Contacts of the helix formed by residues 282 - 295 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93C TYR* 3.6 33.3 + - + +
280C ASP 3.1 6.2 + - - +
281C ASN* 1.3 73.1 + - - +
283C GLU* 1.3 58.3 + - - +
285C PHE* 3.3 9.8 + - + +
286C THR* 2.8 41.7 + - - +
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Residues in contact with GLU 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C TYR* 3.6 25.3 + - + -
117C LYS* 3.4 30.5 + - - +
281C ASN* 3.2 8.9 + - - +
282C GLU* 1.3 79.0 - - - +
284C ILE* 1.3 62.5 + - - +
286C THR* 3.4 6.9 + - - -
287C LEU* 3.0 32.6 + - + +
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Residues in contact with ILE 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C LEU* 3.9 28.0 - - + -
110C VAL* 4.0 12.1 - - + +
111C LEU* 4.2 17.5 - - + -
114C TYR* 3.4 47.3 - - + -
219C PHE* 4.5 13.0 - - + -
278C ILE* 4.1 11.9 - - + -
281C ASN* 3.0 35.1 + - + +
283C GLU* 1.3 73.7 - - - +
285C PHE* 1.3 53.0 + - - +
287C LEU* 3.2 3.0 + - + +
288C ALA* 2.7 37.2 + - - +
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Residues in contact with PHE 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C TYR* 5.1 1.3 - - - -
82C LYS* 6.5 0.9 - - - -
93C TYR* 3.4 50.5 - + + -
94C ILE 3.5 23.6 - - - -
95C ILE* 3.9 13.7 - - + -
278C ILE* 3.6 17.8 - - + +
281C ASN 3.1 13.5 + - - +
282C GLU* 3.3 13.7 - - + +
284C ILE* 1.3 77.2 - - - +
286C THR* 1.3 62.7 + - - +
288C ALA* 3.1 2.6 + - - +
289C ARG* 2.8 77.9 + - - +
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Residues in contact with THR 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282C GLU* 2.8 28.4 + - - +
283C GLU* 3.7 8.0 - - - -
284C ILE 3.3 0.2 - - - -
285C PHE* 1.3 79.5 - - - +
287C LEU* 1.3 62.9 + - + +
289C ARG* 3.3 9.2 + - - +
290C GLN* 3.1 40.5 + - + +
451D TYR* 6.0 1.8 - - - +
456D LEU* 5.1 1.2 - - + +
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Residues in contact with LEU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C VAL* 3.5 33.1 - - + +
113C LYS* 4.0 30.3 - - + +
114C TYR* 4.4 15.7 - - + -
117C LYS* 3.9 24.2 - - - +
283C GLU* 3.0 33.2 + - + +
284C ILE* 4.9 0.2 - - - -
286C THR* 1.3 78.4 - - + +
288C ALA* 1.3 63.2 + - - +
290C GLN* 3.3 25.1 + - - +
291C ARG* 3.2 16.8 + - - +
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Residues in contact with ALA 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ILE* 3.4 21.8 - - + -
106C ILE* 3.5 22.2 - - + +
107C LEU* 4.7 7.0 - - + -
110C VAL* 3.8 16.3 - - + +
276C VAL* 5.3 0.4 - - + -
278C ILE* 4.5 7.2 - - + -
284C ILE 2.7 22.3 + - - +
285C PHE* 3.6 1.8 - - - +
287C LEU* 1.3 71.6 - - - +
289C ARG* 1.3 58.8 + - - +
291C ARG* 3.2 2.1 + - - -
292C CYS* 2.8 28.2 + - - +
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Residues in contact with ARG 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C TYR* 3.2 28.7 + - - -
94C ILE 5.0 1.6 + - - -
95C ILE* 3.7 8.4 - - + +
285C PHE* 2.8 54.5 + - + +
286C THR* 3.5 10.8 - - - +
288C ALA* 1.3 77.6 - - - +
