Contacts of the helix formed by residues 365 - 379 (chain K) in PDB entry 3V3K
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 365 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397I LYS* 4.8 1.4 + - - -
364K GLU* 1.3 73.7 - - - +
366K LEU* 1.3 60.5 + - - +
367K GLN* 3.3 32.2 - - - +
368K SER* 2.7 25.5 + - - -
369K LEU* 2.9 32.7 + - - +
397K LYS* 4.1 22.4 + - + +
398K LEU 3.4 20.6 - - - +
399K PHE* 3.6 26.0 - - + -
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Residues in contact with LEU 366 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279K LEU* 3.4 33.7 - - + -
281K PHE* 4.0 16.6 - - + -
328K PHE* 3.7 28.5 - - + -
357K PHE* 4.1 6.5 - - + -
365K ASP* 1.3 72.4 - - - +
367K GLN* 1.3 61.8 + - - +
369K LEU* 3.2 10.9 + - - +
370K LEU* 3.0 40.0 + - + +
394K LEU* 4.4 2.9 - - + -
398K LEU* 2.9 36.0 + - + +
400K PHE* 3.8 21.1 - - + -
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Residues in contact with GLN 367 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367I GLN* 4.0 28.8 - - + +
371I LEU* 3.2 38.4 - - + +
392I ASN* 5.4 1.2 + - - +
328K PHE* 4.5 8.3 - - + -
365K ASP* 3.3 18.2 - - - +
366K LEU* 1.3 84.9 - - - +
368K SER* 1.3 57.4 + - - +
370K LEU* 4.0 6.8 - - - +
371K LEU* 3.3 33.6 + - + +
389K CYS* 5.9 2.2 - - + -
392K ASN* 3.1 28.6 - - - +
394K LEU* 4.6 6.9 - - - +
396K LYS 4.8 0.8 + - - -
397K LYS* 4.3 2.2 - - - -
398K LEU 4.2 15.6 + - - -
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Residues in contact with SER 368 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397I LYS* 3.1 27.8 + - - +
364K GLU* 3.7 21.2 - - - +
365K ASP* 2.7 36.1 + - - -
366K LEU 3.2 0.8 - - - -
367K GLN* 1.3 77.8 - - - +
369K LEU* 1.3 62.9 + - - +
371K LEU* 3.5 17.9 + - - +
372K ARG* 3.5 18.4 + - - +
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Residues in contact with LEU 369 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356K ILE* 3.5 38.8 - - + +
357K PHE* 3.7 37.0 - - + -
360K TRP* 3.6 24.7 - - + +
361K ALA* 3.7 19.3 - - + +
364K GLU* 4.2 10.1 - - + +
365K ASP 2.9 21.7 + - - +
366K LEU* 3.2 8.5 + - - +
368K SER* 1.3 76.2 - - - +
370K LEU* 1.3 57.7 + - - +
372K ARG* 3.2 9.5 + - - +
373K VAL* 3.1 29.4 + - - +
400K PHE* 4.5 7.0 - - + -
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Residues in contact with LEU 370 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281K PHE* 4.3 5.6 - - + -
328K PHE* 3.4 38.8 - - + -
330K SER* 3.4 20.6 - - - +
349K TYR* 3.8 17.5 - - + +
353K LEU* 4.4 11.2 - - + -
357K PHE* 5.0 4.0 - - + -
366K LEU* 3.0 29.5 + - + +
367K GLN* 4.1 4.5 - - - +
369K LEU* 1.3 72.5 - - - +
371K LEU* 1.3 59.6 - - - +
373K VAL* 3.7 19.3 - - + +
374K ALA* 2.9 27.9 + - - +
387K PRO* 5.5 1.3 - - + +
389K CYS* 3.7 19.2 - - - -
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Residues in contact with LEU 371 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365I ASP* 5.5 2.0 - - - +
367I GLN* 5.4 7.9 - - + -
392I ASN* 4.6 15.5 - - - +
394I LEU* 3.2 29.6 - - + +
395I ARG 3.0 29.4 - - - +
396I LYS* 3.6 12.3 - - - +
397I LYS* 3.8 32.5 - - + +
367K GLN* 3.3 24.8 + - + +
368K SER* 3.6 14.4 - - - +
369K LEU 3.2 0.6 - - - -
370K LEU* 1.3 75.3 - - - +
372K ARG* 1.3 55.2 + - + +
374K ALA* 3.3 3.3 + - - +
375K ASN* 2.7 31.0 + - - +
