Contacts of the helix formed by residues 305 - 318 (chain A) in PDB entry 3IKM
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 305 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304A LEU* 1.3 73.4 - - - +
306A SER* 1.3 71.5 + - - +
307A PHE* 3.5 10.8 - - - -
308A GLN* 3.0 38.8 + - - -
309A ARG* 3.0 22.1 + - - +
850A ILE* 3.9 17.9 - - - +
1025A LEU* 6.1 0.3 - - - +
1095A SER* 4.2 13.5 - - - -
1099A TRP* 5.0 4.3 - - - -
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Residues in contact with SER 306 (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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304A LEU 4.1 0.2 + - - -
305A SER* 1.3 75.5 - - - +
307A PHE* 1.3 83.4 + - - -
309A ARG* 3.3 14.6 - - - +
310A SER* 3.3 10.7 + - - -
850A ILE* 4.3 9.3 - - - +
1055A SER* 3.9 2.9 + - - -
1059A ASN* 3.9 24.9 + - - -
1099A TRP* 4.9 9.0 - - - -
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Residues in contact with PHE 307 (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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305A SER* 4.8 9.9 - - - -
306A SER* 1.3 87.8 + - - +
308A GLN* 1.3 72.7 + - + +
310A SER* 2.4 25.8 + - - +
311A LEU* 2.9 23.3 - - + +
1048A ALA* 4.2 7.9 - - - -
1051A GLY* 3.4 31.9 - - - -
1052A GLY* 4.0 11.0 - - - -
1055A SER* 2.9 31.2 + - - +
1056A GLU* 5.5 2.0 - - - -
1090A GLU* 3.3 27.1 - - - -
1091A GLU 5.6 0.9 - - - -
1094A THR* 5.4 9.0 - - + -
1095A SER* 4.9 19.3 - - - -
1099A TRP* 5.4 6.3 - + - -
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Residues in contact with GLN 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LEU* 4.2 11.4 - - - +
305A SER* 3.0 46.6 + - - +
307A PHE* 1.3 80.4 - - + +
309A ARG* 1.3 52.1 + - - +
311A LEU* 3.1 13.3 + - - +
312A TRP* 2.7 41.8 + - + +
1025A LEU* 4.5 9.4 - - - +
1090A GLU* 3.1 31.9 - - + +
1091A GLU* 2.3 51.7 - - - +
1095A SER* 4.5 4.4 + - - -
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Residues in contact with ARG 309 (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 HIS* 4.1 7.3 - - - -
299A MET* 4.2 12.3 - - - +
303A GLY* 3.8 3.4 - - - -
304A LEU* 2.9 72.1 + - + +
305A SER 3.0 24.8 + - - +
306A SER* 3.3 8.7 - - - +
308A GLN* 1.3 75.2 - - - +
310A SER* 1.3 54.5 + - - +
312A TRP* 2.8 11.6 + - - +
313A ILE* 2.3 46.2 + - + +
351A SER 3.5 11.1 + - - -
352A SER* 2.7 42.0 + - - +
353A VAL* 4.0 14.3 - - - +
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Residues in contact with SER 310 (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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306A SER 3.3 4.8 + - - -
307A PHE* 2.4 38.3 + - - +
309A ARG* 1.3 81.0 - - - +
311A LEU* 1.3 60.9 + - - +
313A ILE* 2.6 35.3 - - - +
314A ALA* 3.1 6.6 + - - +
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Residues in contact with LEU 311 (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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307A PHE* 2.9 32.8 - - + +
308A GLN* 3.1 17.2 + - - +
310A SER* 1.3 78.3 - - - +
312A TRP* 1.3 63.4 + - - +
313A ILE 3.3 0.3 + - - -
314A ALA* 3.4 5.5 + - - +
315A ALA* 3.4 24.1 + - - +
1047A ARG* 3.7 45.1 - - + +
1051A GLY* 5.9 2.7 - - - -
1090A GLU* 4.3 17.5 - - + +
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Residues in contact with TRP 312 (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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304A LEU* 4.4 16.5 - - + +
308A GLN* 2.7 21.9 + - + +
309A ARG* 2.9 14.8 - - - +
311A LEU* 1.3 78.1 - - - +
313A ILE* 1.3 48.9 + - - -
315A ALA* 5.5 5.4 - - + -
316A LYS* 2.7 44.6 + - + +
345A TRP* 4.4 7.6 - - + -
346A ASP* 2.5 60.0 + - - -
347A TRP 3.3 15.3 + - - -
348A LEU* 3.3 35.9 - - + -
350A ILE* 3.7 17.7 - - + -
1025A LEU* 5.9 0.4 - - - +
1044A VAL* 5.3 1.6 - - + -
1090A GLU* 2.7 31.4 + - + +
1091A GLU* 4.7 6.9 + - - -
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Residues in contact with ILE 313 (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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309A ARG* 2.3 53.4 + - + +
310A SER* 2.6 25.8 - - - +
311A LEU 3.1 0.4 - - - -
312A TRP* 1.3 67.8 - - - +
314A ALA* 1.3 87.7 - - + +
316A LYS* 3.0 41.9 + - - +
317A GLN* 3.3 9.8 + - + +
352A SER* 4.3 6.1 - - - +
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Residues in contact with ALA 314 (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 SER 3.1 7.3 + - - +
311A LEU* 3.4 9.4 + - - +
313A ILE* 1.3 95.3 - - + +
315A ALA* 1.3 62.7 + - - +
318A GLY 2.8 27.9 + - - +
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Residues in contact with ALA 315 (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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311A LEU 3.4 11.9 + - - +
312A TRP* 4.6 7.4 - - + +
314A ALA* 1.3 81.4 - - + +
316A LYS* 1.3 62.7 + - - +
317A GLN 3.7 1.0 + - - +
318A GLY* 4.3 6.5 + - - -
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Residues in contact with LYS 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LEU* 4.3 2.4 - - - +
312A TRP* 2.7 25.7 + - - +
313A ILE* 3.0 29.5 - - - +
315A ALA* 1.3 74.5 - - - +
317A GLN* 1.3 97.7 + - + +
348A LEU* 3.0 26.8 - - + +
350A ILE* 2.8 40.9 - - + +
352A SER* 2.4 40.1 + - - -
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Residues in contact with GLN 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ILE* 3.3 7.3 + - + +
315A ALA 4.3 1.0 - - - +
316A LYS* 1.3 108.8 - - + +
318A GLY* 1.3 60.8 + - - +
350A ILE* 5.2 1.8 - - - +
357A SER* 3.6 16.2 + - - -
360A GLU* 3.3 33.0 + - - +
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Residues in contact with GLY 318 (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 ALA* 2.8 21.6 + - - +
315A ALA* 4.7 4.7 - - - -
316A LYS 3.8 0.2 - - - -
317A GLN* 1.3 83.5 - - - +
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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