Contacts of the helix formed by residues 394 - 405 (chain C) in PDB entry 3V81
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 GLN 394 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318B TYR* 3.4 43.4 - - - +
319B TYR 5.1 0.5 - - - +
393C ILE* 1.3 78.6 - - - +
395C LYS* 1.3 65.0 + - - +
396C GLU* 3.6 19.7 - - + +
397C THR* 3.0 28.2 + - - +
398C TRP* 3.1 11.1 + - - +
414C TRP* 4.0 0.7 - - - -
416C PHE* 3.6 27.8 - - - -
422C LEU* 3.9 14.3 - - + +
423C VAL 4.7 2.4 + - - +
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Residues in contact with LYS 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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98B ALA* 6.4 3.1 - - + -
393C ILE 3.7 1.0 + - - -
394C GLN* 1.3 72.4 + - - +
396C GLU* 1.3 68.5 + - - +
398C TRP* 3.6 2.0 + - + +
399C GLU* 3.0 35.8 + - - +
414C TRP* 3.0 76.6 + - + +
415C GLU* 4.7 3.4 - - - +
416C PHE* 4.9 9.4 - - + +
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Residues in contact with GLU 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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98B ALA* 5.9 3.3 - - - +
101B LYS* 5.8 2.1 + - - -
394C GLN* 3.6 22.9 - - + +
395C LYS* 1.3 86.0 + - - +
397C THR* 1.3 67.7 + - - +
399C GLU* 3.4 5.6 + - - +
400C THR* 2.9 29.9 + - - +
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Residues in contact with THR 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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365C VAL* 4.7 2.7 - - + -
393C ILE* 3.6 21.1 - - + -
394C GLN* 3.0 28.4 + - - +
396C GLU* 1.3 79.8 - - - +
398C TRP* 1.3 64.6 + - - +
400C THR* 3.3 6.7 + - - -
401C TRP* 3.1 19.9 + - - +
423C VAL 3.6 15.2 + - - +
424C LYS* 4.0 15.0 - - - +
425C LEU* 4.1 18.0 - - + +
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Residues in contact with TRP 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C VAL* 3.8 23.8 - - + -
368C LEU* 6.1 1.3 - - + -
369C THR* 3.0 28.7 - - - -
393C ILE* 3.9 15.9 - - + +
394C GLN 3.1 7.5 + - - +
395C LYS 4.0 1.8 - - - +
397C THR* 1.3 80.5 - - - +
399C GLU* 1.3 67.3 + - - +
401C TRP* 3.0 20.9 + + - +
402C TRP* 3.0 57.7 + + + +
409C THR* 3.8 20.9 - - + -
410C TRP* 4.2 7.0 - - - -
411C ILE* 3.0 47.7 + - + +
414C TRP* 3.8 37.1 - + + +
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Residues in contact with GLU 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C LYS* 3.0 23.8 + - - +
396C GLU* 3.6 6.7 - - - +
397C THR 3.3 0.2 - - - -
398C TRP* 1.3 80.4 - - - +
400C THR* 1.3 60.8 + - - +
402C TRP* 3.0 35.3 + - - +
403C THR* 2.8 39.4 + - + +
361D HIS 4.7 5.4 - - - +
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Residues in contact with THR 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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396C GLU* 2.9 17.4 + - - +
397C THR* 3.5 10.5 - - - -
399C GLU* 1.3 78.5 - - - +
401C TRP* 1.3 59.9 + - - +
403C THR* 4.2 2.7 - - - -
404C GLU* 3.0 39.0 + - + +
425C LEU* 4.0 17.5 - - + -
428C GLN* 4.0 25.1 - - - +
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Residues in contact with TRP 401 (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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363C ASN* 3.4 24.7 - - - -
365C VAL* 3.3 36.0 - - + +
366C LYS* 3.9 20.4 - - + +
369C THR* 5.2 1.6 + - - -
397C THR 3.1 11.4 + - - +
398C TRP* 3.0 22.4 + + - +
400C THR* 1.3 75.1 - - - +
402C TRP* 1.3 72.3 + - + +
404C GLU* 3.1 6.2 + - + +
405C TYR* 3.0 77.7 + + + +
409C THR* 4.7 4.0 - - + +
425C LEU* 3.9 24.9 - - + -
507C GLN 5.5 1.1 - - - -
508C ALA* 3.4 18.2 - - - -
509C GLN* 4.2 14.1 - - - -
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Residues in contact with TRP 402 (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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398C TRP* 3.0 60.6 + + + +
399C GLU* 3.0 31.7 + - - +
401C TRP* 1.3 81.9 - - + +
403C THR* 1.3 82.6 + - + +
405C TYR* 3.3 6.4 + - - +
409C THR* 3.8 28.0 - - + +
410C TRP* 6.5 0.9 - + - -
331D LYS* 2.6 33.9 + - - -
361D HIS* 3.9 35.9 - - - -
362D THR* 4.2 15.5 - - - -
363D ASN 6.0 0.2 - - - -
364D ASP* 3.7 31.2 - - + -
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Residues in contact with THR 403 (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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399C GLU* 2.8 30.8 + - + +
400C THR* 3.6 5.5 + - - -
402C TRP* 1.3 118.9 - - + +
404C GLU* 1.3 67.6 + - - +
405C TYR 3.8 0.2 + - - -
331D LYS* 4.4 9.3 - - - +
333D GLY* 4.9 10.7 - - - -
334D GLN* 5.1 14.5 + - - +
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Residues in contact with GLU 404 (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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400C THR* 3.0 29.6 - - + +
401C TRP* 3.1 5.3 + - + +
403C THR* 1.3 82.9 + - - +
405C TYR* 1.3 60.1 + - - +
406C TRP* 3.7 1.2 + - - -
431C LYS* 3.1 39.2 + - - +
424D LYS* 5.4 5.2 + - - -
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Residues in contact with TYR 405 (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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366C LYS* 3.0 32.7 + - + -
401C TRP* 3.0 60.7 + + + +
402C TRP* 3.3 7.4 + - - +
403C THR 4.7 0.2 - - - +
404C GLU* 1.3 78.4 - - - +
406C TRP* 1.3 99.7 + + - +
407C GLN* 3.3 39.4 + - + +
409C THR* 4.5 9.2 - - + -
507C GLN 5.8 0.7 - - - -
508C ALA* 4.7 11.8 - - + +
331D LYS* 2.9 28.4 + - - +
394D GLN* 5.4 0.7 + - - -
424D LYS* 6.0 0.4 - - - -
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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