Contacts of the helix formed by residues 385 - 395 (chain C) in PDB entry 3WTV
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 385 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369C ASP* 5.7 2.9 - - - +
372C ALA* 3.4 11.2 - - - -
383C LYS 4.1 5.4 - - - +
384C MET* 1.3 78.0 - - - +
386C TYR* 1.3 65.4 + - - +
387C GLU* 3.1 34.7 - - - +
388C LYS* 3.0 51.5 + - - +
389C LEU* 3.1 9.5 + - - +
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Residues in contact with TYR 386 (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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365C LEU* 4.0 23.3 - - + -
368C PRO* 3.6 39.0 - - + +
369C ASP* 4.4 10.2 + - - +
372C ALA* 3.2 12.0 - - - +
385C ASN* 1.3 74.8 - - - +
387C GLU* 1.3 70.9 - - + +
389C LEU* 4.1 13.2 - - + -
390C SER* 2.8 45.2 + - - -
410C TYR* 3.5 35.3 - + - -
412C TYR* 3.1 26.7 + + - -
1E A 6.1 2.7 - - - -
2E G 3.7 7.2 + - - -
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Residues in contact with GLU 387 (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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385C ASN* 3.1 24.1 - - - +
386C TYR* 1.3 87.6 - - + +
388C LYS* 1.3 63.0 + - + +
390C SER* 3.3 16.6 + - - -
391C ARG* 3.5 8.0 + - - +
394C ARG* 4.6 2.9 + - - -
12D C 5.1 10.6 + - - -
2E G 5.5 5.2 - - - +
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Residues in contact with LYS 388 (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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383C LYS* 3.5 25.7 + - - +
384C MET* 3.3 21.3 - - + -
385C ASN* 3.0 24.1 + - - +
387C GLU* 1.3 74.8 - - + +
389C LEU* 1.3 65.8 + - - +
391C ARG* 3.1 15.4 + - - +
392C GLY* 3.3 8.0 + - - -
9D A 4.6 4.8 + - + -
10D T 2.5 89.9 + - + +
11D C 4.0 10.7 + - + -
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Residues in contact with LEU 389 (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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337C LEU* 3.8 17.9 - - + +
341C LEU* 5.2 2.9 - - + -
365C LEU* 4.6 8.7 - - + -
371C VAL* 4.0 15.9 - - + -
372C ALA* 3.9 15.5 - - + +
375C TRP* 3.8 43.5 - - + +
384C MET* 3.8 4.9 - - - -
385C ASN 3.1 11.9 + - - +
386C TYR* 3.6 21.1 - - + +
388C LYS* 1.3 76.7 - - - +
390C SER* 1.3 59.7 + - - +
392C GLY* 2.8 19.0 + - - +
393C LEU* 3.1 32.0 + - + -
9D A 5.1 1.6 - - - -
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Residues in contact with SER 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C TYR* 2.8 42.8 + - - -
387C GLU* 3.3 10.9 + - - -
389C LEU* 1.3 78.8 - - - +
391C ARG* 1.3 58.7 + - - +
393C LEU* 3.0 8.7 + - - +
394C ARG* 2.7 60.1 + - - +
412C TYR* 4.0 9.8 + - - -
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Residues in contact with ARG 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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387C GLU 3.5 5.6 + - - +
388C LYS 3.1 12.1 + - - +
390C SER* 1.3 80.6 + - - +
392C GLY* 1.3 60.3 + - - +
394C ARG* 3.6 23.4 - - - +
395C TYR* 3.0 67.6 + - + +
9D A 5.3 0.4 - - - +
10D T 3.6 27.1 - - + +
11D C 3.7 4.5 - - - +
12D C 6.0 0.2 - - - +
4E G 3.3 44.5 + - - +
5E G 2.5 50.9 + - - -
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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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337C LEU* 4.1 14.1 - - - -
388C LYS 3.3 4.9 + - - -
389C LEU* 2.8 10.3 + - - -
391C ARG* 1.3 77.0 - - - +
393C LEU* 1.3 66.8 + - - +
395C TYR* 3.1 24.5 + - - +
396C TYR* 3.7 11.5 + - - -
8D C 4.5 18.5 - - - +
9D A 5.5 2.9 - - - -
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Residues in contact with LEU 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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337C LEU* 3.5 21.5 - - + -
341C LEU* 3.6 26.0 - - + -
363C PHE* 5.1 1.1 - - + -
365C LEU* 5.0 4.3 - - + -
386C TYR* 5.6 0.2 - - + -
389C LEU* 3.1 24.3 + - + +
390C SER* 3.0 8.8 + - - +
392C GLY* 1.3 77.7 - - - +
394C ARG* 1.3 53.3 + - - +
396C TYR* 2.6 51.8 + - + +
397C TYR* 3.7 6.9 + - - -
402C ILE* 4.3 6.9 - - + +
412C TYR* 3.6 54.3 - - + +
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Residues in contact with ARG 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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387C GLU 4.6 3.0 + - - -
390C SER* 2.7 39.2 + - - +
391C ARG* 3.6 32.9 - - - +
392C GLY 3.3 0.4 - - - -
393C LEU* 1.3 76.0 - - - +
395C TYR* 1.3 59.9 + - - +
396C TYR 3.0 1.3 + - - -
397C TYR* 3.2 48.5 + - + +
398C ASP 4.6 0.7 + - - -
412C TYR* 5.3 2.5 + - - +
12D C 4.9 2.0 - - - +
2E G 4.1 14.6 - - - +
3E A 3.4 48.8 + - + +
4E G 2.8 50.4 + - + +
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Residues in contact with TYR 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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391C ARG* 3.0 60.0 + - + +
392C GLY* 3.1 13.6 + - - +
393C LEU 2.9 1.2 + - - -
394C ARG* 1.3 76.5 - - - +
396C TYR* 1.3 62.8 + - + +
397C TYR 3.4 0.4 - - - -
398C ASP* 4.3 4.2 + - - +
399C LYS* 3.4 33.3 + - + +
8D C 4.4 27.1 - + + +
9D A 3.5 20.2 + - - -
10D T 4.6 0.4 - - - -
5E G 5.5 0.2 - - - -
6E A 2.8 30.0 + - - -
7E T 3.8 4.5 + - - +
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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