Contacts of the helix formed by residues 424 - 434 (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 SER 424 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423F SER* 1.3 83.9 + - - +
425F LEU* 1.3 63.3 + - - +
426F GLU* 4.0 3.6 + - - +
427F GLN* 2.5 51.3 + - - +
428F LEU* 3.3 3.4 - - - +
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Residues in contact with LEU 425 (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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424F SER* 1.3 74.6 + - - +
426F GLU* 1.3 62.5 + - - +
428F LEU* 3.1 32.8 - - + +
429F TYR* 2.9 52.8 + - + +
432F TYR* 5.9 0.2 - - + -
442F LEU* 3.5 31.4 - - + -
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Residues in contact with GLU 426 (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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369F ARG* 4.9 11.9 + - - +
424F SER* 3.0 7.1 + - - +
425F LEU* 1.3 74.5 - - - +
427F GLN* 1.3 67.1 + - + +
429F TYR* 2.7 46.9 - - - +
430F SER* 3.0 23.2 + - - -
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Residues in contact with GLN 427 (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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423F SER* 2.8 18.3 - - - -
424F SER* 2.5 69.3 + - - +
426F GLU* 1.3 80.0 - - + +
428F LEU* 1.3 57.4 + - - +
430F SER* 2.3 33.3 + - - +
431F LYS* 2.5 21.3 + - + +
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Residues in contact with LEU 428 (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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419F GLU* 2.6 28.5 - - + +
420F THR* 5.8 1.3 - - - +
422F GLN* 4.0 6.5 - - + +
423F SER* 2.6 37.9 - - - +
424F SER 3.3 6.5 - - - +
425F LEU* 3.1 31.6 + - + +
427F GLN* 1.3 77.6 - - - +
429F TYR* 1.3 75.1 + - - +
431F LYS* 4.6 2.9 - - + -
432F TYR* 2.8 51.5 + - + +
442F LEU* 5.3 1.3 - - + -
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Residues in contact with TYR 429 (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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425F LEU* 2.9 53.7 - - + +
426F GLU* 2.7 32.3 - - - +
428F LEU* 1.3 83.5 - - + +
430F SER* 1.3 63.4 + - - +
432F TYR* 3.0 10.9 + + - +
433F ASP* 2.8 33.6 + - - +
440F THR* 4.8 9.6 - - - -
442F LEU* 5.0 3.2 - - + +
456F ARG* 5.6 6.1 - - - +
457F SER* 4.5 21.5 + - - -
459F ASP* 5.4 6.5 - - - +
463F LYS* 5.6 8.6 + - - +
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Residues in contact with SER 430 (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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426F GLU* 3.0 4.8 + - - -
427F GLN* 2.3 37.9 + - - +
428F LEU 3.0 0.2 - - - -
429F TYR* 1.3 79.6 - - - +
431F LYS* 1.3 59.0 + - - +
433F ASP* 2.8 11.9 + - - +
434F GLU* 2.6 53.5 + - - +
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Residues in contact with LYS 431 (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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199E LEU* 5.7 11.2 - - + +
76F ARG* 3.8 34.0 + - + +
102F LEU* 5.6 0.4 - - - +
414F TRP* 5.9 8.3 - - - +
427F GLN 2.5 13.1 + - - +
428F LEU* 3.6 4.5 - - + +
430F SER* 1.3 79.8 + - - +
432F TYR* 1.3 73.6 + - + +
434F GLU* 2.5 23.2 - - - +
435F MET* 2.6 62.5 + - - +
437F ILE* 5.4 0.4 - - - +
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Residues in contact with TYR 432 (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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384F ALA* 4.8 6.3 - - + -
386F ASP* 4.7 5.2 - - - -
414F TRP* 5.3 8.7 - + - -
419F GLU* 2.7 40.0 + - + +
425F LEU* 5.9 0.4 - - + -
428F LEU* 2.8 50.1 + - + +
429F TYR* 3.0 15.7 - + - +
431F LYS* 1.3 90.9 - - + +
433F ASP* 1.3 55.9 + - - +
435F MET* 2.5 26.9 + - - +
436F SER 2.5 19.1 + - - -
437F ILE* 3.1 31.2 + - + +
440F THR* 3.6 29.2 - - + -
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Residues in contact with ASP 433 (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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370F LYS 4.6 4.9 - - - +
371F VAL* 2.6 43.1 - - + +
372F LEU 3.4 4.0 + - - -
429F TYR* 2.8 34.3 + - - +
430F SER* 3.4 7.7 + - - +
432F TYR* 1.3 68.3 - - - +
434F GLU* 1.3 57.3 + - + +
435F MET 2.6 14.1 + - - -
436F SER* 3.0 9.7 + - - +
437F ILE 5.3 4.3 - - - +
438F LEU 5.4 2.4 - - - +
459F ASP* 4.0 26.5 - - - +
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Residues in contact with GLU 434 (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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72F ILE* 3.6 21.3 - - + +
76F ARG* 2.5 69.0 + - - +
369F ARG 5.8 2.5 - - - +
370F LYS 5.4 4.0 - - - +
371F VAL* 4.6 8.0 - - - +
372F LEU* 2.8 15.7 - - - +
430F SER* 2.6 33.6 + - - +
431F LYS* 2.5 30.2 + - - +
433F ASP* 1.3 73.4 - - + +
435F MET* 1.3 57.3 + - - +
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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