Contacts of the helix formed by residues 364 - 374 (chain I) in PDB entry 4KRM
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 364 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329I ALA* 5.0 1.0 - - - +
362I PRO 3.4 5.5 + - - +
363I LEU* 1.3 78.0 - - - +
365I PRO* 1.4 71.6 - - - +
366I GLN* 3.4 24.8 + - - +
367I GLU* 2.9 42.8 + - + +
368I LEU 4.1 0.5 + - - -
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Residues in contact with PRO 365 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352I PHE* 5.1 3.8 - - + -
363I LEU 3.4 9.1 - - - +
364I ASP* 1.4 89.0 - - - +
366I GLN* 1.3 61.7 + - - +
367I GLU 3.2 0.4 - - - -
368I LEU* 3.3 25.3 + - + +
387I PRO* 3.6 35.4 - - + -
389I ASN* 5.8 2.7 - - - +
390I ARG* 3.4 20.7 + - - +
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Residues in contact with GLN 366 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364I ASP* 3.0 21.3 + - - +
365I PRO* 1.3 78.8 - - - +
367I GLU* 1.3 60.4 + - - +
369I ASP* 2.9 41.2 + - - +
390I ARG* 4.7 4.3 - - - +
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Residues in contact with GLU 367 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329I ALA* 5.5 1.3 - - - +
332I ILE* 3.2 32.4 - - + +
333I LYS* 5.5 3.8 - - - +
363I LEU* 4.2 7.6 - - + -
364I ASP* 2.9 32.3 + - + +
366I GLN* 1.3 78.6 - - - +
368I LEU* 1.3 60.5 + - - +
369I ASP 3.0 0.7 - - - -
370I ILE* 3.0 41.5 + - + +
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Residues in contact with LEU 368 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327I ILE* 4.8 4.5 - - + -
332I ILE* 4.1 7.4 - - + -
347I ILE* 5.0 5.4 - - + -
352I PHE* 4.0 22.2 - - + -
363I LEU* 4.0 24.5 - - + -
365I PRO* 3.3 19.2 + - + +
366I GLN 2.9 1.2 + - - -
367I GLU* 1.3 76.9 - - - +
369I ASP* 1.3 55.3 + - - +
370I ILE 3.0 1.3 - - - -
371I LEU* 3.1 39.3 + - + +
386I TRP* 3.9 33.0 - - + -
387I PRO* 4.0 14.4 - - + -
390I ARG* 4.3 6.1 - - - +
395I ALA* 3.2 24.1 - - + +
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Residues in contact with ASP 369 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366I GLN* 2.9 22.6 + - - +
368I LEU* 1.3 72.7 - - - +
370I ILE* 1.3 63.2 + - - +
371I LEU 3.1 2.5 - - - -
372I LYS* 3.2 54.2 + - + +
373I THR* 6.0 0.3 - - - +
390I ARG* 2.7 30.2 + - - -
394I HIS* 5.7 1.0 - - - +
395I ALA* 4.7 4.2 + - - +
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Residues in contact with ILE 370 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332I ILE* 3.9 30.5 - - + +
333I LYS* 4.3 9.0 - - + -
335I PHE* 3.5 35.0 - - + +
336I LYS* 3.7 30.2 - - + +
337I ASN 4.9 0.7 + - - -
367I GLU* 3.0 41.9 + - - +
368I LEU 3.0 0.4 - - - -
369I ASP* 1.3 79.5 - - - +
371I LEU* 1.3 59.8 + - + +
372I LYS 3.1 1.9 + - - -
373I THR* 3.3 20.4 + - - +
374I VAL* 5.0 0.2 - - - +
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Residues in contact with LEU 371 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327I ILE* 5.0 12.6 - - + -
332I ILE* 5.2 4.7 - - + -
335I PHE* 4.3 29.6 - - + -
345I LEU* 4.9 11.4 - - + -
347I ILE* 4.7 6.5 - - + -
368I LEU* 3.1 36.7 + - + +
370I ILE* 1.3 78.0 - - + +
372I LYS* 1.3 54.8 + - - +
373I THR 3.1 5.8 - - - -
374I VAL* 3.0 43.1 + - + +
395I ALA* 3.1 17.0 - - + +
396I PHE* 3.7 34.0 - - + -
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Residues in contact with LYS 372 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369I ASP* 3.3 48.2 + - + +
370I ILE 3.1 1.2 - - - -
371I LEU* 1.3 77.3 - - - +
373I THR* 1.3 61.8 + - + +
374I VAL 3.3 0.4 - - - -
394I HIS* 4.4 11.4 - - - +
395I ALA* 3.3 18.4 + - - +
397I GLU* 3.8 25.0 + - + +
398I ASN* 2.7 41.6 + - - +
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Residues in contact with THR 373 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335I PHE 4.4 0.5 + - - -
336I LYS* 6.4 0.9 - - + +
337I ASN* 3.8 25.5 - - - +
338I CYS 2.8 31.6 + - - +
339I THR* 3.3 19.5 - - - +
369I ASP 6.0 0.2 - - - +
370I ILE 3.3 15.9 + - - +
372I LYS* 1.3 79.1 - - + +
374I VAL* 1.3 63.6 + - - +
375I LYS* 3.5 10.1 + - - +
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Residues in contact with VAL 374 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335I PHE* 5.4 1.3 - - + +
338I CYS* 3.5 18.2 - - + +
339I THR 3.7 3.1 - - - +
341I ILE* 3.9 27.8 - - + -
345I LEU* 5.2 2.7 - - + -
370I ILE 5.0 0.2 - - - +
371I LEU* 3.0 40.8 + - + +
373I THR* 1.3 79.0 - - - +
375I LYS* 1.3 61.5 + - - +
376I GLU 3.8 20.9 - - - +
377I ILE* 4.2 12.1 - - + -
396I PHE* 5.2 6.4 - - + -
398I ASN* 3.5 5.4 + - - +
399I LEU* 3.5 25.7 + - + +
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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