Contacts of the helix formed by residues 395 - 404 (chain C) in PDB entry 1YA8
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 LEU 395 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391C ILE* 3.8 12.6 - - + -
392C ALA* 2.8 36.6 + - + +
394C GLU* 1.3 89.0 - - + +
396C ILE* 1.3 67.5 + - - +
397C PRO* 3.3 2.9 - - - -
398C GLU* 2.9 19.7 + - - +
399C ALA* 3.1 9.6 + - - -
550C LEU* 3.5 47.6 - - + +
551C PHE* 4.5 14.6 - - + +
553C LYS* 5.1 18.4 - - + +
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Residues in contact with ILE 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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379C MET* 3.3 44.6 - - + +
382C LEU* 3.7 26.5 - - + -
383C TRP* 4.1 14.6 - - + +
391C ILE* 3.5 32.3 - - + +
392C ALA 3.4 0.2 + - - -
393C LYS* 3.2 27.4 - - + +
395C LEU* 1.3 75.4 - - - +
397C PRO* 1.3 60.2 - - + +
399C ALA* 3.0 4.7 + - - +
400C THR* 2.7 41.0 + - - +
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Residues in contact with PRO 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C MET* 4.0 27.6 - - + -
393C LYS 3.7 8.5 - - - +
394C GLU 4.2 7.0 - - - +
395C LEU 3.4 5.2 - - - -
396C ILE* 1.3 94.4 - - + +
398C GLU* 1.3 56.8 + - - +
400C THR* 3.3 1.0 + - - -
401C GLU* 2.7 35.0 + - - +
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Residues in contact with GLU 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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394C GLU 5.5 1.1 + - - +
395C LEU* 2.9 13.8 + - - +
397C PRO* 1.3 76.5 - - - +
399C ALA* 1.3 63.7 + - - +
401C GLU* 3.4 7.1 + - - +
402C LYS* 3.1 22.2 + - - +
546C PHE* 3.9 18.5 - - + -
549C ASN* 5.2 6.2 + - - -
550C LEU* 3.5 28.3 - - + +
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Residues in contact with ALA 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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382C LEU* 4.5 9.9 - - + -
391C ILE* 5.0 3.4 - - + -
395C LEU 3.1 7.9 + - - +
396C ILE* 3.0 12.4 + - - +
398C GLU* 1.3 78.4 - - - +
400C THR* 1.3 62.2 + - - +
402C LYS* 3.0 18.4 + - - +
403C TYR* 3.4 13.0 + - - -
420C LEU* 3.9 3.0 - - + +
546C PHE* 4.0 11.6 - - - -
547C TRP* 3.8 27.1 - - + -
550C LEU* 3.9 12.1 - - + +
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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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375C GLN* 3.3 21.9 + - - +
378C ALA* 3.9 13.5 - - + -
379C MET* 3.6 24.6 + - + +
382C LEU* 3.6 17.9 - - - +
396C ILE* 2.7 22.1 + - - +
397C PRO 3.9 1.6 - - - -
399C ALA* 1.3 73.1 - - - +
401C GLU* 1.3 56.9 - - - +
403C TYR 4.8 0.2 - - - +
404C LEU* 3.0 53.5 + - + +
417C PHE* 5.6 2.3 - - + -
420C LEU* 5.1 6.2 - - - +
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Residues in contact with GLU 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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375C GLN* 4.5 16.2 + - - +
397C PRO 2.7 23.5 + - - +
398C GLU* 3.7 7.9 - - + +
400C THR* 1.3 74.3 - - - +
402C LYS* 1.3 60.1 + - - +
405C GLY* 3.3 26.4 + - - +
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Residues in contact with LYS 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 GLU 3.1 11.3 + - - +
399C ALA 3.0 11.1 + - - +
401C GLU* 1.3 81.2 - - - +
403C TYR* 1.3 70.1 + - + +
405C GLY* 4.4 1.7 + - - -
406C GLY 5.3 0.7 + - - -
542C LYS* 4.3 30.2 - - - +
546C PHE* 3.8 48.2 - - + +
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Residues in contact with TYR 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 ALA 3.4 6.9 + - - +
400C THR* 5.3 0.4 - - - -
402C LYS* 1.3 96.7 - - + +
404C LEU* 1.3 68.4 + - + +
405C GLY 3.3 1.0 + - - -
406C GLY* 3.9 3.1 + - - -
416C LEU* 3.0 42.7 - - + +
419C ASP* 4.0 7.6 - - + -
420C LEU* 3.2 57.2 - - + -
423C ASP* 2.6 31.6 + - - -
542C LYS* 6.0 3.1 - - - -
543C GLU* 3.7 12.0 - - + +
546C PHE* 4.4 3.6 - + - -
547C TRP* 2.8 33.9 + + - -
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Residues in contact with LEU 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C LEU* 5.4 1.1 - - + -
374C ASP 5.3 0.4 - - - -
375C GLN* 2.9 18.5 - - - +
378C ALA* 3.4 33.2 - - + -
400C THR* 3.0 20.5 + - + +
403C TYR* 1.3 77.0 - - + +
405C GLY* 1.3 56.1 + - - +
406C GLY* 2.8 11.8 + - - -
407C THR 3.9 0.2 - - - +
413C LYS* 2.7 75.7 + - + +
416C LEU* 3.3 25.2 - - + +
417C PHE* 3.5 17.7 - - + +
420C LEU* 6.3 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