Contacts of the helix formed by residues 293 - 302 (chain A) in PDB entry 1I4A
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 SER 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283A ARG 5.7 0.4 - - - -
286A PHE* 3.9 1.9 - - - -
287A LYS* 4.5 6.3 - - - +
292A LYS* 1.3 76.9 - - - +
294A LEU* 1.3 64.3 + - - +
295A TYR 4.1 2.0 - - - -
296A SER* 2.7 36.1 + - - -
297A PHE* 3.2 8.0 + - - +
317A ASP* 2.5 29.3 + - - -
318A ASP* 3.6 36.3 - - - -
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Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LEU* 3.9 26.5 - - + -
257A MET* 3.9 18.4 - - + -
271A MET* 4.1 7.0 - - + -
279A MET* 3.9 20.0 - - - -
282A ILE* 4.5 4.7 - - + -
283A ARG* 4.1 15.8 + - + -
286A PHE* 3.6 43.9 - - + +
293A SER* 1.3 72.2 - - - +
295A TYR* 1.3 65.4 + - - +
297A PHE* 3.0 4.3 + - - +
298A ILE* 2.9 30.9 + - + +
314A CYS* 3.8 21.5 - - - -
318A ASP* 4.8 2.8 + - - -
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Residues in contact with TYR 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A SER* 3.9 1.3 - - - +
294A LEU* 1.3 80.4 - - - +
296A SER* 1.3 61.0 + - - +
298A ILE* 3.2 0.8 + - - -
299A LYS* 2.9 49.3 + - + +
308A LYS* 5.2 2.6 + - - -
311A LEU* 3.5 57.5 - - + +
314A CYS* 3.7 9.5 - - - -
316A GLY* 3.4 37.0 - - - +
317A ASP* 3.3 36.6 - - + +
318A ASP* 5.5 0.6 + - - +
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Residues in contact with SER 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LYS* 3.8 13.6 - - - +
293A SER* 2.7 41.0 + - - -
295A TYR* 1.3 79.5 - - - +
297A PHE* 1.3 61.4 + - - +
299A LYS* 3.9 8.0 - - - +
300A GLY* 3.2 18.9 + - - -
317A ASP* 4.3 3.6 - - - -
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Residues in contact with PHE 297 (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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254A TYR* 3.5 33.7 - + - -
257A MET* 3.7 27.3 - - + +
258A LYS* 3.9 28.7 - - + -
286A PHE* 3.5 31.9 - + + -
290A TYR* 4.8 3.6 - - + -
292A LYS* 3.8 31.9 - - + -
293A SER 3.2 2.2 + - - +
294A LEU 3.0 9.5 + - - +
296A SER* 1.3 80.4 + - - +
298A ILE* 1.3 64.4 + - - +
300A GLY 3.5 1.6 + - - -
301A ASP* 3.2 26.8 + - + +
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Residues in contact with ILE 298 (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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257A MET* 3.7 20.6 - - + -
267A LEU* 4.6 2.9 - - + -
271A MET* 3.8 30.1 - - + -
294A LEU* 2.9 41.2 + - + +
295A TYR 3.7 3.6 - - - +
297A PHE* 1.3 75.2 - - - +
299A LYS* 1.3 63.2 + - - +
301A ASP 3.2 0.3 + - - -
302A THR* 2.8 40.9 + - + +
307A ARG 4.7 0.2 - - - +
310A LEU* 3.8 35.4 - - + +
311A LEU* 3.7 15.3 - - + -
314A CYS* 4.2 7.9 - - + -
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Residues in contact with LYS 299 (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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295A TYR* 2.9 36.9 + - + +
296A SER* 3.9 8.1 - - - +
298A ILE* 1.3 78.3 - - - +
300A GLY* 1.3 56.3 + - - +
302A THR 3.3 5.2 - - - +
307A ARG* 3.0 54.6 + - - +
311A LEU* 4.1 13.5 - - + -
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Residues in contact with GLY 300 (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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296A SER 3.2 13.6 + - - -
297A PHE 3.9 1.3 - - - -
298A ILE 3.3 0.2 - - - -
299A LYS* 1.3 79.6 - - - +
301A ASP* 1.3 59.3 + - - +
302A THR 3.6 0.9 - - - -
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Residues in contact with ASP 301 (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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257A MET* 3.1 31.0 - - + +
261A GLY 3.6 0.5 - - - +
262A THR* 2.4 43.8 + - - +
297A PHE* 3.2 17.2 + - + +
298A ILE 3.2 3.4 + - - +
300A GLY* 1.3 78.7 - - - +
302A THR* 1.3 66.0 + - + +
410A CA 2.5 24.3 - - - -
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Residues in contact with THR 302 (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 THR* 5.0 0.9 - - + -
264A ASP* 4.9 2.5 - - - +
267A LEU* 3.9 23.6 - - + -
298A ILE* 2.8 23.7 + - + +
299A LYS 3.3 6.4 - - - +
300A GLY 3.6 0.9 - - - -
301A ASP* 1.3 86.0 - - + +
303A SER* 1.3 65.3 + - - +
306A TYR* 3.7 31.6 - - + -
307A ARG* 3.2 37.2 + - - +
310A LEU* 4.0 3.8 - - + -
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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
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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