Contacts of the helix formed by residues 370 - 377 (chain P) in PDB entry 1K4U
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 370 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368P ARG* 3.6 2.4 + - - +
369P PRO* 1.3 69.5 - - - +
371P ALA* 1.3 68.7 + - - +
372P ASP* 2.6 7.3 + - - -
373P LEU* 2.7 28.3 + - - +
374P ILE* 3.2 6.3 + - - -
390P VAL* 3.1 25.9 + - - -
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Residues in contact with ALA 371 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368P ARG* 4.9 11.4 - - - +
369P PRO 3.1 5.5 + - - -
370P SER* 1.3 69.0 + - - +
372P ASP* 1.3 50.4 + - - +
374P ILE* 3.0 9.4 + - - -
375P LEU* 2.6 32.8 + - - +
386P LEU* 2.7 46.2 - - + +
388P SER* 3.2 20.4 - - - +
389P ALA* 3.9 7.0 - - - +
390P VAL* 5.0 1.7 + - - +
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Residues in contact with ASP 372 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370P SER* 2.6 9.4 + - - +
371P ALA* 1.3 73.1 - - - +
373P LEU* 1.3 54.8 + - - +
375P LEU* 2.6 38.5 + - - +
376P ASN* 2.7 18.4 + - - +
389P ALA* 2.7 35.5 - - - +
390P VAL* 3.4 15.9 + - - +
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Residues in contact with LEU 373 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369P PRO* 3.2 29.8 - - + -
370P SER* 2.7 21.5 + - - +
372P ASP* 1.3 74.9 - - - +
374P ILE* 1.3 64.4 + - + +
376P ASN* 3.0 4.4 + - - -
377P ARG* 2.6 58.0 + - - +
490S VAL* 3.2 17.3 - - + +
491S ASN* 3.2 26.2 - - + +
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Residues in contact with ILE 374 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368P ARG* 5.3 2.2 - - - +
369P PRO* 2.7 44.9 - - + +
370P SER 3.2 8.3 + - - +
371P ALA* 3.0 12.7 + - - +
372P ASP 2.9 0.6 - - - -
373P LEU* 1.3 81.3 - - + +
375P LEU* 1.3 50.8 + - - +
376P ASN 2.9 4.3 - - - -
377P ARG 2.7 3.8 + - - -
378P CYS* 2.6 61.8 + - + +
382P THR* 4.1 3.8 - - + -
383P LYS* 5.2 0.4 - - + -
386P LEU* 3.4 27.6 - - + -
474S GLU* 5.5 0.9 - - + -
490S VAL* 3.1 25.8 - - + -
505S ILE* 4.0 18.4 - - + -
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Residues in contact with LEU 375 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371P ALA 2.6 24.2 + - - +
372P ASP* 2.6 37.8 + - - +
374P ILE* 1.3 70.5 - - - +
376P ASN* 1.3 58.5 + - - +
378P CYS 4.4 2.6 - - - +
383P LYS* 3.2 62.3 - - + +
386P LEU* 3.4 7.4 - - + -
387P ALA* 3.8 23.3 - - + -
389P ALA* 3.6 18.6 - - + +
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Residues in contact with ASN 376 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372P ASP* 2.7 11.0 + - - +
373P LEU* 3.1 12.3 - - - +
374P ILE 2.9 0.2 - - - -
375P LEU* 1.3 83.6 + - - +
377P ARG* 1.3 87.5 + - - +
378P CYS 3.8 0.7 - - - -
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Residues in contact with ARG 377 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373P LEU* 2.6 39.1 + - - +
374P ILE 2.7 6.8 + - - +
376P ASN* 1.3 109.8 + - - +
378P CYS* 1.3 55.4 + - - -
488S SER* 4.3 7.7 - - - -
489S LYS* 3.2 22.1 - - + +
490S VAL* 2.7 46.7 - - + +
491S ASN* 5.0 0.7 - - - +
496S GLU* 4.3 3.5 - - - +
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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