Contacts of the helix formed by residues 311 - 323 (chain B) in PDB entry 1IAX
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 SER 311 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284A GLY 3.6 10.4 + - - -
285A PHE* 3.7 19.5 - - - -
286A ARG* 5.0 0.9 - - - +
311A SER* 4.0 12.2 - - - -
314A THR* 2.7 28.2 + - - -
285B PHE 5.3 0.2 + - - -
309B LEU 3.7 2.0 + - - -
310B VAL* 1.3 75.1 - - - +
312B THR* 1.3 55.1 + - - +
313B GLN 3.5 6.8 + - - -
314B THR* 2.6 36.4 + - - -
315B GLN* 2.6 18.6 + - - +
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Residues in contact with THR 312 (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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284A GLY* 2.7 25.7 + - - +
285A PHE* 3.4 8.1 - - - -
86B ILE* 2.7 37.9 + - - +
89B PHE* 3.4 35.2 - - + +
90B GLN* 5.4 0.4 - - - -
95B LEU* 4.4 4.4 - - + +
310B VAL 3.3 2.2 + - - +
311B SER* 1.3 70.2 - - - +
313B GLN* 1.3 57.9 + - - +
315B GLN* 3.5 20.8 - - - +
316B TYR* 2.8 32.9 + - - +
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Residues in contact with GLN 313 (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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74A SER* 4.2 14.6 - - - -
285A PHE* 3.8 26.2 - - + -
313A GLN* 3.1 41.2 - - - +
314A THR* 2.8 39.6 + - - +
317A PHE* 4.2 9.6 - - - +
74B SER* 5.6 4.4 - - - -
75B ILE 5.8 8.0 - - - +
86B ILE* 5.1 9.4 - - + -
311B SER* 3.0 4.4 + - - +
312B THR* 1.3 82.9 + - - +
314B THR* 1.3 56.6 + - - +
316B TYR* 3.7 7.0 - - - +
317B PHE* 3.1 20.1 + - - +
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Residues in contact with THR 314 (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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311A SER* 2.9 26.6 + - - +
313A GLN* 3.0 15.8 + - - +
314A THR* 4.3 0.9 + - - -
285B PHE* 3.3 49.6 - - + +
310B VAL* 4.0 8.5 - - + -
311B SER* 2.6 17.0 + - - -
313B GLN* 1.3 72.4 - - - +
315B GLN* 1.3 59.0 + - - -
317B PHE* 3.1 2.0 + - - +
318B LEU* 2.8 38.0 + - + +
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Residues in contact with GLN 315 (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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89B PHE* 5.7 0.8 - - - -
91B ASP 5.7 0.2 + - - -
94B GLY* 3.2 7.5 - - - -
95B LEU* 2.9 37.8 + - + +
98B PHE* 3.8 31.2 - - + +
123B MET* 3.5 23.9 - - - +
309B LEU* 5.5 1.0 - - - +
310B VAL* 2.9 36.2 + - + +
311B SER 2.6 15.7 + - - +
312B THR* 3.5 22.5 - - - +
314B THR* 1.3 72.8 - - - +
316B TYR* 1.3 53.7 + - - +
318B LEU* 3.0 3.3 + - - +
319B ALA* 2.8 36.1 + - - +
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Residues in contact with TYR 316 (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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73B GLY 3.2 26.8 + - - -
74B SER* 4.7 5.2 - - - -
75B ILE* 4.2 15.8 - - + +
82B SER* 3.7 24.0 + - - -
86B ILE* 3.6 35.9 - - + -
95B LEU* 3.9 14.9 - - + +
312B THR 2.8 17.2 + - - +
313B GLN 3.7 4.9 - - - +
315B GLN* 1.3 75.6 - - - +
317B PHE* 1.3 64.6 + - - +
319B ALA* 3.8 5.1 - - + +
320B ALA* 3.3 24.2 + - + +
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Residues in contact with PHE 317 (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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75A ILE 5.4 1.3 - - - -
83A PHE* 4.8 5.8 - + - -
