Contacts of the helix formed by residues 264 - 273 (chain A) in PDB entry 1SLL
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 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A LYS* 3.0 25.8 + - - +
205A ARG* 2.7 34.6 + - - -
207A PHE* 3.4 31.1 - - + -
212A LEU* 4.8 4.1 - - + +
263A SER* 1.3 73.0 - - - +
265A GLU* 1.3 66.2 + - - +
267A LEU* 3.1 2.6 + - - +
268A ILE* 2.7 43.2 + - + +
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Residues in contact with GLU 265 (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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263A SER* 3.3 21.8 - - - +
264A ASP* 1.3 91.6 + - - +
266A GLU* 1.3 62.8 + - + +
268A ILE* 3.3 7.5 + - - +
269A GLN* 3.1 24.1 + - - +
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Residues in contact with GLU 266 (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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262A LEU* 3.6 34.1 - - + +
263A SER* 3.1 38.1 + - - +
265A GLU* 1.3 76.8 - - + +
267A LEU* 1.3 53.5 + - + +
269A GLN* 3.4 7.3 + - - +
270A ALA* 2.7 36.9 + - - +
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Residues in contact with LEU 267 (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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118A THR* 3.8 26.0 - - + -
120A ILE* 4.9 5.2 - - + -
194A ALA* 3.9 16.6 - - + -
196A LYS* 3.8 26.5 - - + -
207A PHE* 3.6 38.8 - - + -
262A LEU* 4.1 21.1 - - + +
263A SER 3.1 13.7 + - - +
264A ASP 3.7 6.5 - - - +
266A GLU* 1.3 76.5 - - - +
268A ILE* 1.3 59.4 + - - +
270A ALA* 4.0 9.6 - - + -
271A THR* 2.8 35.4 + - - +
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Residues in contact with ILE 268 (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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207A PHE* 3.8 14.4 - - + -
210A GLY* 3.4 31.4 - - - +
212A LEU* 3.7 26.9 - - + +
264A ASP* 2.7 28.2 + - + +
265A GLU* 3.7 7.4 - - - +
266A GLU 3.3 0.2 - - - -
267A LEU* 1.3 71.5 - - - +
269A GLN* 1.3 59.5 + - - +
271A THR* 4.1 2.9 - - - -
272A GLY* 2.8 26.2 + - - -
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Residues in contact with GLN 269 (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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265A GLU 3.1 16.6 + - - +
266A GLU* 3.7 6.6 - - - +
268A ILE* 1.3 79.1 - - - +
270A ALA* 1.3 70.6 + - - +
272A GLY* 3.4 9.0 + - - -
273A VAL* 3.7 20.2 + - - +
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Residues in contact with ALA 270 (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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120A ILE* 3.3 28.2 - - + +
192A THR* 3.8 7.8 - - - +
262A LEU* 6.4 0.4 - - + -
266A GLU 2.7 22.2 + - - +
267A LEU* 3.7 10.8 - - + +
268A ILE 3.4 0.2 - - - -
269A GLN* 1.3 82.0 + - - +
271A THR* 1.3 60.7 + - - +
273A VAL* 3.3 21.9 - - - +
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Residues in contact with THR 271 (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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120A ILE* 4.4 3.1 - - + -
192A THR* 3.3 36.8 - - + +
193A VAL* 3.8 22.7 - - - +
194A ALA* 3.8 14.1 - - + +
207A PHE* 4.0 12.6 - - + +
208A ALA 4.2 0.4 - - - -
209A ASN* 3.2 16.6 + - - -
210A GLY* 3.0 25.7 + - - -
267A LEU 2.8 28.3 + - - +
268A ILE* 4.1 0.5 - - - -
270A ALA* 1.3 70.3 - - - +
272A GLY* 1.3 57.0 + - - +
273A VAL 3.0 11.2 + - - -
274A THR* 3.5 6.8 + - - -
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Residues in contact with GLY 272 (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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209A ASN 3.9 3.6 - - - -
210A GLY* 3.3 14.8 - - - +
268A ILE 2.8 18.4 + - - -
269A GLN* 3.4 5.1 + - - -
270A ALA 3.3 0.8 - - - -
271A THR* 1.3 73.1 - - - +
273A VAL* 1.3 62.7 + - - +
274A THR 3.1 4.0 + - - -
275A THR* 3.5 17.2 + - - +
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Residues in contact with VAL 273 (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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192A THR* 4.7 5.6 - - + +
269A GLN* 3.7 21.3 - - - +
270A ALA* 3.3 21.1 - - - +
271A THR 3.0 1.4 + - - +
272A GLY* 1.3 77.4 - - - +
274A THR* 1.3 66.7 + - + +
275A THR 4.1 1.5 + - - -
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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