Contacts of the helix formed by residues 390 - 400 (chain C) in PDB entry 6RKU
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 ILE 390 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A ILE* 5.8 1.3 - - + -
398A ARG* 4.5 35.4 - - + +
386C ALA 4.4 2.9 - - - +
387C LEU* 4.4 11.4 - - - +
388C ALA 3.6 5.9 + - - +
389C ASN* 1.3 73.9 - - - +
391C ASP* 1.3 69.5 + - + +
392C PRO* 3.5 1.1 - - - +
393C ILE* 3.3 6.6 + - - +
394C ILE* 2.9 50.2 + - + +
466C LEU* 3.6 39.5 - - + -
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Residues in contact with ASP 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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398A ARG* 5.4 8.4 + - - +
390C ILE* 1.3 84.2 - - + +
392C PRO* 1.3 66.9 - - + +
394C ILE* 3.0 16.8 + - + +
395C GLU* 2.5 55.7 + - - +
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Residues in contact with PRO 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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389C ASN* 4.6 13.7 - - + +
390C ILE 3.8 6.3 - - - +
391C ASP* 1.3 94.3 - - + +
393C ILE* 1.3 57.7 + - - +
395C GLU* 3.4 11.2 + - + +
396C LEU* 2.9 30.6 + - - +
415C TRP* 4.7 15.7 - - + -
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Residues in contact with ILE 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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463A LEU* 5.6 3.6 - - + -
386C ALA* 4.0 24.5 - - + +
389C ASN* 3.2 22.4 - - + +
390C ILE* 3.3 8.6 + - - +
391C ASP 3.2 0.8 - - - -
392C PRO* 1.3 74.2 - - - +
394C ILE* 1.3 67.1 + - + +
396C LEU* 3.8 5.3 - - - -
397C ILE* 2.9 44.3 + - + +
410C LEU* 4.3 13.9 - - + -
415C TRP* 3.5 36.6 - - + -
458C ILE* 5.0 14.4 - - + -
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Residues in contact with ILE 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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390A ILE* 5.9 1.6 - - + -
394A ILE* 4.5 34.3 - - + -
398A ARG* 6.0 2.0 - - - +
463A LEU* 6.1 4.5 - - + -
466A LEU* 6.1 4.5 - - + -
390C ILE* 2.9 46.9 + - + +
391C ASP* 3.0 19.5 + - + +
393C ILE* 1.3 78.1 - - + +
395C GLU* 1.3 59.8 + - - +
397C ILE* 3.3 6.3 + - - +
398C ARG* 2.9 55.4 + - + +
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Residues in contact with GLU 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 ASP* 2.5 58.9 + - - +
392C PRO* 3.6 9.0 - - + +
393C ILE 3.3 0.2 - - - -
394C ILE* 1.3 79.9 - - + +
396C LEU* 1.3 57.5 + - - +
398C ARG* 3.2 13.4 + - - +
399C HIS* 2.9 51.5 + - + +
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Residues in contact with LEU 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 PRO 2.9 18.1 + - - +
393C ILE* 3.8 6.1 - - - +
395C GLU* 1.3 75.7 - - - +
397C ILE* 1.3 65.3 + - + +
399C HIS* 3.7 4.8 + - - +
400C ALA* 3.1 26.4 + - + +
406C ALA* 4.0 28.9 - - + +
409C ALA* 4.0 26.0 - - + +
410C LEU* 4.0 22.0 - - + -
413C ASN* 4.7 12.6 - - - +
415C TRP* 5.1 9.2 - - + -
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Residues in contact with ILE 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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463A LEU* 4.0 31.2 - - + +
466A LEU* 3.2 39.8 - - + +
467A THR* 4.7 6.1 - - + +
393C ILE* 2.9 40.1 + - + +
394C ILE* 3.8 5.8 - - + +
396C LEU* 1.3 81.7 - - + +
398C ARG* 1.3 66.1 + - + +
400C ALA* 3.3 20.4 + - - +
406C ALA* 5.0 8.3 - - + -
410C LEU* 5.4 2.7 - - + -
458C ILE* 6.4 0.4 - - + -
459C LEU* 4.2 25.8 - - + -
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Residues in contact with ARG 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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390A ILE* 4.6 30.5 - - + +
391A ASP* 5.4 9.7 + - - +
394A ILE* 6.1 2.6 - - - +
466A LEU* 4.2 21.6 - - + +
467A THR* 5.8 1.0 - - - -
394C ILE* 2.9 41.2 + - + +
395C GLU* 3.2 14.3 + - - +
397C ILE* 1.3 76.1 - - + +
399C HIS* 1.3 65.0 + - + +
400C ALA 4.4 2.3 - - - +
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Residues in contact with HIS 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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395C GLU* 2.9 44.5 + - + +
396C LEU* 4.3 4.7 - - - +
398C ARG* 1.3 82.4 - - + +
400C ALA* 1.3 63.9 + - - +
401C PRO* 3.2 12.1 - - - +
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Residues in contact with ALA 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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467A THR* 4.0 13.5 - - + +
468A GLY 4.6 0.5 + - - -
396C LEU* 3.1 22.1 + - + +
397C ILE 3.3 13.0 + - - +
398C ARG 4.4 1.6 - - - +
399C HIS* 1.3 75.2 - - - +
401C PRO* 1.3 70.1 - - + +
402C THR 4.2 4.0 - - - +
405C GLU* 5.0 2.5 - - + -
406C ALA* 3.7 34.1 - - + +
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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