Contacts of the helix formed by residues 286 - 293 (chain D) in PDB entry 1INL
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 PRO 286 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A PHE* 4.9 2.0 - - + -
273A TYR* 3.3 58.3 - - + +
278A VAL* 3.8 7.4 - - + -
233D LEU* 3.6 21.1 - - + -
243D MET* 4.2 9.2 - - + -
284D ALA 3.9 3.4 - - - +
285D LEU* 1.3 87.9 - - + +
287D ASN* 1.3 67.0 + - - +
288D PHE* 3.9 12.3 - - + -
289D VAL* 3.1 17.6 + - + +
290D LYS* 3.1 8.5 + - - +
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Residues in contact with ASN 287 (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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271A LEU* 2.9 29.2 + - - +
272A LYS* 3.5 12.1 - - - +
273A TYR 3.0 8.5 + - - -
274A TYR 3.4 19.0 + - - -
275A ASN* 2.9 27.5 + - - +
286D PRO* 1.3 70.3 - - - +
288D PHE* 1.3 58.2 + - - +
290D LYS* 3.2 6.5 + - - +
291D LYS* 2.9 29.1 + - - +
296D MET* 3.4 37.3 - - - +
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Residues in contact with PHE 288 (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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74A PHE* 3.7 20.9 - + + -
75A MET* 3.7 22.0 - - + -
237A THR* 5.6 0.2 - - + -
272A LYS* 2.8 30.9 + - + +
273A TYR* 3.8 21.5 - + - -
208D PRO* 3.7 23.6 - - + -
209D PHE* 5.4 2.2 - + - -
243D MET* 3.7 30.5 - - + -
286D PRO* 3.9 13.9 - - + -
287D ASN* 1.3 73.7 - - - +
289D VAL* 1.3 71.6 + - + +
291D LYS* 3.6 8.5 + - - +
292D GLU* 3.2 34.8 + - + +
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Residues in contact with VAL 289 (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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208D PRO* 4.5 9.4 - - + -
215D PHE* 3.9 27.6 - - + -
233D LEU* 4.7 4.7 - - + -
243D MET* 3.8 17.9 - - + -
285D LEU* 4.1 25.4 - - + -
286D PRO* 3.1 16.7 + - + +
288D PHE* 1.3 105.0 - - + +
290D LYS* 1.3 67.9 - - - +
292D GLU* 3.2 6.8 + - - +
293D LEU* 3.1 23.5 + - + +
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Residues in contact with LYS 290 (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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275A ASN* 3.9 11.9 - - - +
276A GLU* 5.9 1.8 + - - -
277A GLU* 3.1 25.0 + - - +
285D LEU* 3.2 38.1 - - + +
286D PRO 3.1 9.3 + - - +
287D ASN* 3.2 10.9 + - - +
289D VAL* 1.3 75.4 - - - +
291D LYS* 1.3 61.7 + - - +
293D LEU* 3.2 3.6 + - - +
294D GLY 3.1 3.5 + - - -
295D LEU* 2.8 53.6 + - + +
296D MET* 3.8 31.0 - - + +
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Residues in contact with LYS 291 (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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287D ASN 2.9 16.0 + - - +
288D PHE* 3.7 9.6 - - - +
290D LYS* 1.3 76.8 - - - +
292D GLU* 1.3 64.2 + - + +
294D GLY* 3.2 12.3 + - - -
296D MET* 4.0 26.6 - - + +
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Residues in contact with GLU 292 (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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208D PRO* 6.2 0.4 - - + -
212D ILE* 3.7 32.1 - - + +
215D PHE* 4.8 4.0 - - + -
216D LYS* 3.5 52.7 + - + +
220D ARG* 4.2 6.8 + - - -
288D PHE* 3.2 23.7 + - + +
289D VAL* 3.2 10.5 + - - +
291D LYS* 1.3 78.9 + - - +
293D LEU* 1.3 58.8 + - - +
294D GLY 3.3 1.2 + - - -
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Residues in contact with LEU 293 (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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215D PHE* 3.6 33.0 - - + -
216D LYS* 4.8 5.2 - - - -
219D TYR* 3.7 46.3 - - + -
220D ARG* 3.9 15.8 + - - +
231D VAL* 3.8 23.8 - - + -
285D LEU* 4.0 21.1 - - + -
289D VAL* 3.1 17.7 + - + +
290D LYS 3.2 3.8 + - - +
291D LYS 3.2 0.2 - - - -
292D GLU* 1.3 79.0 - - - +
294D GLY* 1.3 59.9 + - - +
295D LEU* 3.2 24.3 + - + +
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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