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Residues in contact with ARG 372 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145I LEU* 5.3 2.0 - - - +
151I LEU* 3.3 46.3 - - + +
356K ILE* 3.3 18.4 - - + -
360K TRP* 3.1 55.0 - - - +
364K GLU* 2.9 36.1 + - - -
368K SER 3.5 11.6 + - - +
369K LEU* 3.2 7.5 + - - +
371K LEU* 1.3 76.8 - - + +
373K VAL* 1.3 53.8 + - - +
375K ASN* 3.7 8.0 - - - +
376K ALA* 2.8 36.7 + - - +
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Residues in contact with VAL 373 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349K TYR* 4.0 39.7 - - + +
352K THR* 3.9 10.8 - - + -
353K LEU* 4.0 19.7 - - + +
356K ILE* 3.4 22.0 - - + -
357K PHE* 5.2 2.0 - - + -
369K LEU 3.1 16.5 + - - +
370K LEU* 3.7 20.4 - - + +
371K LEU 3.2 0.2 - - - -
372K ARG* 1.3 73.7 - - - +
374K ALA* 1.3 60.4 + - - +
377K VAL* 2.9 40.9 + - + +
387K PRO* 4.8 2.5 - - + -
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Residues in contact with ALA 374 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394I LEU 3.6 16.4 - - - +
395I ARG* 4.1 0.8 - - - +
370K LEU 2.9 19.0 + - - +
371K LEU 3.6 4.0 - - - +
373K VAL* 1.3 76.4 - - - +
375K ASN* 1.3 61.6 + - - +
378K SER* 3.4 16.6 + - - -
386K MET* 3.2 37.9 - - + +
387K PRO* 3.5 22.5 - - + +
388K GLY* 5.5 1.3 - - - -
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Residues in contact with ASN 375 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150I ASP* 3.3 33.2 + - - +
151I LEU* 6.1 0.8 - - - +
395I ARG* 3.6 42.3 + - - +
396I LYS* 4.6 3.0 - - - +
371K LEU 2.7 21.0 + - - +
372K ARG* 3.7 9.4 - - - +
374K ALA* 1.3 73.7 - - - +
376K ALA* 1.3 60.7 + - - +
378K SER* 2.7 21.0 + - - -
379K VAL* 3.8 12.2 - - - +
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Residues in contact with ALA 376 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352K THR* 3.4 23.8 - - + +
356K ILE* 4.6 2.9 - - + -
372K ARG 2.8 22.4 + - - +
373K VAL 3.4 0.2 + - - -
375K ASN* 1.3 72.8 - - - +
377K VAL* 1.3 60.5 + - - +
379K VAL* 3.1 28.0 - - - +
380K LYS* 3.9 10.9 - - - +
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Residues in contact with VAL 377 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348K TRP* 3.8 22.9 - - + +
349K TYR* 4.3 2.7 - - - -
352K THR* 3.5 26.9 - - - +
373K VAL* 2.9 26.6 + - + +
376K ALA* 1.3 74.6 - - - +
378K SER* 1.3 64.2 + - - +
380K LYS* 3.3 23.4 + - + +
385K GLN* 3.4 40.8 + - + +
387K PRO* 3.6 22.9 - - + -
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Residues in contact with SER 378 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320I SER* 2.8 23.5 + - - +
321I LEU* 4.5 2.9 - - - +
322I PRO* 3.9 27.7 - - - +
395I ARG* 3.6 21.1 + - - -
374K ALA 3.4 15.1 + - - -
375K ASN* 2.7 22.7 + - - -
377K VAL* 1.3 79.9 - - - +
379K VAL* 1.3 61.1 + - - +
380K LYS 3.4 2.6 + - - +
384K LYS* 4.4 4.3 - - - +
385K GLN 3.8 10.7 + - - -
386K MET* 4.5 4.5 - - - -
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Residues in contact with VAL 379 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320I SER* 3.3 28.2 - - - +
321I LEU* 6.0 1.8 - - + -
375K ASN* 3.8 15.7 - - - +
376K ALA* 3.1 21.3 - - - +
378K SER* 1.3 78.3 - - - +
380K LYS* 1.3 66.4 + - + +
381K GLY 3.6 1.6 + - - -
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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