Contacts of the helix formed by residues 282 - 295 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B TYR* 3.5 33.3 + - + +
280B ASP 3.1 8.0 + - - +
281B ASN* 1.3 72.0 + - - +
283B GLU* 1.3 56.5 + - - +
285B PHE* 3.3 11.0 - - + +
286B THR* 2.8 42.6 + - - +
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Residues in contact with GLU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B TYR* 3.6 25.8 + - + -
117B LYS* 3.4 30.5 + - - +
281B ASN* 3.1 9.7 + - - +
282B GLU* 1.3 75.6 - - - +
284B ILE* 1.3 66.6 + - - +
286B THR* 3.7 6.5 - - - -
287B LEU* 3.0 33.2 + - + +
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Residues in contact with ILE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LEU* 3.9 26.9 - - + -
110B VAL* 3.9 12.2 - - + +
111B LEU* 4.0 17.0 - - + -
114B TYR* 3.4 45.8 - - + -
219B PHE* 4.4 13.9 - - + -
278B ILE* 4.1 12.1 - - + -
281B ASN* 3.1 35.2 + - + +
283B GLU* 1.3 76.7 - - - +
285B PHE* 1.3 53.6 - - - +
287B LEU* 3.3 3.0 + - + +
288B ALA* 2.7 32.9 + - - +
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Residues in contact with PHE 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B TYR* 5.1 1.8 - - - -
82B LYS* 6.5 0.7 - - - -
93B TYR* 3.4 50.3 - + + -
94B ILE 3.5 24.0 - - - -
95B ILE* 3.9 11.4 - - + -
278B ILE* 3.6 15.9 - - + +
281B ASN 3.2 10.0 + - - +
282B GLU* 3.3 16.4 - - + +
284B ILE* 1.3 80.2 - - - +
286B THR* 1.3 58.0 - - - +
288B ALA* 3.1 2.1 + - - +
289B ARG* 2.7 83.5 + - - +
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Residues in contact with THR 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A PRO* 6.4 2.2 - - + -
456A LEU* 6.4 0.9 - - + -
282B GLU* 2.8 28.4 + - - +
283B GLU* 3.7 8.0 - - - -
285B PHE* 1.3 81.0 - - - +
287B LEU* 1.4 65.7 + - + +
289B ARG* 3.3 9.1 + - - +
290B GLN* 3.1 44.4 + - - +
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B VAL* 3.5 33.1 - - + +
113B LYS* 4.0 31.2 - - + +
114B TYR* 4.4 16.6 - - + +
117B LYS* 4.0 22.7 - - - +
283B GLU* 3.0 30.9 + - + +
284B ILE* 4.8 0.2 - - - -
286B THR* 1.4 79.1 - - + +
288B ALA* 1.4 63.8 + - - +
290B GLN* 3.3 24.3 + - - +
291B ARG* 3.2 16.6 + - - +
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ILE* 3.5 22.2 - - + -
106B ILE* 3.6 23.0 - - + +
107B LEU* 4.6 7.6 - - + -
110B VAL* 3.8 14.5 - - + +
276B VAL* 5.4 0.2 - - + -
278B ILE* 4.5 7.2 - - + -
284B ILE 2.7 22.5 + - - +
285B PHE* 3.6 1.6 - - - +
287B LEU* 1.4 73.8 - - - +
289B ARG* 1.3 59.2 + - - +
291B ARG* 3.2 1.9 + - - -
292B CYS* 2.9 27.9 + - - +
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Residues in contact with ARG 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 5.8 5.7 - - - +
456A LEU* 5.1 14.0 - - + +
460A THR* 5.3 11.5 - - - +
78B TYR* 3.2 28.3 + - - -
94B ILE 4.9 1.6 + - - -
95B ILE* 3.7 13.6 - - + +
285B PHE* 2.7 56.4 + - + +
286B THR* 3.5 8.5 - - - +
287B LEU 3.2 0.2 - - - -
288B ALA* 1.3 74.1 - - - +
