Contacts of the helix formed by residues 282 - 295 (chain D) in PDB entry 1AX4
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 GLU 282 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93D TYR* 3.6 34.4 + - + +
280D ASP 3.2 7.2 + - - +
281D ASN* 1.3 72.0 + - - +
283D GLU* 1.3 58.2 + - - +
285D PHE* 3.4 10.2 - - + +
286D THR* 2.9 41.7 + - - +
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Residues in contact with GLU 283 (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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114D TYR* 3.6 24.2 + - + +
117D LYS* 3.4 31.7 + - - +
281D ASN* 3.2 9.7 + - - +
282D GLU* 1.3 75.1 - - - +
284D ILE* 1.3 64.6 + - - +
286D THR* 3.3 6.9 + - - -
287D LEU* 3.0 32.8 + - + +
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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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107D LEU* 3.9 27.1 - - + -
110D VAL* 4.0 12.9 - - + +
111D LEU* 4.1 16.4 - - + -
114D TYR* 3.4 46.9 - - + -
219D PHE* 4.4 12.1 - - + -
278D ILE* 4.1 12.1 - - + -
281D ASN* 3.1 36.0 + - + +
283D GLU* 1.3 74.4 - - - +
285D PHE* 1.3 52.9 + - - +
287D LEU* 3.2 3.4 + - - +
288D ALA* 2.7 36.9 + - - +
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Residues in contact with PHE 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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78D TYR* 5.2 1.6 - - - -
82D LYS* 6.5 0.4 - - - -
93D TYR* 3.3 52.9 - + + -
94D ILE 3.6 23.1 - - - -
95D ILE* 3.9 13.5 - - + -
278D ILE* 3.6 16.3 - - + +
281D ASN 3.1 10.9 + - - +
282D GLU* 3.4 14.4 - - + +
284D ILE* 1.3 78.7 - - - +
286D THR* 1.3 60.3 + - - +
288D ALA* 3.1 2.4 + - - +
289D ARG* 2.7 84.0 + - - +
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Residues in contact with THR 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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451C TYR* 5.0 11.2 - - - +
282D GLU* 2.9 26.3 + - - +
283D GLU* 3.6 7.9 - - - -
285D PHE* 1.3 82.6 - - - +
287D LEU* 1.3 64.7 + - + +
289D ARG* 3.3 8.8 + - - +
290D GLN* 3.2 43.5 + - + +
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Residues in contact with LEU 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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110D VAL* 3.6 29.5 - - + +
113D LYS* 3.9 30.5 - - + +
114D TYR* 4.4 15.7 - - + -
117D LYS* 3.9 23.8 - - - +
283D GLU* 3.0 31.5 + - + +
284D ILE* 3.7 3.6 - - - +
286D THR* 1.3 78.9 - - + +
288D ALA* 1.3 61.7 + - - +
290D GLN* 3.3 24.5 + - - +
291D ARG* 3.2 16.5 + - - +
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Residues in contact with ALA 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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95D ILE* 3.5 20.9 - - + -
106D ILE* 3.7 19.5 - - + +
107D LEU* 4.7 7.0 - - + -
110D VAL* 3.8 15.4 - - + +
276D VAL* 5.4 0.2 - - + -
278D ILE* 4.5 7.0 - - + -
284D ILE 2.7 22.6 + - - +
285D PHE* 3.5 3.1 - - - +
287D LEU* 1.3 69.7 - - - +
289D ARG* 1.4 62.3 + - - +
291D ARG* 3.0 4.7 + - - +
292D CYS* 2.8 28.4 + - - +
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Residues in contact with ARG 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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38C LEU* 5.9 2.0 - - - +
460C THR* 4.4 19.3 - - - +
78D TYR* 3.2 28.5 + - - -
94D ILE 4.9 2.0 + - - -
95D ILE* 3.7 8.4 - - + +
