Contacts of the helix formed by residues 274 - 280 (chain A) in PDB entry 1JS6
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 TYR 274 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A PHE* 3.3 63.0 - + + -
81A PRO* 3.6 26.0 - - + +
243A LEU 5.1 0.8 + - - -
244A GLY 4.6 3.6 - - - +
249A CYS* 4.0 20.2 - - - -
272A ALA 2.9 3.0 + - - -
273A ALA* 1.3 75.2 - - - +
275A ALA* 1.3 74.6 + - + +
276A GLY 3.2 3.4 + - - -
277A SER* 3.6 9.0 + - - -
303A LYS* 4.2 9.0 - - + -
304A TRP* 3.6 56.8 - + + +
406A LEU* 4.2 4.7 - - + -
407A GLY* 3.1 31.6 + - - -
408A LEU 5.2 0.4 - - - -
450A ILE 4.9 2.3 + - - -
601A PLP 4.1 6.0 + - - +
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Residues in contact with ALA 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A LEU 3.3 23.6 + - - +
244A GLY* 4.0 5.8 - - - -
251A PHE* 3.8 15.5 - - + -
272A ALA 3.5 0.8 + - - -
274A TYR* 1.3 80.9 - - + +
276A GLY* 1.3 64.9 + - - +
277A SER 3.2 0.2 - - - -
278A ALA* 3.0 22.8 + - - +
279A PHE* 3.6 12.0 - - + -
304A TRP* 4.6 0.7 - - - -
406A LEU* 3.4 29.2 - - + -
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Residues in contact with GLY 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LEU* 3.4 17.3 - - - +
272A ALA* 2.9 21.8 + - - +
274A TYR 3.2 0.6 + - - -
275A ALA* 1.3 77.1 - - - +
277A SER* 1.3 62.8 + - - +
279A PHE* 3.0 28.9 + - - +
297A PHE* 4.9 0.4 - - - -
299A PHE* 3.7 20.2 - - - -
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Residues in contact with SER 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A TYR 3.6 2.1 + - - -
275A ALA 3.1 0.8 + - - -
276A GLY* 1.3 75.4 - - - +
278A ALA* 1.3 62.7 + - - +
279A PHE 3.2 0.9 + - - -
280A ILE* 3.3 19.7 + - - +
299A PHE* 3.3 28.3 - - - -
300A ASN 3.9 3.5 + - - -
304A TRP* 3.2 49.9 - - - +
305A LEU* 3.3 10.5 + - - +
378A ILE* 3.0 17.5 - - - +
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Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ALA 3.0 13.2 + - - +
277A SER* 1.3 80.6 - - - +
279A PHE* 1.3 57.9 + - + +
280A ILE 3.0 0.2 - - - -
281A CYS* 2.8 30.8 + - - +
284A PHE* 3.6 17.5 - - + -
304A TRP* 3.7 21.4 - - + -
378A ILE* 3.4 14.9 - - + +
406A LEU* 3.8 20.4 - - + -
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Residues in contact with PHE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A MET 4.1 1.2 - - - +
126A LEU* 3.5 16.8 - - + +
127A GLN* 5.9 0.3 - - - +
243A LEU* 3.8 33.7 - - + -
251A PHE* 4.5 1.1 - + - -
272A ALA* 4.3 4.9 - - + -
275A ALA* 3.6 26.2 - - + -
276A GLY* 3.0 28.5 + - - +
278A ALA* 1.3 74.6 - - + +
280A ILE* 1.3 58.5 + - - +
281A CYS 3.0 13.7 + - - +
284A PHE* 4.0 13.5 - - + -
285A ARG* 3.8 24.2 - - - +
287A LEU* 3.6 34.8 - - + -
288A LEU* 3.6 34.8 - - + -
297A PHE* 4.5 3.8 - + - -
406A LEU* 5.5 0.4 - - + -
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Residues in contact with ILE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LEU* 4.8 9.0 - - + -
125A MET* 3.5 37.7 - - + +
126A LEU* 3.9 17.7 - - + -
277A SER* 3.4 20.4 - - - +
278A ALA 2.9 2.2 + - - -
279A PHE* 1.3 77.5 - - - +
281A CYS* 1.3 68.8 + - - +
282A PRO* 3.9 2.6 - - - +
299A PHE* 5.6 0.2 - - + -
305A LEU* 4.5 12.6 - - + -
371A VAL* 4.6 7.4 - - + +
374A LEU* 3.7 35.4 - - + +
375A GLN* 3.1 35.2 + - + +
378A ILE* 4.4 2.0 - - + -
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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