Contacts of the helix formed by residues 296 - 307 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83J ASN* 5.0 2.4 + - - -
294J ALA 4.1 1.8 + - - -
295J LEU* 1.3 75.1 - - - +
297J PRO* 1.3 69.3 - - - +
298J ASN* 3.1 41.4 + - - +
299J ALA* 2.8 28.8 + - + +
300J ALA* 2.9 10.4 + - - +
268L ASP 5.3 1.0 + - - -
269L VAL* 4.3 13.5 - - - +
270L LEU 5.2 3.2 + - - +
296L ASN* 4.0 25.0 - - + +
298L ASN* 4.6 1.6 - - - +
299L ALA* 3.7 25.7 - - + +
302L LEU* 5.7 1.0 - - - +
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Residues in contact with PRO 297 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81J VAL* 4.0 9.8 - - + +
82J VAL 3.2 13.0 - - - +
83J ASN* 4.6 7.9 - - - +
84J THR 5.3 1.8 - - - +
113J ASN* 3.1 28.7 - - + +
115J THR* 3.3 27.8 + - + -
116J THR* 4.4 2.2 - - - +
295J LEU 3.5 4.9 - - - +
296J ASN* 1.3 99.2 - - - +
298J ASN* 1.3 55.7 + - - +
300J ALA* 3.2 11.5 + - + +
301J TYR* 3.0 27.9 + - - +
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Residues in contact with ASN 298 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298I ASN* 5.5 2.6 - - - +
81J VAL* 3.8 17.6 - - - +
83J ASN* 3.0 31.7 + - - +
296J ASN* 3.1 19.9 + - - +
297J PRO* 1.3 74.3 - - - +
299J ALA* 1.3 64.2 + - - +
301J TYR* 3.4 5.8 + - - +
302J LEU* 3.2 27.1 + - - +
298L ASN* 4.0 33.8 - - + +
302L LEU* 4.6 8.9 - - - +
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Residues in contact with ALA 299 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269J VAL* 3.5 27.3 - - + +
270J LEU 4.6 1.1 - - - +
295J LEU* 4.0 16.8 - - + -
296J ASN* 2.8 14.0 + - + +
298J ASN* 1.3 76.0 - - - +
300J ALA* 1.3 68.2 + - - +
302J LEU* 3.0 17.9 + - - +
303J ILE* 3.2 18.1 + - - +
296L ASN* 3.9 19.4 + - + +
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Residues in contact with ALA 300 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115J THR 3.6 19.7 - - - +
116J THR* 3.7 15.3 - - - +
119J LEU* 3.7 11.7 - - + +
295J LEU* 3.6 25.9 - - + +
296J ASN 2.9 7.2 + - - +
297J PRO* 3.3 10.5 - - + +
299J ALA* 1.3 78.2 - - - +
301J TYR* 1.3 60.0 + - - +
303J ILE* 3.5 0.9 + - - -
304J ILE* 3.2 28.0 + - - +
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Residues in contact with TYR 301 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I ASN* 3.8 19.8 + - + +
78J THR* 4.1 12.9 - - + +
79J THR* 3.5 35.0 - - - -
81J VAL* 4.0 21.8 - - + -
115J THR* 4.5 4.0 + - - +
297J PRO 3.0 14.2 + - - +
298J ASN* 3.8 5.4 - - - +
299J ALA 3.1 0.2 - - - -
300J ALA* 1.3 74.0 - - - +
302J LEU* 1.3 75.0 + - + +
303J ILE 3.0 2.0 - - - -
304J ILE* 3.1 15.2 + - + +
305J ARG* 2.9 42.7 + - + +
268K ASP* 2.7 42.3 + - - +
302K LEU* 4.8 9.9 - - + -
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Residues in contact with LEU 302 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268J ASP* 4.2 17.3 - - - +
