Contacts of the helix formed by residues 282 - 295 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A TYR* 3.5 36.1 + - + +
280A ASP 3.2 6.9 + - - +
281A ASN* 1.3 72.9 + - - +
283A GLU* 1.3 57.2 + - - +
285A PHE* 3.3 9.9 + - + +
286A THR* 2.8 42.5 + - - +
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Residues in contact with GLU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A TYR* 3.6 25.1 + - + -
117A LYS* 3.4 31.2 + - - +
281A ASN* 3.2 9.3 + - - +
282A GLU* 1.3 75.1 - - - +
284A ILE* 1.3 65.4 + - - +
286A THR* 3.3 6.5 + - - -
287A LEU* 3.0 32.4 + - + +
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Residues in contact with ILE 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU* 3.9 27.6 - - + -
110A VAL* 4.0 11.7 - - + +
111A LEU* 4.2 17.7 - - + -
114A TYR* 3.4 45.8 - - + -
219A PHE* 4.5 12.8 - - + -
278A ILE* 4.1 12.8 - - + -
281A ASN* 3.0 35.0 + - + +
283A GLU* 1.3 74.8 - - - +
285A PHE* 1.3 52.9 + - - +
287A LEU* 3.2 2.7 + - + +
288A ALA* 2.7 37.8 + - - +
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Residues in contact with PHE 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A TYR* 5.2 1.3 - - - -
82A LYS* 6.6 0.2 - - - -
93A TYR* 3.4 51.1 - + + -
94A ILE 3.6 23.6 - - - -
95A ILE* 3.9 15.3 - - + -
278A ILE* 3.6 15.7 - - + +
281A ASN 3.1 10.3 + - - +
282A GLU* 3.3 13.5 - - + +
284A ILE* 1.3 79.6 - - - +
286A THR* 1.3 63.9 + - - +
288A ALA* 3.1 1.6 + - - +
289A ARG* 2.8 76.9 + - - +
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Residues in contact with THR 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A GLU* 2.8 29.3 + - - +
283A GLU* 3.8 7.4 - - - -
284A ILE 3.3 0.2 - - - -
285A PHE* 1.3 78.8 - - - +
287A LEU* 1.3 64.9 + - + +
289A ARG* 3.3 9.9 + - + +
290A GLN* 3.1 43.8 + - + +
451B TYR* 4.9 12.3 - - - +
454B PRO* 6.4 1.1 - - + -
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A VAL* 3.6 31.8 - - + +
113A LYS* 3.9 31.2 - - + +
114A TYR* 4.4 16.2 - - + -
117A LYS* 3.9 22.7 - - - +
283A GLU* 3.0 31.5 + - + +
284A ILE* 3.8 0.4 - - - +
286A THR* 1.3 79.1 - - + +
288A ALA* 1.3 63.1 + - - +
290A GLN* 3.2 24.8 + - - +
291A ARG* 3.2 16.5 + - - +
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ILE* 3.4 23.3 - - + -
106A ILE* 3.7 20.1 - - + +
107A LEU* 4.7 7.2 - - + -
110A VAL* 3.9 14.6 - - + +
276A VAL* 5.3 0.4 - - + -
278A ILE* 4.5 6.7 - - + -
284A ILE 2.7 21.9 + - - +
285A PHE* 3.6 2.2 - - - +
287A LEU* 1.3 73.1 - - - +
289A ARG* 1.3 58.3 + - - +
291A ARG* 3.1 2.8 + - - -
292A CYS* 2.8 28.1 + - - +
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Residues in contact with ARG 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A TYR* 3.3 28.7 + - - -
94A ILE 5.0 1.6 + - - -
95A ILE* 4.1 8.3 - - + -
285A PHE* 2.8 58.1 + - + +
286A THR* 3.5 9.4 - - + +
288A ALA* 1.3 78.1 - - - +
290A GLN* 1.3 62.2 + - + +
292A CYS* 3.2 16.6 + - - +
