Contacts of the helix formed by residues 343 - 356 (chain F) 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 343 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F HIS* 5.6 3.1 + - - -
99F PHE* 3.3 33.9 - - + -
107F ARG* 3.9 24.1 + - - +
110F LEU* 5.0 0.9 - - - +
233F GLU 4.4 1.9 - - - +
234F LYS* 3.7 28.3 - - - +
235F THR* 4.1 17.6 + - - -
341F ASP* 3.8 0.9 - - - -
342F LEU* 1.3 75.9 - - - +
344F ARG* 1.3 58.7 + - - +
346F MET* 2.8 30.1 + - + +
347F LEU* 2.7 27.9 - - + +
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Residues in contact with ARG 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F LEU* 3.0 18.1 - - + +
234F LYS* 2.6 32.8 - - - +
293F PHE* 4.9 6.6 - - + -
298F GLU* 2.3 58.5 + - - +
299F LEU* 3.6 4.9 - - - +
300F ILE* 2.8 42.8 + - + +
341F ASP 5.2 0.2 + - - -
342F LEU* 2.6 23.6 - - + +
343F ASP* 1.3 73.9 - - - +
345F GLY* 1.3 66.2 + - - +
346F MET 2.8 1.6 - - - -
347F LEU* 2.6 37.8 + - + +
348F ALA* 2.6 16.2 + - - +
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Residues in contact with GLY 345 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110F LEU* 5.1 0.9 - - - -
263F TRP* 3.6 26.4 - - - -
300F ILE* 4.6 7.4 - - - -
342F LEU* 2.5 30.5 - - - +
344F ARG* 1.3 72.2 - - - +
346F MET* 1.3 60.2 + - - +
348F ALA* 3.1 7.9 + - - +
349F TYR* 3.1 28.0 + - - -
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Residues in contact with MET 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F PHE* 3.1 31.6 - - + -
99F PHE* 4.4 11.4 - - + -
106F LEU* 3.3 45.8 - - + -
107F ARG* 4.4 14.1 - - + +
110F LEU* 3.4 24.5 - - + +
343F ASP* 2.8 16.9 + - + +
345F GLY* 1.3 72.4 - - - +
347F LEU* 1.3 82.2 + - + +
348F ALA 2.9 4.7 - - - -
349F TYR* 2.7 16.1 + - + +
350F LEU* 2.5 36.1 + - - +
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Residues in contact with LEU 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F LEU* 5.0 26.2 - - + +
92F LEU* 5.4 5.6 - - + -
99F PHE* 4.8 3.6 - - + -
234F LYS* 4.8 3.6 - - - +
293F PHE* 4.4 7.0 - - + -
343F ASP* 2.7 46.0 - - + +
344F ARG* 2.6 41.9 + - + +
346F MET* 1.3 87.6 - - + +
348F ALA* 1.3 53.0 + - - -
350F LEU* 2.5 28.3 - - + +
351F TYR* 3.1 20.1 - - - -
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Residues in contact with ALA 348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273F PHE* 4.7 4.7 - - + -
291F TYR* 3.4 42.3 + - + -
293F PHE* 3.9 7.6 - - + -
300F ILE* 4.8 2.7 - - + -
344F ARG 2.6 13.0 + - - +
345F GLY* 3.4 11.9 - - - +
347F LEU* 1.3 73.7 - - - +
349F TYR* 1.3 53.2 + - - +
351F TYR* 2.6 13.5 - - - +
352F ASP* 2.4 35.0 + - - -
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Residues in contact with TYR 349 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F LEU* 5.5 5.6 - - + -
110F LEU* 4.1 25.1 - - + -
262F TRP* 4.1 4.0 + + - -
263F TRP* 2.8 53.5 - + - -
266F PHE* 2.9 53.2 - - + +
267F ALA* 3.8 13.5 - - + -
273F PHE* 4.6 4.5 - + - -
345F GLY 3.1 20.5 + - - -
346F MET* 2.7 14.0 + - + +
348F ALA* 1.3 71.2 - - - +
350F LEU* 1.3 63.7 + - - +
351F TYR 2.6 5.3 + - - -
352F ASP* 2.7 21.4 + - + +
353F SER* 2.8 14.8 + - - -
374F LEU* 5.1 3.4 - - + -
378F LEU* 4.5 14.8 - - + -
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Residues in contact with LEU 350 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F LEU* 3.7 17.0 - - + +
73F CYS* 4.9 6.7 - - - -
78F PHE* 3.0 41.5 - - + -
79F LEU* 5.4 0.7 - - + -