269J VAL* 4.1 23.8 - - + -
298J ASN 3.2 15.4 + - - +
299J ALA* 3.0 10.4 + - - +
301J TYR* 1.3 88.1 - - + +
303J ILE* 1.3 56.8 + - - +
305J ARG* 4.5 2.0 - - - -
306J GLY* 3.2 5.2 + - - -
301K TYR* 4.8 9.6 - - + -
302K LEU* 5.1 11.2 - - + -
305K ARG* 2.6 59.6 + - - +
83L ASN* 4.3 18.4 - - - +
296L ASN* 5.8 1.1 - - - +
298L ASN* 4.6 8.7 - - - +
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Residues in contact with ILE 303 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119J LEU* 3.4 33.9 - - + -
123J ILE* 5.3 1.3 - - + -
134J LEU* 4.8 0.4 - - + -
259J ALA* 3.7 14.8 - - + +
263J LEU* 4.2 8.7 - - + +
264J GLY* 4.4 12.3 - - - -
269J VAL* 4.1 19.3 - - + -
271J ALA* 3.4 33.0 - - + -
295J LEU* 4.9 1.3 - - + -
299J ALA 3.2 15.7 + - - +
300J ALA 3.8 6.5 - - - +
301J TYR 3.0 0.6 - - - -
302J LEU* 1.3 77.6 - - - +
304J ILE* 1.3 56.2 + - - +
305J ARG 3.0 1.3 - - - -
306J GLY 3.6 0.6 - - - +
307J MET* 2.7 46.6 + - + +
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Residues in contact with ILE 304 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66J GLU* 4.0 28.7 - - - +
79J THR* 4.5 11.7 - - + +
115J THR* 3.6 26.0 - - - +
118J VAL* 4.2 18.2 - - + -
119J LEU* 3.8 29.8 - - + -
122J LYS* 4.1 9.0 + - + +
300J ALA 3.2 18.1 + - - +
301J TYR* 3.1 17.2 + - + +
303J ILE* 1.3 78.6 - - - +
305J ARG* 1.3 63.5 + - - +
307J MET* 3.4 5.4 + - - +
308J LYS* 3.3 24.8 + - - +
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Residues in contact with ARG 305 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301J TYR* 2.9 31.4 + - + +
302J LEU* 3.9 7.2 - - - +
304J ILE* 1.3 75.4 - - - +
306J GLY* 1.3 60.8 + - - +
307J MET 3.0 1.6 - - - -
308J LYS* 2.9 33.3 + - + +
309J THR 4.2 0.2 + - - -
264K GLY 4.0 5.3 + - - -
266K HIS* 3.5 46.1 + - + +
268K ASP* 2.5 44.1 + - - +
269K VAL* 4.2 4.2 - - - +
302K LEU* 2.8 49.5 + - - +
305K ARG* 3.9 21.1 - - - +
306K GLY* 3.5 15.0 - - - +
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Residues in contact with GLY 306 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263J LEU 3.9 2.7 - - - -
264J GLY 3.6 13.2 - - - -
266J HIS* 3.8 9.9 - - - -
302J LEU 3.2 6.4 + - - -
303J ILE 3.1 5.4 + - - -
305J ARG* 1.3 78.9 - - - +
307J MET* 1.3 54.2 + - - +
309J THR* 3.4 5.6 + - - -
313J ARG* 2.6 36.3 + - - -
305K ARG* 3.3 15.8 - - - +
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Residues in contact with MET 307 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61J ALA* 3.3 23.6 - - + +
119J LEU* 3.8 26.0 - - - -
122J LYS* 4.0 23.1 - - + -
123J ILE* 4.0 15.3 - - + -
126J LEU* 3.7 30.1 - - + -
263J LEU* 3.2 42.4 - - + +
303J ILE* 2.7 17.2 + - - +
304J ILE* 3.7 6.3 - - - +
306J GLY* 1.3 73.7 - - - +
308J LYS* 1.3 61.0 + - - +
309J THR 2.9 7.0 + - - -
310J LEU* 3.1 22.2 + - + +
313J ARG* 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