Contacts of the helix formed by residues 325 - 337 (chain A) in PDB entry 3IML
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 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324A VAL* 1.3 80.1 - - - +
326A ASP* 1.3 64.4 + - - +
327A GLU* 3.7 10.7 + - - +
328A THR* 2.7 42.7 + - - -
329A ILE* 3.1 9.4 + - - +
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Residues in contact with ASP 326 (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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315A MET* 5.4 0.8 - - - +
316A VAL 3.0 25.8 - - - +
317A ASN* 3.2 9.0 - - - +
318A THR* 2.8 46.2 + - - +
319A PHE 4.7 0.5 + - - -
320A GLY 5.6 0.6 + - - -
322A GLY* 4.9 0.2 - - - -
324A VAL 3.5 2.4 + - - +
325A SER* 1.3 71.5 - - - +
327A GLU* 1.3 58.6 + - - +
329A ILE* 2.9 11.3 + - - +
330A THR* 2.8 32.2 + - - -
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Residues in contact with GLU 327 (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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325A SER* 3.1 9.4 + - - +
326A ASP* 1.3 78.4 - - - +
328A THR* 1.3 57.4 + - - +
330A THR* 3.2 8.1 + - - -
331A LYS* 2.8 47.7 + - + +
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Residues in contact with THR 328 (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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324A VAL* 3.9 21.1 - - + +
325A SER* 2.7 30.7 + - - -
327A GLU* 1.3 76.0 - - - +
329A ILE* 1.3 57.8 + - - +
331A LYS* 3.4 12.4 + - + +
332A LEU* 2.8 44.0 + - + +
386A ALA* 5.7 3.1 - - - -
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Residues in contact with ILE 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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289A ILE* 3.7 25.4 - - + -
294A LEU* 4.4 31.6 - - + +
316A VAL* 3.6 23.6 - - + -
318A THR* 3.7 26.2 - - + -
322A GLY* 4.6 0.4 - - - -
324A VAL* 3.6 30.5 - - + +
325A SER 3.1 9.6 + - - +
326A ASP* 2.9 10.4 + - - +
328A THR* 1.3 73.9 - - - +
330A THR* 1.3 58.8 - - - +
332A LEU* 3.0 10.1 + - + +
333A VAL* 2.8 32.3 + - + +
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Residues in contact with THR 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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314A VAL* 3.1 36.8 - - + +
315A MET* 4.0 5.8 - - + +
316A VAL* 3.1 31.3 + - - +
326A ASP 2.8 18.9 + - - -
327A GLU* 3.6 10.6 - - - -
329A ILE* 1.3 72.5 - - - +
331A LYS* 1.3 62.1 + - - +
333A VAL* 3.3 11.9 + - - +
334A ARG* 3.4 19.8 + - + +
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Residues in contact with LYS 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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327A GLU* 2.8 40.0 + - + +
328A THR* 3.6 11.2 - - + +
330A THR* 1.3 73.6 - - - +
332A LEU* 1.3 64.7 + - + +
334A ARG* 3.2 16.6 + - - +
335A GLU* 3.2 32.8 + - - +
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Residues in contact with LEU 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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294A LEU* 4.0 25.8 - - + -
328A THR* 2.8 32.4 + - + +
329A ILE* 3.0 12.1 + - + +
331A LYS* 1.3 78.7 - - + +
333A VAL* 1.3 61.0 + - + +
335A GLU* 3.4 8.9 + - - +
336A HIS* 3.1 38.8 + - + +
382A LEU* 4.2 22.2 - - + +
385A ALA* 4.3 19.7 - - + -
386A ALA* 4.2 17.9 - - + +
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Residues in contact with VAL 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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285A VAL* 3.6 36.3 - - + -
289A ILE* 4.1 9.2 - - + -
300A ILE* 4.0 12.3 - - + -
314A VAL* 4.4 6.3 - - + -
316A VAL* 4.0 18.4 - - + -
329A ILE* 2.8 19.7 + - + +
330A THR* 3.5 9.4 - - - +
331A LYS 3.2 0.2 - - - -
332A LEU* 1.3 77.7 - - + +
334A ARG* 1.3 58.1 + - - +
337A PHE* 3.0 42.6 + - + +
339A LEU* 4.3 14.8 - - + +
382A LEU* 6.2 1.3 - - + -
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Residues in contact with ARG 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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310A GLU* 2.8 29.7 + - - +
311A PRO* 3.6 27.7 + - - +
312A THR 5.5 0.2 + - - -
313A SER* 5.0 0.6 - - - +
314A VAL* 3.1 46.7 + - + +
330A THR* 3.4 15.0 + - - +
331A LYS* 3.2 10.5 + - - +
333A VAL* 1.3 77.5 - - + +
335A GLU* 1.3 63.1 + - - +
336A HIS 3.3 0.2 - - - -
337A PHE 3.5 13.9 + - - +
339A LEU* 5.4 7.8 - - + +
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Residues in contact with GLU 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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331A LYS* 3.2 35.6 + - - +
332A LEU* 3.8 14.6 - - - +
333A VAL 3.4 0.2 - - - -
334A ARG* 1.3 77.5 - - - +
336A HIS* 1.3 74.9 + - + +
337A PHE 3.7 0.4 - - - -
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Residues in contact with HIS 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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332A LEU* 3.1 28.8 + - + +
334A ARG 3.3 0.2 - - - -
335A GLU* 1.3 90.9 - - + +
337A PHE* 1.3 74.5 + - + +
378A LYS* 3.2 39.6 + - + +
381A ALA* 4.1 28.5 + - + +
382A LEU* 3.8 19.0 - - + +
385A ALA* 4.7 17.7 - - + -
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Residues in contact with PHE 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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284A TYR* 3.5 35.2 - + - -
285A VAL* 3.8 27.8 - - + -
288A ASN* 4.1 22.9 - - + -
333A VAL* 3.0 39.6 + - + +
334A ARG* 3.5 17.5 + - - +
335A GLU 3.7 0.4 - - - -
336A HIS* 1.3 89.7 - - + +
338A ASP* 1.3 60.3 + - - +
339A LEU* 3.6 21.3 + - + +
347A MET* 3.8 9.2 - - - -
378A LYS* 3.5 28.9 - - + -
382A LEU* 4.2 15.0 - - + -
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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