Contacts of the helix formed by residues 328 - 343 (chain A) in PDB entry 3I5G
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 ASP 328 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327A ILE* 1.3 73.8 - - - +
329A ASP* 1.3 68.4 + - - +
330A GLU* 3.7 24.1 + - - +
331A GLU* 3.3 25.4 + - + +
332A GLU* 3.0 28.5 + - - +
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Residues in contact with ASP 329 (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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285A ARG* 3.1 28.6 + - - -
288A HIS* 4.8 1.2 + - - +
291A TYR* 3.4 32.5 - - - +
292A GLN* 3.8 6.9 + - - +
295A SER* 4.3 7.0 - - - -
323A THR* 3.5 27.0 - - - +
327A ILE* 3.8 13.5 + - - +
328A ASP* 1.3 72.4 + - - +
330A GLU* 1.3 54.4 + - - +
332A GLU* 3.0 8.6 + - - +
333A MET* 2.6 36.3 + - - +
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Residues in contact with GLU 330 (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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295A SER* 3.6 12.5 + - - +
296A PRO* 3.4 52.7 - - + +
297A ALA* 4.1 9.6 - - + +
328A ASP* 3.4 12.8 + - - +
329A ASP* 1.3 76.5 - - - +
331A GLU* 1.3 63.5 + - - +
333A MET* 3.3 3.1 + - - +
334A GLY* 2.9 19.4 + - - -
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Residues in contact with GLU 331 (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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328A ASP* 3.3 28.6 + - + +
329A ASP 3.2 0.4 - - - -
330A GLU* 1.3 80.0 - - - +
332A GLU* 1.3 65.1 + - + +
334A GLY* 3.0 5.1 + - - -
335A LEU* 2.8 45.6 + - + +
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Residues in contact with GLU 332 (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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292A GLN* 3.3 25.2 + - + +
327A ILE* 4.6 17.9 - - + +
328A ASP 3.0 20.7 + - - +
329A ASP* 3.0 8.4 + - - +
331A GLU* 1.3 81.7 - - - +
333A MET* 1.3 55.2 + - - +
334A GLY 2.8 5.1 + - - -
335A LEU* 3.1 20.2 + - - +
336A THR* 2.6 38.7 + - - +
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Residues in contact with MET 333 (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 ILE* 4.2 5.2 - - + +
292A GLN* 3.1 38.5 + - + +
293A LEU* 2.9 58.8 - - + +
295A SER* 3.9 4.3 - - - +
297A ALA* 4.2 4.0 - - + -
298A PHE* 3.8 26.1 - - + +
329A ASP 2.6 19.2 + - - +
330A GLU 3.6 5.2 - - - +
332A GLU* 1.3 71.6 - - - +
334A GLY* 1.3 57.0 + - - +
336A THR* 4.0 3.1 - - + -
337A ASP* 3.1 22.1 + - - +
354A TYR* 4.1 20.2 - - + -
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Residues in contact with GLY 334 (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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298A PHE* 4.1 15.3 - - - -
330A GLU 2.9 13.3 + - - -
331A GLU* 3.2 5.8 - - - -
332A GLU 2.8 2.4 - - - -
333A MET* 1.3 75.4 - - - +
335A LEU* 1.3 59.1 + - - -
337A ASP* 3.0 5.4 + - - +
338A THR* 2.8 31.6 + - - -
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Residues in contact with LEU 335 (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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229A PRO* 4.6 10.3 - - + -
331A GLU* 2.8 37.8 + - + +
332A GLU* 3.9 23.3 - - - +
334A GLY* 1.3 71.9 - - - -
336A THR* 1.3 54.6 + - - +
338A THR* 3.1 12.9 + - + +
339A ALA* 2.7 37.0 + - - +
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Residues in contact with THR 336 (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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229A PRO* 3.9 18.7 + - - +
230A VAL* 3.8 6.0 - - + +
