Contacts of the helix formed by residues 274 - 282 (chain D) 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 ASP 274 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269D HIS* 2.4 32.3 - - + +
270D ASN 2.3 34.2 + - - +
271D VAL 2.4 31.6 + - - +
272D SER 2.9 0.4 - - - -
273D PHE* 1.3 70.2 - - - +
275D ARG* 1.3 67.8 + - - +
276D ALA 3.0 0.2 - - - -
277D HIS* 3.4 12.1 - - - +
278D ILE* 2.4 43.4 + - + +
291D PHE* 3.7 7.1 - - + +
293D ASP* 2.5 25.0 - - + -
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Residues in contact with ARG 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D VAL 3.7 1.4 + - - -
272D SER 3.7 0.6 - - - -
273D PHE* 3.0 4.9 - - + +
274D ASP* 1.3 82.4 - - - +
276D ALA* 1.3 54.0 + - - +
278D ILE* 2.6 10.9 + - - -
279D ARG* 2.4 51.2 + - + -
812D MET* 6.3 3.8 - - - -
841D LEU 3.4 5.3 + - - +
842D PRO* 2.7 37.8 - - - +
843D GLN* 2.1 122.4 + - + +
856D GLU* 4.2 10.1 - - - +
857D PRO* 5.2 9.3 - - - +
858D THR* 5.2 3.4 + - - -
859D TRP* 4.9 3.6 - - - -
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Residues in contact with ALA 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D VAL* 5.1 15.0 - - + -
253D ALA* 4.7 5.6 - - - +
273D PHE* 3.0 38.9 - - + +
275D ARG* 1.3 83.0 - - - +
277D HIS* 1.3 68.4 + - + +
279D ARG* 3.8 6.0 + - - +
280D GLU* 3.9 17.3 + - - +
812D MET* 6.2 4.0 - - - -
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Residues in contact with HIS 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D PHE* 3.0 55.5 + + + +
199D VAL* 4.3 8.4 - - + +
253D ALA* 4.4 11.3 - - - +
267D VAL* 4.7 4.0 - - + +
269D HIS* 3.0 37.9 - + + +
270D ASN 4.4 1.4 + - - -
273D PHE 2.5 30.2 + - - -
274D ASP* 3.2 4.2 + - - +
275D ARG 3.2 0.4 - - - -
276D ALA* 1.3 83.6 - - + +
278D ILE* 1.3 67.5 + - - +
281D GLN* 4.2 8.8 - - - +
291D PHE* 2.9 40.3 - - + -
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Residues in contact with ILE 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D ASP* 2.4 40.1 + - + +
275D ARG* 2.6 5.9 + - - +
277D HIS* 1.3 69.3 - - - +
279D ARG* 1.3 81.4 + - - +
281D GLN 3.3 4.0 + - - -
282D TYR* 2.3 70.8 - - + +
291D PHE* 2.9 37.8 - - + +
428D LEU 4.7 0.9 - - - +
431D GLY* 2.9 43.5 - - - +
432D VAL* 3.8 1.8 - - + +
843D GLN* 6.3 0.2 - - - -
844D VAL 6.3 0.2 - - - +
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Residues in contact with ARG 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D ARG* 2.4 40.1 + - + +
276D ALA* 4.5 2.5 - - - +
278D ILE* 1.3 81.4 - - - +
280D GLU* 1.3 61.8 + - + +
283D LEU* 3.8 3.1 - - - +
431D GLY 3.8 1.6 + - - -
433D SER* 2.3 42.2 + - - -
434D TYR* 3.5 5.1 - - - +
812D MET* 6.2 4.0 - - + -
814D VAL* 4.7 2.6 - - - +
839D ALA 4.8 0.3 - - - +
841D LEU* 2.5 87.8 + - + +
842D PRO* 2.7 34.8 + - - +
843D GLN* 4.1 0.8 - - - +
844D VAL* 2.8 19.4 - - - +
856D GLU* 3.2 5.1 + - - -
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Residues in contact with GLU 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D THR 5.7 0.5 - - - +
209D PRO* 5.4 4.9 - - - +
249D VAL* 3.4 7.0 - - - +
251D THR* 2.8 23.1 - - - +
252D GLY* 3.9 3.2 - - - +
253D ALA* 2.4 48.3 + - - +
256D PRO* 3.8 1.2 - - - +
276D ALA* 3.9 9.5 + - - +
278D ILE 3.3 2.2 + - - -
279D ARG* 1.3 76.3 - - + +
281D GLN* 1.4 50.7 + - - +
282D TYR 3.3 3.1 - - - -
283D LEU* 3.3 14.8 - - - +
284D ILE* 2.8 27.0 - - - +
812D MET* 3.6 26.8 - - + +
814D VAL* 3.5 31.0 - - + +
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Residues in contact with GLN 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D ALA* 3.0 12.0 - - + +
256D PRO* 2.9 33.4 + - + +
257D THR* 2.2 33.7 + - - +
277D HIS 4.2 2.4 - - - +
278D ILE 3.3 8.6 + - - +
280D GLU* 1.4 73.1 - - - +
282D TYR* 1.3 62.4 + - + +
284D ILE* 3.1 23.1 - - - +
285D GLN 3.6 1.9 + - - -
286D GLY 3.4 13.5 - - - +
287D SER* 2.5 21.8 + - - +
289D MET* 3.4 34.2 - - - +
291D PHE* 3.9 9.5 - - - -
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Residues in contact with TYR 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D ILE* 2.3 61.9 - - + +
280D GLU 3.3 0.2 - - - -
281D GLN* 1.3 89.5 - - + +
283D LEU* 1.3 53.7 + - - +
285D GLN* 2.7 26.6 - - + +
287D SER* 5.5 0.7 - - - -
289D MET 2.6 25.7 + - - -
290D ARG* 3.4 6.1 - - - -
291D PHE* 3.3 15.4 - + - -
432D VAL* 2.7 62.9 - - + +
434D TYR* 2.5 29.6 - - + -
841D LEU* 3.1 21.5 - - + -
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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