Contacts of the helix formed by residues 296 - 307 (chain K) in PDB entry 1I43
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 ASN 296 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268I ASP 5.2 0.8 + - - -
269I VAL* 4.2 15.6 - - - +
270I LEU 5.2 2.4 + - - +
296I ASN* 4.0 24.9 - - + +
298I ASN* 4.5 1.4 - - - +
299I ALA* 3.9 24.9 - - + +
302I LEU* 5.5 1.0 - - - +
83K ASN* 4.8 3.8 + - - -
294K ALA 4.0 2.6 + - - -
295K LEU* 1.3 76.9 - - - +
297K PRO* 1.3 70.8 - - - +
298K ASN* 3.1 41.1 + - - +
299K ALA* 2.7 29.1 + - + +
300K ALA* 3.0 9.4 + - - -
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Residues in contact with PRO 297 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81K VAL* 3.9 10.1 - - + +
82K VAL 3.2 13.9 - - - +
83K ASN* 4.6 8.1 - - - +
84K THR 5.3 2.2 - - - +
113K ASN* 3.1 28.5 - - - +
115K THR* 3.4 27.7 + - + -
116K THR* 4.5 2.5 - - - +
295K LEU 3.6 5.6 - - - +
296K ASN* 1.3 98.3 - - - +
298K ASN* 1.3 60.8 + - - +
300K ALA* 3.3 8.3 + - + +
301K TYR* 3.1 22.7 + - - +
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Residues in contact with ASN 298 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296I ASN* 4.6 0.4 - - - +
298I ASN* 3.7 35.3 - - + +
302I LEU* 4.5 9.3 - - - +
81K VAL* 3.6 18.7 - - - +
83K ASN* 3.3 25.7 + - - +
296K ASN* 3.1 21.8 + - - +
297K PRO* 1.3 77.7 - - - +
299K ALA* 1.3 60.9 + - - +
301K TYR* 3.6 5.1 + - - +
302K LEU* 3.3 28.3 + - - +
298L ASN* 5.5 2.6 - - - +
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Residues in contact with ALA 299 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296I ASN* 3.8 18.3 + - - +
269K VAL* 3.4 28.0 - - + +
270K LEU 4.6 0.4 - - - +
295K LEU* 3.8 18.2 - - + -
296K ASN* 2.7 14.6 + - + +
298K ASN* 1.3 78.4 - - - +
300K ALA* 1.3 65.1 + - - +
302K LEU* 3.0 17.8 + - - +
303K ILE* 3.1 18.0 + - - +
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Residues in contact with ALA 300 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115K THR 3.7 19.5 - - - +
116K THR* 3.7 15.9 - - - +
119K LEU* 3.9 10.0 - - + +
295K LEU* 3.7 25.0 - - + +
296K ASN 3.0 6.8 + - - +
297K PRO* 3.3 10.7 + - + +
299K ALA* 1.3 77.4 - - - +
301K TYR* 1.3 56.4 + - - +
303K ILE* 3.4 3.7 + - - +
304K ILE* 3.0 32.6 + - - +
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Residues in contact with TYR 301 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268J ASP* 2.6 42.5 + - - +
302J LEU* 4.8 9.6 - - + -
78K THR* 4.2 11.7 - - - +
79K THR* 3.5 35.2 - - - -
81K VAL* 4.0 23.6 - - + -
115K THR* 4.5 4.4 + - - +
297K PRO 3.1 15.4 + - - +
298K ASN 3.9 5.2 - - - +
299K ALA 3.1 0.2 - - - -
300K ALA* 1.3 72.7 - - - +
302K LEU* 1.3 71.1 + - + +
303K ILE 3.0 2.0 - - - -
304K ILE* 3.6 14.9 - - + +
305K ARG* 2.8 47.9 + - + +
83L ASN* 3.9 18.2 + - + -
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Residues in contact with LEU 302 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83I ASN* 4.2 17.0 - - - +
