Contacts of the helix formed by residues 324 - 336 (chain A) in PDB entry 1IK2
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 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321A ALA 5.2 0.8 + - - +
322A SER 4.2 0.4 - - - -
323A ILE* 1.3 70.9 - - - +
325A ASP* 1.3 66.8 + - - +
326A ALA* 3.2 17.7 + - - +
327A GLU* 3.5 38.6 + - - +
328A GLU* 3.2 22.2 + - - +
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Residues in contact with ASP 325 (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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281A ARG* 3.8 18.4 + - - -
284A HIS* 5.2 2.1 + - - +
287A TYR* 3.4 20.3 - - - +
288A GLN* 3.6 23.9 - - - +
291A SER* 2.8 37.9 + - - +
318A THR 5.3 0.3 - - - +
319A THR* 5.0 11.9 - - - +
323A ILE* 3.7 8.8 + - - +
324A ASP* 1.3 75.1 + - - +
326A ALA* 1.3 64.9 + - - +
328A GLU* 3.0 15.5 + - - +
329A LEU* 3.1 11.4 + - - +
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Residues in contact with ALA 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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288A GLN 6.0 0.7 - - - -
293A LYS* 5.4 11.0 - - + +
324A ASP* 3.2 12.4 + - - +
325A ASP* 1.3 80.6 - - - +
327A GLU* 1.3 62.3 + - + +
329A LEU* 4.0 7.6 - - - +
330A MET* 3.7 23.7 + - - +
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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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323A ILE* 5.7 0.2 - - - -
324A ASP* 3.5 37.3 + - - +
325A ASP 3.1 0.4 - - - -
326A ALA* 1.3 80.3 - - + +
328A GLU* 1.3 78.1 + - - +
330A MET* 3.8 4.3 + - - +
331A ALA* 3.1 25.1 + - - +
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Residues in contact with GLU 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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225A PRO* 5.3 0.3 - - - +
229A ALA* 5.3 4.2 - - + +
284A HIS* 5.4 5.8 - - + -
288A GLN* 3.3 21.0 + - - +
323A ILE* 3.5 27.0 - - + +
324A ASP 3.2 23.0 + - - +
325A ASP* 3.0 5.3 + - - +
327A GLU* 1.3 94.0 - - - +
329A LEU* 1.3 61.2 + - - +
331A ALA* 3.1 11.1 + - + +
332A THR* 2.9 31.5 + - - -
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Residues in contact with LEU 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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288A GLN* 3.2 47.2 - - + +
289A ILE* 3.8 8.5 - - - +
293A LYS* 3.6 42.6 - - + +
297A LEU* 4.0 15.9 - - + -
325A ASP 3.1 13.3 + - - +
326A ALA* 4.2 6.5 - - - +
327A GLU 3.3 0.2 - - - -
328A GLU* 1.3 79.6 - - - +
330A MET* 1.3 63.6 + - - +
332A THR* 3.2 10.9 + - - -
333A ASP* 3.3 11.2 + - + +
348A SER 4.5 6.7 - - - +
350A TYR* 3.3 26.8 + - + +
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Residues in contact with MET 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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293A LYS* 3.5 28.3 - - - +
326A ALA 3.7 15.5 + - - +
327A GLU* 3.9 4.9 - - - +
329A LEU* 1.3 78.9 - - - +
331A ALA* 1.3 61.6 + - - +
333A ASP* 3.1 26.1 + - - +
334A ASN* 3.2 22.2 + - - +
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Residues in contact with ALA 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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225A PRO* 3.5 29.1 - - + +
327A GLU 3.1 19.7 + - - +
328A GLU* 3.1 15.6 + - + +
330A MET* 1.3 75.1 - - - +
332A THR* 1.3 64.4 + - - +
334A ASN* 3.1 18.3 + - - +
335A ALA 3.4 10.6 + - - -
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Residues in contact with THR 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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225A PRO* 3.5 22.6 - - - +
229A ALA* 3.9 14.1 - - + +
230A PHE* 4.7 0.9 - - + -
285A ILE* 4.0 13.5 - - + -
288A GLN* 3.8 5.2 + - - -
328A GLU 2.9 16.5 + - - -
329A LEU 3.2 2.6 + - - -
331A ALA* 1.3 76.6 - - - +
333A ASP* 1.3 58.8 + - - +
334A ASN 3.1 7.8 + - - +
335A ALA* 3.7 10.7 - - - +
336A PHE* 4.0 21.4 - - + -
346A LYS* 3.3 15.2 - - - +
350A TYR* 3.1 24.4 + - + -
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Residues in contact with ASP 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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293A LYS* 5.1 5.1 + - - +
329A LEU* 3.3 9.5 + - + +
330A MET* 3.1 26.5 + - - +
331A ALA 3.1 0.8 - - - -
332A THR* 1.3 75.0 - - - +
334A ASN* 1.3 66.5 + - - +
337A ASP* 4.8 7.3 - - - +
346A LYS* 3.7 19.9 + - - +
348A SER* 3.9 26.3 - - - +
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Residues in contact with ASN 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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222A GLN* 3.9 15.5 + - - +
225A PRO* 5.9 0.9 - - + -
330A MET* 3.3 18.0 + - - +
331A ALA* 3.1 12.0 + - - +
332A THR 3.6 1.4 - - - +
333A ASP* 1.3 82.9 + - - +
335A ALA* 1.3 69.7 + - - +
336A PHE 3.0 3.5 + - - -
337A ASP* 3.3 12.3 + - - +
338A VAL* 3.6 17.8 - - + +
346A LYS* 5.2 0.2 - - - -
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Residues in contact with ALA 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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222A GLN* 3.6 34.6 + - - +
225A PRO* 4.1 2.9 - - + +
226A ALA* 3.7 23.6 - - + +
331A ALA 3.4 8.5 + - - +
332A THR 3.7 11.7 - - - +
334A ASN* 1.3 76.3 - - - +
336A PHE* 1.3 68.1 + - + +
338A VAL* 3.2 13.7 + - - +
339A LEU* 3.2 20.4 + - - +
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Residues in contact with PHE 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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226A ALA* 3.7 37.2 - - + -
230A PHE* 4.2 10.3 - + - -
332A THR* 4.0 26.9 - - + -
334A ASN 3.0 2.2 + - - -
335A ALA* 1.3 77.7 - - + +
337A ASP* 1.3 67.8 + - - +
339A LEU* 3.0 16.7 + - - +
340A GLY 3.1 9.9 + - - -
341A PHE* 3.2 53.1 + + + +
345A GLU 5.6 0.9 - - - -
346A LYS* 4.2 26.2 - - + -
439A MET* 3.5 43.5 - - + -
443A ILE* 4.6 4.9 - - + -
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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