Contacts of the helix formed by residues 397 - 410 (chain C) in PDB entry 1YAA
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 VAL 397 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333C MET* 3.4 31.2 - - + -
336C ALA* 3.7 35.9 - - + +
337C LEU* 3.9 12.5 - - + +
340C HIS* 4.3 11.2 - - + +
392C LEU* 4.2 9.2 - - + -
393C ASN 2.9 27.5 + - - +
394C GLN* 4.3 9.3 - - - +
395C GLY 3.9 0.2 - - - -
396C ASN* 1.3 82.0 + - - +
398C GLU* 1.3 58.0 + - - +
400C VAL* 3.3 6.2 + - - +
401C ALA* 2.9 27.2 + - - +
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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
----------------------------------------------------------
340C HIS* 3.2 32.0 + - + +
343C LYS* 3.5 18.6 + - - -
394C GLN 5.7 0.8 + - - -
396C ASN 3.3 0.8 - - - -
397C VAL* 1.3 78.5 - - - +
399C TYR* 1.3 59.1 + - - +
401C ALA* 3.0 3.3 + - - +
402C LYS* 2.9 71.0 + - - +
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Residues in contact with TYR 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C THR* 3.5 46.5 + - + -
33C VAL* 4.2 13.2 - - + -
376C THR 5.0 0.5 + - - -
377C HIS* 2.8 44.1 + + + +
379C VAL* 3.9 10.5 - - + -
395C GLY 5.5 1.1 - - - +
396C ASN* 3.1 14.8 + - + +
398C GLU* 1.3 77.1 - - - +
400C VAL* 1.3 63.5 + - - +
402C LYS* 3.5 9.6 + - + +
403C ALA* 3.1 20.6 + - + +
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Residues in contact with VAL 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C VAL* 3.9 30.7 - - + -
35C LEU* 4.1 14.4 - - + -
337C LEU* 4.3 7.0 - - + -
379C VAL* 4.5 11.0 - - + -
381C LEU* 6.1 0.2 - - + -
392C LEU* 3.7 30.1 - - + -
396C ASN 3.0 14.7 + - - +
397C VAL 3.6 6.7 - - - +
399C TYR* 1.3 75.3 - - - +
401C ALA* 1.3 60.3 + - - +
403C ALA* 3.2 5.3 + - - +
404C ILE* 3.0 47.5 + - + +
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Residues in contact with ALA 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C LEU* 4.1 9.8 - - + +
340C HIS* 3.5 30.1 - - + -
341C LEU* 3.4 25.8 - - + +
343C LYS* 5.0 0.2 - - - +
344C LEU* 3.7 7.6 - - + +
397C VAL 2.9 17.4 + - - +
398C GLU* 3.4 5.4 - - - +
400C VAL* 1.3 77.5 - - - +
402C LYS* 1.3 57.2 + - - +
404C ILE* 3.6 0.4 + - - -
405C ASP* 3.1 26.9 + - - +
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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
----------------------------------------------------------
343C LYS* 5.1 0.2 - - - +
344C LEU* 3.8 29.8 - - + -
398C GLU* 2.9 54.6 + - - +
399C TYR* 3.9 8.3 - - + +
401C ALA* 1.3 75.7 - - - +
403C ALA* 1.3 59.4 + - - +
405C ASP* 3.3 3.6 - - - +
406C GLU* 2.9 27.2 + - - +
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Residues in contact with ALA 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C LEU* 3.7 10.5 - - + -
377C HIS* 3.6 42.7 - - + -
379C VAL* 4.4 7.9 - - + -
399C TYR* 3.1 18.8 + - + +
400C VAL 3.2 5.6 + - - +
402C LYS* 1.3 74.8 - - - +
404C ILE* 1.3 66.1 + - - +
406C GLU* 3.2 2.6 + - - +
407C VAL* 3.0 27.9 + - - +
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Residues in contact with ILE 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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35C LEU* 6.1 1.3 - - + -
337C LEU* 4.3 22.9 - - + -
341C LEU* 4.3 15.0 - - + -
346C THR* 5.1 0.2 - - + -
350C TRP* 4.3 19.5 - - + -
363C THR* 5.7 8.1 - - + -
365C LEU* 4.6 20.6 - - + -
373C LEU* 4.0 13.9 - - + +
379C VAL* 6.1 0.2 - - + -
381C LEU* 6.2 3.8 - - + -
400C VAL* 3.0 37.7 + - + +
401C ALA* 3.8 5.2 - - - +
403C ALA* 1.3 74.3 - - - +
405C ASP* 1.3 58.6 + - - +
407C VAL* 3.3 4.9 + - - +
408C VAL* 2.9 47.6 + - + +
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Residues in contact with ASP 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C LEU* 3.8 20.8 - - + +
346C THR* 2.6 31.0 + - - +
401C ALA 3.1 19.3 + - - +
402C LYS* 3.3 10.2 - - - +
404C ILE* 1.3 78.2 - - - +
406C GLU* 1.3 64.1 + - - +
408C VAL* 3.5 0.9 + - - +
409C ARG* 2.5 66.6 + - - +
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Residues in contact with GLU 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C ARG* 2.9 44.3 + - - -
377C HIS* 2.9 27.4 - - - +
402C LYS 2.9 14.6 + - - +
403C ALA 3.2 7.8 + - - +
405C ASP* 1.3 79.7 - - - +
407C VAL* 1.3 59.5 + - - +
409C ARG* 3.3 5.5 + - - +
410C PHE* 2.9 39.2 + - - +
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Residues in contact with VAL 407 (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* 5.0 2.7 - - + -
369C MET* 3.2 45.7 - - + +
372C ARG* 3.6 29.6 - - + -
373C LEU* 3.8 25.4 - - + -
377C HIS* 3.9 3.4 - - + -
403C ALA 3.0 18.1 + - - +
404C ILE 3.6 4.9 - - - +
406C GLU* 1.3 84.1 - - - +
408C VAL* 1.3 63.2 + - + +
410C PHE* 3.3 3.7 + - - -
411C TYR* 3.3 26.8 + - + +
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Residues in contact with VAL 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C THR* 4.1 7.9 - - + -
347C PRO* 4.1 33.9 - - + +
350C TRP* 3.9 25.8 - - + -
365C LEU* 5.0 1.3 - - + -
369C MET* 4.4 23.7 - - + +
404C ILE* 2.9 34.4 + - + +
405C ASP 3.9 4.0 - - - +
407C VAL* 1.3 75.5 - - + +
409C ARG* 1.3 61.3 + - - +
411C TYR* 3.7 8.1 + - - +
412C ALA* 3.9 12.3 + - - +
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Residues in contact with ARG 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C LEU 3.8 7.4 + - - -
345C GLY 3.0 25.5 + - - -
346C THR* 3.4 0.6 - - - +
347C PRO* 3.1 33.2 - - + +
405C ASP* 2.5 50.9 + - - +
406C GLU* 3.7 4.9 - - - +
408C VAL* 1.3 75.0 - - - +
410C PHE* 1.3 66.3 + - - +
411C TYR 3.2 1.2 + - - -
412C ALA* 3.5 19.7 + - - +
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Residues in contact with PHE 410 (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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372C ARG* 3.4 34.5 - - - +
406C GLU* 2.9 36.0 + - - +
407C VAL* 3.3 9.4 + - - +
409C ARG* 1.3 77.7 - - - +
411C TYR* 1.3 96.2 + + - +
412C ALA* 3.7 3.3 + - - +
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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
------------------------------------------------------------
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