293A VAL* 3.3 19.3 + - - +
299A VAL* 3.5 44.3 + - + +
300A THR* 4.8 3.2 - - - +
38B LEU* 5.5 4.6 - - - +
460B THR* 4.3 21.2 - - - +
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Residues in contact with GLN 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LYS* 5.1 4.2 + - - -
286A THR* 3.1 32.8 + - + +
287A LEU* 3.2 26.6 + - - +
289A ARG* 1.3 76.8 - - + +
291A ARG* 1.3 59.3 + - - +
293A VAL* 5.0 0.2 - - - -
294A PRO* 3.1 23.9 - - - +
453B PRO* 5.4 3.6 - - - +
454B PRO* 4.9 12.9 - - - +
455B VAL* 3.1 37.1 + - + +
456B LEU* 3.7 21.5 - - + +
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Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ASN* 2.7 49.9 + - - +
106A ILE* 3.7 17.3 - - - +
109A PRO* 3.5 27.3 - - - +
110A VAL* 4.3 7.6 - - + -
142A ASN* 5.5 0.8 + - - -
287A LEU 3.2 8.0 + - - +
288A ALA 3.1 8.0 + - - +
290A GLN* 1.3 79.3 - - - +
292A CYS* 1.3 65.2 + - - +
294A PRO* 3.2 13.5 - - + +
295A MET* 3.4 43.3 + - + +
141B LEU* 5.7 6.1 - - - +
295B MET* 5.6 2.4 - - - +
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Residues in contact with CYS 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ILE* 3.6 31.6 - - + -
106A ILE* 4.0 16.1 - - + +
288A ALA 2.8 13.6 + - - +
289A ARG* 3.2 13.0 + - - +
291A ARG* 1.3 78.0 - - - +
293A VAL* 1.3 57.1 + - - +
296A GLU* 2.8 43.4 + - - +
297A GLY 3.1 20.4 + - - -
299A VAL* 4.4 10.1 - - + -
302A GLY* 4.2 10.8 - - - -
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Residues in contact with VAL 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A ARG 3.3 14.1 + - - +
290A GLN* 5.0 0.2 - - - -
292A CYS* 1.3 78.0 - - - +
294A PRO* 1.3 70.9 - - + +
297A GLY 3.3 8.9 + - - +
298A PHE* 4.8 7.2 - - + -
299A VAL* 4.0 16.6 - - + -
101B ARG* 2.7 35.8 + - - +
134B THR* 5.9 2.2 - - + -
456B LEU* 4.0 17.5 - - + -
459B PHE* 3.3 45.3 - - + -
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Residues in contact with PRO 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A GLN 3.1 23.3 - - - +
291A ARG* 3.2 13.5 - - + +
293A VAL* 1.3 94.3 - - + +
295A MET* 1.3 59.1 + - + +
101B ARG* 3.2 17.6 - - + +
134B THR* 5.3 5.4 - - + -
137B ALA* 4.5 15.0 - - + -
138B HIS* 2.8 31.3 + - + +
141B LEU* 4.1 24.2 - - + -
456B LEU* 4.7 3.8 - - + -
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Residues in contact with MET 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ASN* 3.6 23.3 - - - +
106A ILE* 5.2 2.7 - - + -
291A ARG* 3.4 48.9 + - + +
292A CYS* 3.3 1.6 + - - -
294A PRO* 1.3 81.1 - - + +
296A GLU* 1.3 72.2 + - + +
98B HIS* 3.4 17.5 - - - -
101B ARG* 4.2 4.6 - - - +
102B GLY* 4.5 4.0 - - - -
105B ASN* 3.5 37.7 + - - +
138B HIS* 3.9 19.1 - - + +
141B LEU* 3.9 21.1 - - + -
291B ARG* 5.7 1.3 - - - +
296B GLU* 4.4 3.8 - - - +
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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