Contacts of the helix formed by residues 281 - 289 (chain D) in PDB entry 1JIQ
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 GLY 281 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D MET* 4.1 5.6 - - - -
276D LEU* 3.2 22.4 + - - -
278D SER 2.8 10.5 + - - -
280D ILE* 1.3 76.9 - - - +
282D LEU* 1.3 63.2 + - - +
283D SER 3.2 2.9 - - - -
284D ILE* 2.9 30.2 + - - +
285D ALA* 3.1 9.4 + - - +
293D PHE* 3.8 6.2 - - - -
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Residues in contact with LEU 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D MET* 3.7 32.9 - - + +
132D PHE* 4.1 21.5 - - + -
133D CYS* 4.0 22.0 - - - -
207D ILE* 4.2 12.3 - - + -
244D VAL* 4.3 4.3 - - + -
246D LEU* 3.7 25.6 - - + -
264D PHE* 3.9 22.2 - - + -
279D ALA 2.8 18.2 + - - +
280D ILE 3.2 1.2 - - - -
281D GLY* 1.3 76.9 - - - +
283D SER* 1.3 59.7 + - - +
285D ALA* 3.0 4.8 + - - +
286D LEU* 2.8 33.4 + - + +
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Residues in contact with SER 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D VAL* 4.5 7.2 - - - -
154D ASN* 3.9 14.0 + - - -
164D PRO* 3.5 16.8 - - - +
181D VAL* 3.8 5.8 - - - +
183D TYR* 2.9 32.5 + - - -
207D ILE* 4.0 22.0 - - - +
246D LEU* 5.6 0.2 - - - +
280D ILE 4.4 2.3 + - - -
282D LEU* 1.3 77.8 - - - +
284D ILE* 1.3 63.2 + - - +
286D LEU* 3.8 5.0 - - - +
287D HIS* 3.0 25.5 + - - +
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Residues in contact with ILE 284 (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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164D PRO* 3.8 31.2 - - + -
167D VAL* 3.7 31.9 - - + -
168D THR* 3.7 17.9 - - + -
171D LEU* 5.1 1.6 - - + -
276D LEU* 4.0 21.5 - - + +
281D GLY* 2.9 24.9 + - - +
283D SER* 1.3 75.5 + - - +
285D ALA* 1.3 59.6 + - - +
287D HIS* 3.1 2.1 + - - +
288D VAL* 2.9 49.5 + - + +
293D PHE* 3.9 18.4 - - + -
296D LEU* 4.4 3.6 - - + -
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Residues in contact with ALA 285 (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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129D MET* 4.7 2.5 - - + -
133D CYS* 3.4 21.5 - - - -
137D ARG* 4.1 1.0 - - - -
281D GLY 3.1 7.9 + - - +
282D LEU* 3.0 13.7 + - + +
284D ILE* 1.3 81.5 - - - +
286D LEU* 1.3 56.9 + - - +
289D GLY* 2.8 33.5 + - - -
290D PHE* 3.5 10.9 + - + -
293D PHE* 4.1 29.6 - - + -
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Residues in contact with LEU 286 (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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132D PHE* 3.9 17.3 - - + -
133D CYS* 3.9 24.2 - - - +
136D VAL* 3.8 34.3 - - + -
137D ARG* 3.0 27.2 + - + +
152D VAL* 3.9 23.6 - - + -
179D PRO* 3.4 15.0 - - + +
181D VAL* 5.5 0.4 - - + -
205D LEU* 4.4 1.6 - - + -
207D ILE* 3.5 32.5 - - + -
282D LEU* 2.8 29.3 + - + +
283D SER* 3.8 3.8 - - - +
285D ALA* 1.3 73.7 - - - +
287D HIS* 1.3 58.6 + - - +
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Residues in contact with HIS 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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137D ARG* 3.3 9.4 + - - -
168D THR* 3.8 23.8 - - + -
172D LYS* 3.0 33.4 + - + +
175D SER* 3.3 51.6 - - - -
178D GLY* 3.8 4.2 - - - -
179D PRO 2.9 30.8 + - - -
180D ARG* 4.4 3.4 - - - -
181D VAL* 3.6 29.7 - - + +
283D SER 3.0 18.2 + - - +
284D ILE 3.6 3.4 - - - +
286D LEU* 1.3 79.0 - - - +
288D VAL* 1.3 64.9 + - + +
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Residues in contact with VAL 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D ARG* 3.8 7.0 + - - -
168D THR* 5.5 2.0 - - - -
171D LEU* 3.7 40.8 - - + +
174D TYR* 3.4 21.4 - - + +
284D ILE* 2.9 38.8 + - + +
287D HIS* 1.3 89.4 - - + +
289D GLY* 1.3 63.4 + - - +
292D ASN* 2.9 46.5 + - + +
293D PHE 4.4 3.4 - - - +
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Residues in contact with GLY 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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137D ARG* 3.3 28.7 - - - +
285D ALA 2.8 17.1 + - - +
288D VAL* 1.3 82.5 - - - +
290D PHE* 1.3 66.3 + - - -
291D ASP* 3.3 3.6 - - - -
292D ASN 3.2 4.1 + - - -
293D PHE* 3.1 17.7 + - - +
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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