285D PHE* 2.7 63.6 + - + +
286D THR* 3.5 8.3 - - + +
288D ALA* 1.4 73.1 - - - +
290D GLN* 1.3 61.6 + - + +
292D CYS* 3.2 19.6 + - - +
293D VAL* 3.3 15.6 + - - +
299D VAL* 3.7 43.0 + - + +
300D THR* 5.0 3.0 - - - +
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Residues in contact with GLN 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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453C PRO* 6.1 1.2 - - - +
454C PRO* 4.8 13.9 - - - +
455C VAL* 3.6 36.4 + - + +
456C LEU* 4.0 18.4 - - + +
113D LYS* 5.0 4.3 + - - -
286D THR* 3.2 32.8 + - + +
287D LEU* 3.6 26.2 - - - +
288D ALA 3.2 0.4 - - - -
289D ARG* 1.3 76.5 - - + +
291D ARG* 1.3 58.2 + - - +
293D VAL 3.8 0.3 + - - -
294D PRO* 3.1 23.6 - - - +
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Residues in contact with ARG 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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141C LEU* 5.6 6.5 - - - +
295C MET* 5.6 2.0 - - - +
105D ASN* 2.8 47.6 + - - +
106D ILE* 3.7 18.6 - - - +
109D PRO* 3.5 26.7 - - - +
110D VAL* 4.3 7.4 - - + -
142D ASN* 5.5 0.6 + - - -
287D LEU 3.2 8.3 + - - +
288D ALA 3.0 7.8 + - - +
290D GLN* 1.3 81.1 - - - +
292D CYS* 1.3 64.1 + - - +
294D PRO* 3.2 14.6 - - + +
295D MET* 3.4 44.0 + - + +
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Residues in contact with CYS 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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95D ILE* 3.5 31.9 - - + -
106D ILE* 4.1 16.9 - - + +
288D ALA 2.8 13.8 + - - +
289D ARG* 3.3 13.5 - - - +
291D ARG* 1.3 75.8 - - - +
293D VAL* 1.3 57.4 + - - +
296D GLU* 2.7 44.3 + - - +
297D GLY 3.1 20.1 + - - -
299D VAL* 4.4 9.6 - - + -
302D GLY* 4.3 10.5 - - - -
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Residues in contact with VAL 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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101C ARG* 2.8 38.4 + - - +
134C THR* 5.8 2.7 - - + -
456C LEU* 3.9 23.8 - - + -
459C PHE* 3.8 33.9 - - + -
289D ARG 3.3 14.0 + - - +
290D GLN 4.1 0.2 - - - +
292D CYS* 1.3 75.6 - - - +
294D PRO* 1.3 73.7 - - + +
297D GLY 3.3 9.1 + - - +
298D PHE* 4.7 7.4 - - + -
299D VAL* 3.9 17.0 - - + -
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Residues in contact with PRO 294 (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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101C ARG* 3.3 17.3 - - + +
134C THR* 5.3 5.2 - - + -
137C ALA* 4.4 15.7 - - + -
138C HIS* 2.6 32.1 + - + +
141C LEU* 4.0 30.3 - - + -
456C LEU* 5.0 2.5 - - + -
290D GLN 3.1 23.3 - - - +
291D ARG* 3.2 13.2 - - + +
293D VAL* 1.3 94.5 - - + +
295D MET* 1.3 56.6 + - + +
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Residues in contact with MET 295 (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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98C HIS* 3.4 17.3 - - - -
101C ARG* 4.1 5.0 - - - +
102C GLY* 4.4 4.5 - - - -
105C ASN* 3.6 36.7 + - - +
138C HIS* 3.9 18.2 - - + +
141C LEU* 3.9 21.3 - - + -
291C ARG* 5.6 2.0 - - - +
295C MET* 5.5 0.2 - - - +
296C GLU* 4.4 3.3 - - - +
105D ASN* 3.6 23.8 - - - +
106D ILE* 5.2 2.7 - - + -
291D ARG* 3.4 50.6 + - + +
292D CYS* 3.2 2.3 + - - +
294D PRO* 1.3 79.7 - - + +
296D GLU* 1.3 73.0 + - + +
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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