + +
280C SER* 3.1 7.7 + - - +
281C ILE* 2.9 46.6 + - + +
296C THR* 4.9 6.9 - - + +
312C MET* 3.9 12.6 - - - +
316C ILE* 3.9 20.6 - - + -
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Residues in contact with PHE 278 (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 HIS 3.0 13.5 + - - +
275C GLU* 3.4 11.7 - - + +
276C THR 3.3 0.2 - - - -
277C THR* 1.3 74.0 - - + +
279C ASN* 1.3 59.9 + - - +
281C ILE* 4.5 5.4 - - + +
282C MET* 2.8 58.3 + - + +
293C TYR* 3.9 19.3 - + - -
316C ILE* 3.9 21.3 - - + -
319C LEU* 3.3 39.0 - - + -
320C ALA* 3.3 39.7 - - + -
321C PRO* 5.4 1.3 - - + -
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Residues in contact with ASN 279 (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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175C LEU* 3.5 27.9 - - + +
275C GLU 2.9 13.5 + - - +
276C THR* 3.2 11.3 + - - +
278C PHE* 1.3 75.9 - - - +
280C SER* 1.3 61.7 + - - +
282C MET* 4.1 4.3 - - - +
283C LYS* 3.3 44.6 + - - +
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Residues in contact with SER 280 (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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150C ILE* 3.6 19.5 - - - -
161C THR* 3.3 16.5 - - - +
163C PRO* 4.6 4.0 - - - -
173C ALA* 3.3 25.2 + - - +
175C LEU* 3.4 12.7 - - - +
276C THR 2.9 15.4 + - - -
277C THR 3.5 7.0 - - - -
279C ASN* 1.3 75.0 - - - +
281C ILE* 1.3 66.1 + - - +
283C LYS* 3.1 16.8 + - - +
284C CYS* 3.1 15.0 - - - -
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Residues in contact with ILE 281 (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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150C ILE* 3.7 25.1 - - + -
277C THR* 2.9 36.8 + - + +
278C PHE* 4.1 5.8 - - + +
280C SER* 1.3 73.7 - - - +
282C MET* 1.3 59.2 + - + +
284C CYS* 3.0 24.5 + - - +
289C ARG* 2.9 44.7 + - + -
292C LEU* 4.2 21.5 - - + +
293C TYR* 3.7 41.7 - - + +
296C THR* 5.0 1.3 - - - +
316C ILE* 5.9 1.8 - - + -
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Residues in contact with MET 282 (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 PHE* 2.8 38.5 + - + +
279C ASN* 4.1 5.2 - - - +
281C ILE* 1.3 77.9 - - + +
283C LYS* 1.3 58.4 + - + +
289C ARG* 2.7 50.7 + - - +
293C TYR* 3.2 27.6 - - - +
321C PRO* 6.2 0.4 - - + -
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Residues in contact with LYS 283 (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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172C HIS* 3.3 47.6 + - + +
173C ALA* 3.9 17.3 - - - +
174C ILE 5.7 0.7 - - - +
175C LEU* 5.5 7.6 - - - -
279C ASN* 3.3 36.5 + - - +
280C SER 3.1 10.0 + - - +
282C MET* 1.3 79.9 - - + +
284C CYS* 1.3 58.2 + - - +
285C ASP* 4.9 1.0 - - - +
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Residues in contact with CYS 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C PRO* 3.9 10.1 - - - -
170C LEU* 3.7 30.7 - - + -
172C HIS* 4.7 1.6 - - - -
173C ALA* 4.0 4.0 - - - -
280C SER 3.1 23.6 - - - -
281C ILE* 3.0 20.2 + - - +
282C MET 3.6 0.2 - - - +
283C LYS* 1.3 80.5 - - - +
285C ASP* 1.3 68.6 + - - +
286C VAL* 5.1 0.2 - - - +
288C ILE* 4.1 8.3 - - + -
289C ARG* 2.8 28.6 + - + -
292C LEU* 3.8 17.0 - - + -
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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