Contacts of the helix formed by residues 296 - 307 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268B ASP 5.4 1.0 + - - -
269B VAL* 4.3 14.1 - - - +
270B LEU 5.2 2.8 + - - +
296B ASN* 3.9 24.8 - - + +
298B ASN* 4.4 1.6 - - - +
299B ALA* 3.9 25.3 - - + +
302B LEU* 5.7 1.2 - - - +
83D ASN* 5.1 2.6 + - - -
294D ALA 4.0 2.2 + - - -
295D LEU* 1.3 77.9 - - - +
297D PRO* 1.3 79.0 - - - +
298D ASN* 3.1 39.5 + - - +
299D ALA* 2.9 18.7 + - + +
300D ALA* 3.0 9.4 + - - -
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Residues in contact with PRO 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B ASP 6.1 0.4 - - - +
81D VAL* 4.0 10.4 - - + +
82D VAL 3.4 13.5 - - - +
83D ASN* 4.5 8.5 - - - +
84D THR 5.3 1.6 - - - +
113D ASN* 3.0 27.6 - - + +
115D THR* 3.4 28.2 + - + -
116D THR* 4.5 2.2 - - - +
295D LEU 3.5 4.2 - - - +
296D ASN* 1.3 98.8 - - - +
298D ASN* 1.3 62.1 + - - +
300D ALA* 3.0 8.7 + - + +
301D TYR* 2.9 23.7 + - - +
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Residues in contact with ASN 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ASN* 4.5 0.4 - - - +
298B ASN* 3.8 35.3 - - + +
302B LEU* 4.6 11.3 - - - +
298C ASN* 5.5 2.6 - - - +
81D VAL* 3.9 17.3 - - - +
83D ASN* 3.3 27.1 + - - +
296D ASN* 3.1 20.2 + - - +
297D PRO* 1.3 79.0 - - - +
299D ALA* 1.3 63.0 + - - +
301D TYR* 3.3 6.7 + - - +
302D LEU* 3.1 27.4 + - - +
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Residues in contact with ALA 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B ASN* 3.8 21.0 + - + +
269D VAL* 3.5 27.0 - - + +
270D LEU 4.6 0.9 - - - +
295D LEU* 4.0 16.2 - - + -
296D ASN* 2.9 14.1 + - + +
298D ASN* 1.3 79.9 - - - +
300D ALA* 1.3 63.5 + - - +
302D LEU* 3.2 15.6 + - - +
303D ILE* 3.2 20.9 + - - +
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Residues in contact with ALA 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D THR 3.8 18.6 - - - +
116D THR* 3.9 14.4 - - - +
119D LEU* 4.0 10.5 - - + +
295D LEU* 3.7 25.7 - - + +
296D ASN 3.0 7.9 + - - +
297D PRO* 3.0 11.0 + - + +
299D ALA* 1.3 77.8 - - - +
301D TYR* 1.3 56.8 + - - +
303D ILE* 3.4 4.4 + - - +
304D ILE* 3.0 32.3 + - - +
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Residues in contact with TYR 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ASP* 2.7 41.7 + - - +
302A LEU* 5.0 8.5 - - + -
83C ASN* 3.9 18.9 + - + -
78D THR* 4.1 12.8 - - - +
79D THR* 3.5 34.3 - - - -
81D VAL* 4.0 22.4 - - + -
115D THR* 4.6 4.9 + - - +
297D PRO 2.9 11.9 + - - +
298D ASN 3.6 8.5 - - - +
299D ALA 3.2 0.2 - - - -
300D ALA* 1.3 76.5 - - - +
302D LEU* 1.3 69.3 + - + +
304D ILE* 3.2 14.7 + - + +
305D ARG* 2.9 44.3 + - + +
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Residues in contact with LEU 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A TYR* 4.8 7.6 - - + -
302A LEU* 5.1 11.2 - - + -
305A ARG* 2.8 57.3 + - - +
