Contacts of the helix formed by residues 280 - 288 (chain C) in PDB entry 1JLH
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 280 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C MET* 5.7 0.2 - - - -
163C PRO* 4.5 1.6 - - - -
275C LEU 3.4 21.2 + - - -
277C SER 2.9 12.0 + - - -
279C ILE* 1.3 77.2 - - - +
281C LEU* 1.3 56.7 + - - +
282C SER 3.2 3.4 - - - -
283C ILE* 2.8 38.8 + - - +
284C ALA* 3.1 5.4 + - - +
292C PHE* 3.8 11.5 - - - -
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Residues in contact with LEU 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C MET* 4.1 30.3 - - + -
131C PHE* 4.1 18.6 - - + -
132C CYS* 3.9 22.2 - - - -
206C ILE* 4.0 15.0 - - + -
243C VAL* 4.3 4.3 - - + -
245C LEU* 3.9 23.3 - - + -
263C PHE* 3.9 22.4 - - + -
277C SER 4.3 0.2 + - - -
278C ALA* 2.9 18.0 + - - +
279C ILE 3.2 1.8 - - - -
280C GLY* 1.3 77.4 - - - +
282C SER* 1.3 56.8 + - - +
284C ALA* 3.1 6.5 + - + +
285C LEU* 2.8 35.2 + - + +
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Residues in contact with SER 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C VAL* 4.5 7.6 - - - -
153C ASN* 4.0 15.9 + - - +
163C PRO* 3.5 16.1 - - - +
180C VAL* 3.9 7.0 - - - +
182C TYR* 2.8 32.0 + - - -
206C ILE* 4.0 20.9 - - - +
279C ILE 4.6 1.5 + - - -
281C LEU* 1.3 78.6 - - - +
283C ILE* 1.3 57.9 + - - +
285C LEU* 3.8 5.8 - - - +
286C HIS* 3.0 30.8 + - - +
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Residues in contact with ILE 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C PRO* 3.6 35.4 - - + +
166C VAL* 3.6 41.7 - - + -
167C THR* 3.8 11.4 - - + -
170C LEU* 5.3 1.8 - - + -
275C LEU* 4.4 11.4 - - + +
280C GLY* 2.8 24.6 + - - +
282C SER* 1.3 78.4 + - - +
284C ALA* 1.3 60.8 + - - +
286C HIS* 3.2 2.1 + - - +
287C VAL* 3.0 42.1 + - + +
292C PHE* 3.8 17.3 - - + -
295C LEU* 4.4 10.1 - - + -
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Residues in contact with ALA 284 (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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128C MET* 5.5 1.1 - - + -
132C CYS* 3.5 23.1 - - - +
136C ARG* 4.2 0.2 - - - -
280C GLY 3.1 5.1 + - - +
281C LEU* 3.1 10.6 + - + +
283C ILE* 1.3 80.1 - - - +
285C LEU* 1.3 54.9 + - - +
288C GLY* 2.8 41.3 + - - -
289C PHE* 3.4 13.9 + - + -
292C PHE* 3.9 26.5 - - + -
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Residues in contact with LEU 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C PHE* 4.1 13.7 - - + -
132C CYS* 3.7 32.3 - - - +
135C VAL* 3.9 26.2 - - + -
136C ARG* 2.8 26.9 - - + +
151C VAL* 4.1 23.3 - - + -
178C PRO* 3.3 13.2 - - + +
204C LEU* 4.4 2.2 - - + -
206C ILE* 3.6 31.4 - - + -
281C LEU* 2.8 26.5 + - + +
282C SER* 3.8 4.5 - - - +
284C ALA* 1.3 77.8 - - - +
286C HIS* 1.3 59.5 + - - +
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Residues in contact with HIS 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C ARG* 3.0 11.6 + - - -
167C THR* 3.9 18.5 + - + +
171C LYS* 3.1 36.0 + - + +
174C SER* 3.2 53.6 + - - +
177C GLY* 3.7 3.1 - - - -
178C PRO* 2.7 31.6 + - - -
179C ARG* 4.2 3.0 - - - -
180C VAL* 3.6 28.9 + - + +
282C SER 3.0 18.7 + - - +
283C ILE 3.7 2.5 - - - +
285C LEU* 1.3 78.6 - - - +
287C VAL* 1.3 63.0 + - + +
288C GLY 3.5 0.2 - - - -
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Residues in contact with VAL 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C ARG* 3.6 7.9 + - - +
167C THR* 5.6 3.6 - - - -
170C LEU* 3.6 38.8 - - + +
173C TYR* 3.4 25.2 - - + +
174C SER* 3.9 4.7 - - - +
283C ILE* 3.0 30.1 + - + +
286C HIS* 1.3 85.7 - - + +
288C GLY* 1.3 63.5 + - - +
291C ASN* 2.7 48.9 + - + +
292C PHE 4.6 1.8 - - - +
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Residues in contact with GLY 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C ARG* 3.2 28.1 - - - +
284C ALA* 2.8 20.3 + - - +
287C VAL* 1.3 87.5 - - - +
289C PHE* 1.3 64.7 + - - -
290C ASP* 3.3 3.1 - - - -
291C ASN 3.4 0.7 + - - -
292C PHE 3.3 14.7 + - - -
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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