Contacts of the helix formed by residues 365 - 374 (chain B) in PDB entry 1GKU
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 365 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B SER 4.1 0.8 + - - -
364B LEU* 1.3 75.9 - - - +
366B PRO* 1.3 77.6 - - - +
367B GLN* 2.7 36.5 + - - +
368B MET* 3.0 21.5 + - - +
369B VAL* 3.2 10.7 + - - +
397B ARG* 4.7 0.2 - - - -
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Residues in contact with PRO 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B LEU 4.0 1.1 - - - +
365B SER* 1.3 86.3 - - - -
367B GLN* 1.3 62.8 + - - +
369B VAL* 3.0 23.5 - - + +
370B LYS* 3.4 15.9 - - + +
393B ILE* 3.4 34.3 - - + -
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Residues in contact with GLN 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B SER* 2.7 28.5 + - - +
366B PRO* 1.3 81.8 - - - +
368B MET* 1.3 94.8 + - + +
370B LYS* 3.2 9.6 + - - +
371B LEU* 3.1 20.1 + - - +
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Residues in contact with MET 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B VAL* 4.9 23.8 - - - -
364B LEU* 4.1 26.0 - - + -
365B SER* 3.0 22.0 + - - +
367B GLN* 1.3 106.9 - - + +
369B VAL* 1.3 66.5 + - - +
370B LYS 3.1 0.3 + - - -
371B LEU* 3.1 32.5 + - + +
372B LEU* 2.9 32.8 + - + +
423B PHE* 6.1 0.4 - - - -
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Residues in contact with VAL 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B ILE* 4.1 5.6 - - + -
364B LEU* 3.9 11.2 - - + -
365B SER 3.2 5.5 + - - +
366B PRO* 3.0 21.3 - - + +
368B MET* 1.3 75.1 - - - +
370B LYS* 1.3 64.2 + - + +
372B LEU* 4.6 1.8 - - - -
373B ALA* 2.8 27.6 + - - +
393B ILE* 3.7 19.1 - - + -
396B VAL* 5.1 13.4 - - + +
397B ARG* 3.5 42.6 - - - +
400B LEU* 3.8 20.5 - - + +
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Residues in contact with LYS 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B PRO* 3.4 21.1 - - + +
367B GLN* 3.2 8.7 + - - +
368B MET 3.1 0.6 - - - -
369B VAL* 1.3 81.1 - - + +
371B LEU* 1.3 58.8 - - - +
373B ALA* 2.9 10.1 - - - +
374B TYR* 2.9 44.3 + - + +
382B ILE* 4.3 12.3 - - + -
383B GLU* 2.7 46.5 + - - +
387B PRO* 5.3 19.1 - - + +
396B VAL* 6.1 3.1 - - + -
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Residues in contact with LEU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B GLN 3.1 11.8 + - - +
368B MET* 3.1 34.2 + - + +
370B LYS* 1.3 75.8 - - - +
372B LEU* 1.3 64.4 + - + +
374B TYR* 3.4 35.3 + - + +
375B LEU* 3.8 7.0 - - + +
423B PHE* 4.2 31.6 - - + -
860B ARG* 5.4 7.2 - - + +
863B GLN 5.8 1.3 - - - +
864B GLU* 4.4 30.1 - - + +
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Residues in contact with LEU 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B VAL* 4.4 14.6 - - + -
358B ILE* 3.5 30.5 - - + -
361B ILE* 5.6 0.2 - - + -
364B LEU* 3.9 24.5 - - + -
368B MET* 2.9 21.7 + - + +
369B VAL 3.9 3.8 - - - +
371B LEU* 1.3 74.5 - - + +
373B ALA* 1.3 55.5 + - - +
374B TYR 2.3 23.8 - - - +
375B LEU* 3.3 14.2 - - + +
376B TYR* 3.4 14.6 - - + -
400B LEU* 4.2 16.8 - - + -
404B MET* 4.9 4.7 - - + -
421B VAL* 4.3 28.7 - - + -
423B PHE* 4.5 10.8 - - + -
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Residues in contact with ALA 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B VAL 2.8 17.7 + - - +
370B LYS* 2.9 18.4 - - - +
372B LEU* 1.3 73.2 - - - +
374B TYR* 1.3 65.6 + - - +
376B TYR* 3.2 18.4 + - - +
377B ARG* 3.4 8.5 + - - +
382B ILE* 3.6 31.5 - - + +
396B VAL* 6.1 4.7 - - + -
400B LEU* 4.5 14.4 - - + -
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Residues in contact with TYR 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B LYS* 2.9 26.9 + - + +
371B LEU* 3.6 28.0 - - + +
372B LEU 2.3 31.9 - - - +
373B ALA* 1.3 76.6 - - - +
375B LEU* 1.3 65.7 + - - +
377B ARG 3.6 10.8 - - - +
379B VAL* 3.5 38.1 - - + +
382B ILE* 3.5 31.9 - - + -
383B GLU* 2.5 26.0 + - - -
860B ARG* 4.1 22.0 - - + -
863B GLN* 3.8 27.9 + - + -
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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