313A GLN* 3.9 13.9 - - - +
63B ILE* 4.9 0.4 - - + -
66B TRP* 4.5 11.6 - + - -
67B ILE* 3.8 45.1 - - + -
72B LYS 4.8 2.0 - - - -
73B GLY* 5.0 1.0 - - - -
74B SER* 3.8 29.6 - - - +
282B LEU* 5.2 1.1 - - + -
285B PHE* 3.7 28.7 - + - -
313B GLN 3.1 12.6 + - - +
314B THR* 3.1 8.5 + - - +
316B TYR* 1.3 84.7 - - - +
318B LEU* 1.3 63.7 + - + +
320B ALA* 3.8 4.0 + - - +
321B MET* 3.1 49.6 + - + +
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Residues in contact with LEU 318 (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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98B PHE* 3.4 31.0 - - + -
101B ALA* 4.8 1.3 - - - -
276B LEU* 3.7 19.3 - - + -
282B LEU* 4.3 12.3 - - + -
285B PHE* 4.5 2.2 - - + -
287B VAL* 3.6 27.1 - - + -
310B VAL* 5.0 0.9 - - + -
314B THR* 2.8 28.7 + - + +
315B GLN 3.6 2.9 - - - +
317B PHE* 1.3 82.4 - - + +
319B ALA* 1.3 59.9 + - - +
321B MET* 3.1 24.8 + - + +
322B LEU* 2.7 47.0 + - + +
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Residues in contact with ALA 319 (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 LEU* 5.6 2.5 - - + -
97B GLU* 3.5 37.5 - - + -
98B PHE* 3.9 4.4 - - - +
101B ALA* 4.0 14.1 - - - +
315B GLN 2.8 19.9 + - - +
316B TYR* 3.8 9.2 - - + +
318B LEU* 1.3 72.4 - - - +
320B ALA* 1.3 62.4 + - - +
322B LEU 4.0 0.3 - - - -
323B SER* 2.7 30.7 + - - -
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Residues in contact with ALA 320 (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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66B TRP* 3.8 16.0 - - + -
71B PRO* 6.1 2.2 - - + -
73B GLY* 4.5 18.4 - - - +
316B TYR* 3.3 17.7 + - + +
317B PHE 3.9 4.0 - - - +
318B LEU 3.2 0.2 - - - -
319B ALA* 1.3 82.0 - - - +
321B MET* 1.3 63.6 + - - +
323B SER* 3.3 14.3 + - - -
324B ASP* 3.8 4.3 + - - +
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Residues in contact with MET 321 (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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63B ILE* 4.3 15.0 - - + -
66B TRP* 3.2 28.9 - - + -
280B MET* 3.5 35.0 - - + -
282B LEU* 4.2 11.0 - - + -
317B PHE* 3.1 28.2 + - + +
318B LEU* 3.1 25.1 + - + +
320B ALA* 1.3 79.1 - - - +
322B LEU* 1.3 63.6 + - + +
323B SER 3.0 5.2 + - - -
324B ASP* 3.1 18.5 + - - +
327B PHE* 3.3 36.1 - - + -
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Residues in contact with LEU 322 (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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101B ALA* 3.7 25.0 - - + +
102B ILE* 3.9 26.9 - - + -
104B LYS* 5.1 5.5 - - - +
105B PHE* 3.8 39.0 + - + +
276B LEU* 4.7 11.7 - - + -
280B MET* 3.7 30.3 - - + -
318B LEU* 2.7 26.3 + - + +
319B ALA 4.0 0.2 - - - -
321B MET* 1.3 79.8 - - + +
323B SER* 1.3 56.9 + - - +
324B ASP 3.3 0.9 - - - -
325B GLU* 3.6 5.7 - - - +
328B VAL* 3.3 23.9 - - + +
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Residues in contact with SER 323 (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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97B GLU* 5.2 4.3 + - - +
101B ALA* 4.4 7.7 - - - +
319B ALA* 2.7 23.2 + - - +
320B ALA* 3.5 8.3 - - - -
321B MET 3.0 1.4 + - - -
322B LEU* 1.3 77.8 - - - +
324B ASP* 1.3 58.0 + - - +
325B GLU* 2.6 25.4 + - - +
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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