290B GLN* 1.3 61.3 + - + +
292B CYS* 3.3 14.6 + - - +
293B VAL* 3.4 20.5 + - - +
299B VAL* 3.6 43.9 + - + +
300B THR* 5.0 2.8 - - - +
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Residues in contact with GLN 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A PRO* 5.4 9.5 - - - +
455A VAL* 5.1 18.8 - - + +
456A LEU* 4.5 35.0 - - + +
113B LYS* 5.1 4.3 + - - -
286B THR* 3.1 32.7 + - + +
287B LEU* 3.6 25.3 - - - +
288B ALA 3.3 0.2 - - - -
289B ARG* 1.3 76.8 - - + +
291B ARG* 1.3 59.3 + - - +
293B VAL* 3.9 2.0 + - - +
294B PRO* 3.1 23.0 - - - +
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Residues in contact with ARG 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A LEU* 5.6 6.9 - - - +
295A MET* 5.7 2.0 - - - +
105B ASN* 2.7 47.2 + - - +
106B ILE* 3.8 19.1 - - - +
109B PRO* 3.5 27.2 - - - +
110B VAL* 4.3 6.5 - - + -
142B ASN* 5.4 0.8 + - - +
287B LEU 3.2 8.5 + - - +
288B ALA 3.2 7.9 + - - +
290B GLN* 1.3 81.2 - - - +
292B CYS* 1.3 65.1 + - - +
294B PRO* 3.2 13.7 - - + +
295B MET* 3.3 44.2 + - + +
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Residues in contact with CYS 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ILE* 3.5 31.9 - - + -
106B ILE* 4.0 17.6 - - + +
288B ALA 2.9 13.9 + - - +
289B ARG* 3.4 12.3 - - - +
291B ARG* 1.3 76.0 - - - +
293B VAL* 1.3 59.0 + - - +
296B GLU* 2.8 43.1 + - - +
297B GLY 3.1 19.3 + - - -
299B VAL* 4.4 9.4 - - + -
302B GLY* 4.3 10.5 - - - -
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Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ARG* 2.9 37.2 + - - +
134A THR* 5.9 2.5 - - + -
456A LEU* 4.2 18.8 - - + -
459A PHE* 4.2 26.9 - - + -
289B ARG 3.4 15.8 + - - +
290B GLN 4.2 2.0 - - - +
291B ARG 3.3 0.2 - - - -
292B CYS* 1.3 76.4 - - - +
294B PRO* 1.3 71.2 - - + +
297B GLY 3.4 9.0 + - - +
298B PHE* 4.8 5.8 - - + -
299B VAL* 3.9 18.4 - - + +
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Residues in contact with PRO 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ARG* 3.4 16.0 - - + +
134A THR* 5.3 5.2 - - + -
137A ALA* 4.4 16.2 - - + -
138A HIS* 2.6 31.8 + - + +
141A LEU* 4.0 29.6 - - + -
290B GLN 3.1 23.1 - - - +
291B ARG* 3.2 11.2 - - + +
293B VAL* 1.3 95.6 - - + +
295B MET* 1.3 58.1 + - + +
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Residues in contact with MET 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A HIS* 3.5 15.8 - - - -
101A ARG* 4.1 4.8 - - - +
102A GLY* 4.5 4.2 - - - -
105A ASN* 3.5 30.6 + - - +
138A HIS* 3.9 11.2 - - + +
141A LEU* 3.8 29.8 - - + -
291A ARG* 5.6 2.0 - - - +
295A MET* 5.5 0.2 - - - +
296A GLU* 4.4 3.8 - - - +
105B ASN* 3.5 30.7 - - - +
106B ILE* 5.2 2.9 - - + -
291B ARG* 3.3 49.3 + - + +
292B CYS* 3.2 2.0 + - - +
294B PRO* 1.3 82.4 - - + +
296B GLU* 1.3 71.2 + - + +
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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