106F LEU* 4.5 7.1 - - + +
346F MET* 2.5 35.7 - - + +
347F LEU* 2.5 34.8 - - + +
349F TYR* 1.3 74.7 - - - +
351F TYR* 1.3 64.6 + - + +
353F SER* 2.3 24.9 + - - -
354F PHE* 3.3 6.1 + - - +
355F GLN 3.6 1.6 + - - -
372F LEU* 5.4 1.9 - - + +
374F LEU* 4.3 12.5 - - + +
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Residues in contact with TYR 351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F GLY 5.7 0.9 - - - -
66F SER* 4.0 21.5 + - - -
69F LEU* 3.2 30.7 - - + +
70F LEU* 6.0 0.9 - - - +
91F LEU* 5.8 7.4 - - + -
291F TYR* 3.3 7.9 - - + +
293F PHE* 3.2 24.2 - + - -
294F PRO* 3.5 21.2 - - + +
295F TRP* 3.4 26.6 - + - -
347F LEU 3.1 19.1 - - - -
348F ALA* 2.6 17.9 + - - +
349F TYR 2.6 1.0 - - - -
350F LEU* 1.3 86.7 - - + +
352F ASP* 1.3 59.0 + - - +
353F SER 2.6 0.2 + - - -
355F GLN* 2.0 54.6 + - + +
357F THR* 5.8 0.9 - - - -
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Residues in contact with ASP 352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266F PHE 5.3 0.2 - - - -
267F ALA* 2.9 16.6 - - - +
268F MET* 2.3 52.2 + - - +
269F SER* 3.2 17.2 + - - -
272F ASN* 6.4 0.4 - - - +
273F PHE* 4.8 1.1 - - + -
291F TYR* 2.9 22.8 + - + +
348F ALA 2.4 22.0 + - - +
349F TYR* 2.9 19.1 - - + +
351F TYR* 1.3 71.8 - - - +
353F SER* 1.3 66.9 + - - +
355F GLN* 2.9 6.7 + - - +
356F LEU* 3.1 15.5 + - - +
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Residues in contact with SER 353 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268F MET* 4.3 3.7 - - - +
349F TYR 2.8 3.7 + - - -
350F LEU* 2.3 38.8 + - - -
351F TYR 2.6 1.0 + - - -
352F ASP* 1.3 86.9 + - - +
354F PHE* 1.3 60.8 + - - +
356F LEU* 3.3 19.8 - - - +
371F VAL 5.1 0.5 - - - +
372F LEU* 4.4 1.8 - - - +
373F LYS* 2.5 60.5 + - - +
374F LEU* 3.9 5.4 - - - +
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Residues in contact with PHE 354 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F GLY 4.0 3.6 - - - -
68F ALA* 3.7 18.6 - - + -
69F LEU* 3.4 49.4 - - + -
72F ILE* 5.5 5.8 - - + -
350F LEU 4.0 4.5 - - - +
353F SER* 1.3 82.3 + - - +
355F GLN* 1.3 67.7 - - - +
356F LEU 2.6 11.4 + - - +
357F THR* 3.5 1.2 + - - -
368F HIS* 4.7 1.3 - + - -
369F ARG 4.7 1.6 - - - -
370F LYS* 2.8 53.2 - - + -
371F VAL 2.9 28.0 - - - -
372F LEU* 3.6 19.3 - - + -
373F LYS 4.1 0.2 - - - +
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Residues in contact with GLN 355 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F LEU* 3.9 2.0 - - - -
272F ASN* 6.6 0.2 - - - -
291F TYR* 2.6 25.6 - - + +
292F ASN 3.9 5.0 + - - -
293F PHE 3.8 3.6 + - - -
294F PRO* 3.0 39.2 - - - +
350F LEU 3.6 0.6 + - - -
351F TYR* 2.0 68.3 + - + -
352F ASP* 3.0 4.7 - - - +
354F PHE* 1.3 66.7 - - - +
356F LEU* 1.3 66.2 + - + +
357F THR* 2.2 38.2 + - - +
358F GLU* 4.9 6.0 + - - +
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Residues in contact with LEU 356 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786D ALA* 5.7 0.2 - - + -
790D ARG* 5.6 3.6 - - - +
268F MET* 5.2 4.5 - - + +
269F SER* 3.8 29.6 - - - +
272F ASN* 5.8 2.2 - - - +
352F ASP* 3.1 17.9 + - - +
353F SER 3.3 14.6 - - - +
354F PHE* 3.1 5.7 - - - +
355F GLN* 1.3 88.6 + - + +
357F THR* 1.3 57.3 + - - +
358F GLU* 4.1 7.4 - - - +
359F ASN* 2.8 42.8 - - + +
370F LYS* 2.7 28.4 - - - +
373F LYS* 5.5 9.0 - - + +
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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