Contacts of the helix formed by residues 390 - 400 (chain C) in PDB entry 2W4V
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 ASN 390 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389C ILE* 1.3 93.2 - - - +
391C ALA* 1.3 66.6 + - - +
392C GLY* 3.3 10.9 + - - +
393C ASP* 2.4 52.4 + - + +
394C LEU 2.9 9.7 + - - -
609C LEU* 5.6 1.4 - - + +
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Residues in contact with ALA 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377C THR* 5.1 10.0 - - + +
380C ALA* 4.1 6.4 - - + +
381C GLU* 3.6 34.8 - - + +
384C ALA* 3.2 26.3 - - + +
389C ILE 3.4 0.6 + - - -
390C ASN* 1.3 75.7 + - - +
392C GLY* 1.3 63.4 + - - +
394C LEU* 3.4 3.3 - - - +
395C LEU* 3.3 22.3 + - - +
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Residues in contact with GLY 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390C ASN* 3.0 14.4 + - - -
391C ALA* 1.3 78.6 - - - +
393C ASP* 1.3 54.4 + - - +
394C LEU 2.8 14.2 + - - -
395C LEU* 3.4 2.1 + - - +
396C LYS* 3.1 22.5 + - - +
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Residues in contact with ASP 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390C ASN* 2.4 50.5 + - + +
392C GLY* 1.3 69.8 - - - +
394C LEU* 1.3 62.7 + - - +
396C LYS* 3.6 14.7 - - - +
397C ALA* 3.2 15.8 + - - +
609C LEU* 3.1 34.4 - - + +
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Residues in contact with LEU 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380C ALA 4.8 1.3 - - - +
383C VAL* 4.5 9.6 - - + -
384C ALA* 3.5 22.9 - - + +
387C CYS* 4.3 4.5 - - - -
389C ILE* 2.4 39.7 - - + -
390C ASN 2.9 8.0 + - - +
391C ALA* 3.4 6.7 - - - +
392C GLY 2.8 1.6 + - - -
393C ASP* 1.3 72.0 - - - +
395C LEU* 1.3 57.8 + - - +
396C LYS 2.5 15.7 + - - -
397C ALA* 2.7 16.0 + - + +
398C LEU* 3.0 22.2 + - + +
426C LEU* 6.1 0.2 - - + -
606C VAL* 4.3 21.1 - - + -
609C LEU* 3.1 21.5 - - + -
610C LEU* 6.2 1.3 - - + -
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Residues in contact with LEU 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361C MET* 4.0 22.4 - - + -
374C SER* 3.6 31.6 - - - +
377C THR* 5.2 9.9 - - + +
380C ALA* 5.5 4.7 - - + -
391C ALA 3.3 12.3 + - - +
392C GLY* 4.2 2.0 - - - +
394C LEU* 1.3 77.7 - - - +
396C LYS* 1.3 62.1 + - - +
398C LEU* 3.7 11.7 - - + +
399C LEU* 3.1 39.0 + - + +
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Residues in contact with LYS 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392C GLY 3.1 17.4 + - - +
393C ASP* 3.6 15.0 - - - +
394C LEU 2.5 5.7 + - - -
395C LEU* 1.3 74.8 - - - +
397C ALA* 1.3 59.5 + - - +
398C LEU 2.8 9.5 + - - -
399C LEU* 3.1 11.5 + - - +
400C LYS* 3.2 20.2 + - + +
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Residues in contact with ALA 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393C ASP 3.2 13.2 + - - +
394C LEU* 2.7 6.6 + - + +
396C LYS* 1.3 75.6 - - - +
398C LEU* 1.3 58.5 + - - +
400C LYS 4.8 1.6 - - - -
401C PRO* 3.8 19.1 - - - +
402C LYS 5.4 0.9 - - - +
603C ASN* 3.3 15.6 - - - +
605C ASN* 3.8 30.1 - - + +
606C VAL* 4.5 6.1 - - - +
609C LEU* 4.5 10.1 - - + -
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Residues in contact with LEU 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358C MET* 5.4 3.8 - - + -
361C MET* 5.1 15.3 - - + -
394C LEU* 3.0 26.9 + - + +
395C LEU* 3.7 11.9 - - + +
396C LYS 2.8 0.8 + - - -
397C ALA* 1.3 78.9 - - - +
399C LEU* 1.3 62.5 + - + +
400C LYS 3.6 0.4 - - - -
401C PRO* 4.3 6.3 - - - +
414C GLN* 4.6 3.5 - - - +
419C VAL* 3.8 18.7 - - - +
422C SER* 4.1 22.5 + - - +
423C VAL* 5.2 12.6 - - + -
426C LEU* 4.4 18.8 - - + -
603C ASN* 3.2 28.7 - - + +
606C VAL* 5.2 2.2 - - + -
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Residues in contact with LEU 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361C MET* 6.1 2.7 - - + -
363C PHE* 6.4 1.3 - - + -
371C GLN* 4.5 8.2 - - + +
372C ALA* 2.6 43.7 - - + +
373C GLU* 3.7 21.5 - - - +
374C SER* 4.0 3.4 - - - +
395C LEU* 3.1 35.8 + - + +
396C LYS* 4.2 1.3 - - - +
398C LEU* 1.3 77.3 - - + +
400C LYS* 1.3 62.7 + - + +
401C PRO* 3.6 4.0 - - - -
413C GLY* 3.8 1.2 - - - -
414C GLN 3.3 22.7 + - - +
419C VAL* 3.3 31.9 - - + -
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Residues in contact with LYS 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371C GLN* 6.3 1.6 - - + -
396C LYS* 3.2 16.6 + - + +
397C ALA* 4.8 1.0 - - - -
399C LEU* 1.3 81.6 - - + +
401C PRO* 1.3 72.8 - - - +
402C LYS* 3.3 3.5 + - - +
411C THR* 3.5 37.7 + - + +
412C LYS* 4.1 0.4 - - - +
413C GLY* 3.8 21.9 - - - +
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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