83B ASN* 4.2 17.3 - - - +
296B ASN* 5.8 1.1 - - - +
298B ASN* 4.6 8.7 - - - +
268D ASP* 3.9 28.7 - - - +
269D VAL* 4.1 13.7 - - + -
298D ASN 3.1 17.9 + - - +
299D ALA* 3.2 10.1 + - - +
301D TYR* 1.3 84.7 - - + +
303D ILE* 1.3 58.6 + - - +
305D ARG* 4.5 2.5 - - - -
306D GLY* 3.1 7.8 + - - -
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Residues in contact with ILE 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D LEU* 3.5 36.1 - - + -
123D ILE* 5.2 1.1 - - + -
134D LEU* 4.8 0.7 - - + -
259D ALA* 4.0 16.8 - - + +
263D LEU* 4.3 7.1 - - + +
264D GLY* 4.5 9.0 - - - -
269D VAL* 4.2 18.2 - - + -
270D LEU 4.8 0.2 - - - +
271D ALA* 3.3 34.3 - - + -
295D LEU* 4.8 1.6 - - + -
299D ALA 3.2 18.0 + - - +
300D ALA* 3.7 5.6 - - - +
301D TYR 3.1 0.4 - - - -
302D LEU* 1.3 76.9 - - - +
304D ILE* 1.3 66.1 + - - +
305D ARG 3.1 1.3 - - - -
306D GLY* 3.1 0.7 + - - +
307D MET* 2.8 37.0 + - + +
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Residues in contact with ILE 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D GLU* 3.7 29.6 - - - +
79D THR* 4.5 14.4 - - + +
115D THR* 3.5 26.0 - - - +
118D VAL* 3.9 20.2 - - + -
119D LEU* 3.8 26.2 - - + +
122D LYS* 4.3 8.2 + - + +
300D ALA 3.0 21.2 + - - +
301D TYR* 3.6 17.9 - - + +
303D ILE* 1.3 76.5 - - - +
305D ARG* 1.3 63.8 + - - +
307D MET* 3.6 5.3 + - - +
308D LYS* 3.2 23.6 + - - +
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Residues in contact with ARG 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A GLY 4.0 6.1 + - - -
266A HIS* 3.5 43.7 + - + +
268A ASP* 2.7 44.0 + - - +
269A VAL* 4.4 3.8 - - - +
302A LEU* 2.9 45.8 + - - +
305A ARG* 3.9 22.7 - - - +
306A GLY* 3.4 20.4 - - - +
301D TYR* 2.9 33.1 + - + +
302D LEU* 3.9 7.0 - - - +
304D ILE* 1.3 77.7 - - - +
306D GLY* 1.3 65.5 + - - +
308D LYS* 3.0 27.0 + - + +
309D THR 4.3 0.2 + - - -
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Residues in contact with GLY 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A ARG* 3.7 15.0 - - - -
263D LEU 3.9 2.2 - - - -
264D GLY 3.7 14.8 - - - -
266D HIS* 4.0 8.3 - - - -
302D LEU 3.1 6.0 + - - -
303D ILE 3.1 6.3 + - - -
305D ARG* 1.3 80.2 - - - +
307D MET* 1.3 59.6 + - - +
308D LYS 3.1 1.3 + - - -
309D THR* 3.2 14.6 + - - -
313D ARG* 3.0 21.6 + - - -
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Residues in contact with MET 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D ALA* 3.3 22.5 - - + +
119D LEU* 3.8 26.0 - - - -
122D LYS* 3.8 25.1 - - + -
123D ILE* 3.9 19.3 - - + -
126D LEU* 3.7 31.4 - - + -
263D LEU* 3.4 33.0 - - + +
303D ILE* 2.8 18.0 + - - +
304D ILE 4.0 5.4 - - - +
305D ARG 3.2 0.2 - - - -
306D GLY* 1.3 72.2 - - - +
308D LYS* 1.3 60.0 + - - +
309D THR 3.0 6.5 + - - -
310D LEU* 3.2 25.7 + - + +
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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