290C GLN* 1.4 62.2 + - - +
292C CYS* 3.1 17.5 + - - +
293C VAL* 3.3 17.8 + - - +
299C VAL* 3.6 44.7 + - + +
300C THR* 4.9 2.6 - - - +
38D LEU* 5.9 2.2 - - - +
456D LEU* 4.1 10.8 - - + -
460D THR* 4.3 21.0 - - - +
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Residues in contact with GLN 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C LYS* 5.1 4.2 + - - -
286C THR* 3.1 33.6 + - + +
287C LEU* 3.6 26.0 - - - +
288C ALA 3.3 0.2 - - - -
289C ARG* 1.4 75.2 - - - +
291C ARG* 1.3 58.8 + - - +
293C VAL* 3.7 2.3 + - - +
294C PRO* 3.0 24.6 - - - +
454D PRO* 4.9 10.9 - - - +
455D VAL* 3.6 38.9 + - + +
456D LEU* 3.8 18.6 - - + +
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Residues in contact with ARG 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ASN* 2.8 48.0 + - - +
106C ILE* 3.7 18.6 - - - +
109C PRO* 3.5 27.5 - - - +
110C VAL* 4.4 6.5 - - + -
142C ASN* 5.4 1.0 + - - -
287C LEU 3.2 8.7 + - - +
288C ALA 3.2 7.9 + - - +
290C GLN* 1.3 80.0 - - - +
292C CYS* 1.3 66.0 + - - +
294C PRO* 3.2 13.3 - - + +
295C MET* 3.4 43.7 + - + +
141D LEU* 5.7 6.1 - - - +
295D MET* 5.6 2.4 - - - +
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Residues in contact with CYS 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ILE* 3.6 31.2 - - + -
106C ILE* 4.0 16.1 - - + +
288C ALA 2.8 16.9 + - - +
289C ARG* 3.1 13.0 + - - +
291C ARG* 1.3 71.7 - - - +
293C VAL* 1.3 64.3 + - - +
296C GLU* 2.8 39.2 + - - -
297C GLY 3.1 21.4 + - - -
298C PHE 4.4 2.9 - - - -
299C VAL* 4.3 6.7 - - + -
302C GLY* 4.2 10.8 - - - -
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Residues in contact with VAL 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289C ARG 3.3 13.0 + - - +
290C GLN 4.0 2.5 - - - +
292C CYS* 1.3 76.9 - - - +
294C PRO* 1.3 70.2 - - + +
297C GLY 3.4 9.3 + - - +
298C PHE* 4.7 5.8 - - + -
299C VAL* 3.9 18.2 - - + -
101D ARG* 2.8 38.5 + - - +
134D THR* 6.0 2.2 - - + -
456D LEU* 3.8 22.4 - - + -
459D PHE* 4.0 27.4 - - + -
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Residues in contact with PRO 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C GLN 3.0 24.0 - - - +
291C ARG* 3.2 13.5 - - + +
293C VAL* 1.3 94.3 - - + +
295C MET* 1.3 57.3 + - + +
101D ARG* 3.3 16.0 - - + +
134D THR* 5.4 5.8 - - + -
137D ALA* 4.6 15.3 - - + -
138D HIS* 2.7 31.9 + - + +
141D LEU* 4.1 28.5 - - + -
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Residues in contact with MET 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ASN* 3.6 24.5 - - - +
106C ILE* 5.2 2.7 - - + -
291C ARG* 3.4 51.0 + - + +
292C CYS 3.2 1.8 + - - +
294C PRO* 1.3 79.5 - - + +
296C GLU* 1.3 70.9 + - + +
98D HIS* 3.4 16.6 - - - -
101D ARG* 4.1 5.6 - - - +
102D GLY* 4.4 4.2 - - - -
105D ASN* 3.5 37.6 + - - +
138D HIS* 3.9 17.7 - - + +
141D LEU* 4.0 21.5 - - + -
291D ARG* 5.6 1.6 - - - +
295D MET* 5.5 0.2 - - - +
296D GLU* 4.4 4.0 - - - +
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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