Contacts of the helix formed by residues 415 - 421 (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 PRO 415 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123E GLU* 3.2 18.4 - - + -
385F LEU* 4.0 5.1 - - + -
403F PHE* 3.0 34.5 - - + -
413F VAL* 3.2 23.1 - - + +
414F TRP* 1.3 107.0 + - - +
416F GLY* 1.3 61.1 + - - +
417F TYR* 2.9 30.1 + - + -
418F LEU* 4.1 7.3 + - + +
419F GLU 4.1 5.7 + - - -
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Residues in contact with GLY 416 (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 4.9 0.2 - - - -
385F LEU* 2.4 34.5 + - - +
386F ASP* 4.2 0.2 - - - -
387F VAL* 3.1 11.8 - - - +
414F TRP* 5.2 1.6 - - - -
415F PRO* 1.3 71.6 - - - +
417F TYR* 1.3 66.1 + - - +
418F LEU 3.1 1.6 - - - -
419F GLU* 2.8 39.9 + - - +
420F THR 3.1 0.9 + - - -
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Residues in contact with TYR 417 (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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387F VAL* 2.7 21.2 - - + +
396F ARG* 4.5 20.0 - - + -
399F CYS* 3.0 27.8 - - + -
400F GLN* 3.9 19.8 - - + -
403F PHE* 2.4 41.2 - + + +
404F ASN* 4.9 0.7 + - - -
415F PRO* 2.9 36.6 - - + -
416F GLY 1.3 64.9 - - - +
418F LEU* 1.3 72.0 + - + +
420F THR* 3.2 13.5 + - - -
421F MET 4.5 0.5 + - - -
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Residues in contact with LEU 418 (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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200E VAL* 2.8 51.1 - - + +
201E ASN* 3.7 6.1 - - - +
203E ARG* 2.8 42.8 - - - +
414F TRP* 6.0 2.5 - - + +
415F PRO* 4.2 10.1 - - + +
417F TYR* 1.3 87.5 - - + +
419F GLU* 1.3 56.3 + - - +
420F THR 2.9 0.3 + - - -
421F MET* 2.5 49.0 + - + +
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Residues in contact with GLU 419 (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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201E ASN* 4.9 4.0 - - - +
384F ALA* 5.9 0.4 - - + -
386F ASP* 4.2 8.2 - - - +
387F VAL 4.1 1.7 + - - -
414F TRP* 5.2 9.1 - - + +
415F PRO 4.1 2.2 + - - +
416F GLY* 2.8 32.9 + - - +
418F LEU* 1.3 80.8 - - - +
420F THR* 1.3 84.4 + - - -
421F MET* 3.1 1.8 + - - -
422F GLN* 3.4 17.7 + - - +
428F LEU* 2.6 35.9 - - + +
432F TYR* 2.7 26.7 + - + +
442F LEU* 3.9 21.8 - - - +
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Residues in contact with THR 420 (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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387F VAL* 1.9 38.2 + - - +
388F GLY* 4.3 9.9 - - - -
389F ARG 5.3 1.8 - - - +
392F THR* 6.5 0.4 - - + -
416F GLY 3.1 3.1 + - - -
417F TYR 3.2 12.0 + - - -
418F LEU 2.9 3.2 + - - -
419F GLU* 1.3 87.5 + - - +
421F MET* 1.3 62.7 + - - +
422F GLN 3.9 3.6 - - - +
423F SER 5.3 1.9 - - - +
428F LEU* 5.8 1.0 - - - +
442F LEU* 5.9 1.6 - - + -
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Residues in contact with MET 421 (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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201E ASN* 3.1 41.3 - - + +
203E ARG* 3.8 7.4 - - - -
417F TYR 4.5 0.2 + - - -
418F LEU* 2.5 40.8 + - + +
420F THR* 1.3 75.0 - - - +
422F GLN* 1.3 79.3 + - + +
423F SER 3.7 5.2 + - - +
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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