296I ASN* 5.7 1.3 - - - +
298I ASN* 4.6 7.4 - - - +
301J TYR* 4.8 9.2 - - + -
302J LEU* 5.1 11.2 - - + -
305J ARG* 2.8 57.5 + - - +
268K ASP* 4.0 26.9 - - - +
269K VAL* 4.1 12.3 - - + -
298K ASN 3.3 16.1 + - - +
299K ALA* 3.0 11.3 + - - +
301K TYR* 1.3 87.1 - - + +
303K ILE* 1.3 57.5 + - - +
305K ARG* 4.4 2.2 - - - -
306K GLY* 3.0 9.5 + - - -
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Residues in contact with ILE 303 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119K LEU* 3.4 33.7 - - + -
123K ILE* 5.2 1.6 - - + -
259K ALA* 3.9 16.6 - - + +
263K LEU* 4.1 7.3 - - + +
264K GLY* 4.3 12.8 - - - -
269K VAL* 4.0 22.9 - - + -
271K ALA* 3.3 33.9 - - + -
295K LEU* 4.8 2.7 - - + -
299K ALA 3.1 15.7 + - - +
300K ALA 3.8 5.8 - - - +
301K TYR 3.0 0.2 - - - -
302K LEU* 1.3 76.0 - - - +
304K ILE* 1.3 64.8 + - - +
305K ARG 3.1 1.1 - - - -
306K GLY 3.8 0.6 - - - +
307K MET* 2.9 34.9 + - + +
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Residues in contact with ILE 304 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66K GLU* 3.9 28.5 - - - +
79K THR* 4.4 15.0 - - + +
115K THR 3.5 23.8 - - - +
118K VAL* 3.9 21.1 - - + -
119K LEU* 3.8 24.5 - - + +
122K LYS* 4.3 9.0 + - + -
300K ALA 3.0 21.4 + - - +
301K TYR* 3.6 17.9 - - + +
303K ILE* 1.3 76.7 - - - +
305K ARG* 1.3 62.2 + - - +
307K MET* 3.5 9.2 + - - +
308K LYS* 3.4 21.0 + - - +
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Residues in contact with ARG 305 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264J GLY 4.0 7.1 + - - -
266J HIS* 3.5 41.8 + - + +
268J ASP* 2.7 42.7 + - - +
269J VAL* 4.2 4.8 - - - +
302J LEU* 2.6 50.2 + - - +
305J ARG* 3.9 20.5 - - - +
306J GLY* 3.3 21.8 - - - +
301K TYR* 2.8 31.9 + - + +
302K LEU* 3.7 7.6 - - - +
304K ILE* 1.3 76.9 - - - +
306K GLY* 1.3 64.8 + - - +
308K LYS* 3.0 26.4 + - + +
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Residues in contact with GLY 306 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305J ARG* 3.5 9.4 - - - +
263K LEU 4.0 1.6 - - - -
264K GLY 3.5 19.3 - - - -
266K HIS* 3.9 10.5 - - - -
302K LEU 3.0 10.1 + - - -
303K ILE 3.3 1.7 + - - -
305K ARG* 1.3 79.6 - - - +
307K MET* 1.3 60.2 + - - +
309K THR* 3.2 15.3 + - - -
313K ARG* 3.0 22.7 + - - -
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Residues in contact with MET 307 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61K ALA* 3.5 22.2 - - + +
119K LEU* 3.5 30.7 - - - -
122K LYS* 4.0 19.5 - - + -
123K ILE* 3.9 19.7 - - + -
126K LEU* 3.5 32.1 - - + -
263K LEU* 3.4 31.0 - - + +
303K ILE* 2.9 19.6 + - + +
304K ILE* 3.7 6.1 - - - +
305K ARG 3.1 0.2 - - - -
306K GLY* 1.3 72.2 - - - +
308K LYS* 1.3 61.7 + - - +
309K THR 2.9 7.9 + - - -
310K LEU* 3.0 25.1 + - + +
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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