233A ALA* 3.8 22.4 - - + +
234A TYR* 5.6 1.3 - - + -
289A ILE* 5.5 3.6 - - + -
292A GLN* 2.6 33.3 + - - +
332A GLU* 2.6 22.8 + - - +
333A MET* 3.8 5.2 - - + +
335A LEU* 1.3 72.2 - - - +
337A ASP* 1.3 63.9 + - - +
339A ALA* 3.4 3.1 + - - +
340A PHE* 3.0 35.5 + - + +
354A TYR* 4.5 7.2 - - + +
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Residues in contact with ASP 337 (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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298A PHE* 3.1 35.6 - - + -
301A ASN* 5.0 0.2 + - - -
333A MET* 3.1 16.4 + - - +
334A GLY 3.0 4.5 + - - +
336A THR* 1.3 79.9 - - - +
338A THR* 1.3 57.8 + - - +
340A PHE* 2.9 14.0 + - - +
341A ASP* 2.4 26.3 - - - +
350A LYS* 2.6 45.6 + - - -
354A TYR* 3.6 18.6 + - - +
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Residues in contact with THR 338 (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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334A GLY 2.8 18.8 + - - -
335A LEU* 3.6 16.9 - - + +
337A ASP* 1.3 72.6 - - - +
339A ALA* 1.3 63.2 + - - +
341A ASP* 2.9 21.2 + - + +
342A VAL* 3.0 23.5 + - + +
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Residues in contact with ALA 339 (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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226A GLN 3.9 14.8 - - - +
229A PRO* 3.5 28.5 - - + -
230A VAL* 4.4 7.0 - - + -
335A LEU 2.7 20.6 + - - +
336A THR 3.6 2.9 - - - +
338A THR* 1.3 73.6 - - - +
340A PHE* 1.3 58.0 + - - +
342A VAL* 3.0 10.6 + - - +
343A LEU* 2.9 36.1 + - - +
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Residues in contact with PHE 340 (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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230A VAL* 3.8 21.9 - - + +
234A TYR* 4.4 11.2 - + - -
336A THR* 3.0 15.5 + - + +
337A ASP* 2.9 17.5 + - - +
339A ALA* 1.3 76.3 - - - +
341A ASP* 1.3 59.9 + - - +
343A LEU* 4.1 9.1 + - + +
344A GLY 3.9 2.3 + - - -
345A PHE* 3.6 33.7 + + + +
350A LYS* 4.5 21.8 - - + -
353A MET* 3.7 31.6 - - + -
354A TYR* 3.7 35.7 - + - -
440A TRP* 5.8 2.5 - + - -
441A LEU* 4.0 26.0 - - + -
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Residues in contact with ASP 341 (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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337A ASP* 2.4 39.0 - - - +
338A THR* 2.9 10.5 + - + +
340A PHE* 1.3 77.0 - - - +
342A VAL* 1.3 56.6 + - + +
343A LEU 3.2 1.6 - - - -
344A GLY* 2.6 27.6 + - - -
345A PHE 4.6 3.6 - - - +
347A ASP* 3.0 26.2 - - - +
350A LYS* 3.9 7.7 + - - -
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Residues in contact with VAL 342 (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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226A GLN* 3.7 39.5 - - + +
338A THR* 3.0 28.5 + - + +
339A ALA* 3.0 9.8 + - - +
341A ASP* 1.3 72.0 - - + +
343A LEU* 1.3 60.3 + - + +
344A GLY* 2.7 11.3 + - - -
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Residues in contact with LEU 343 (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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226A GLN* 4.3 16.6 - - + +
227A CYS* 3.8 41.3 - - - +
230A VAL* 4.1 24.7 - - + -
339A ALA 2.9 19.7 + - - +
340A PHE* 4.3 9.2 - - + +
342A VAL* 1.3 75.2 - - - +
344A GLY* 1.3 64.5 + - - +
345A PHE* 3.8 18.6 - - + -
441A LEU* 5.8 1.3 - - + -
444A ARG* 6.5 0.2 - - + -
445A VAL* 3.8 21.8 - - + -
448A THR* 2.9 39.2 + - + +
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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