Contacts of the helix formed by residues 426 - 440 (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 PHE 426 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C SER* 4.7 4.7 - - - -
247C SER* 3.4 39.9 - - - -
248C GLY* 4.0 5.4 - - - -
252C THR* 5.0 7.0 - - + -
350C ILE* 4.2 6.7 - - + -
354C GLU* 3.7 36.3 - - + +
359C ILE* 3.9 15.7 - - + -
422C ALA* 2.8 12.7 + - - +
424C VAL 3.6 0.6 - - - -
425C MET* 1.3 116.6 - - + +
427C GLY* 1.3 67.9 + - - +
428C VAL 3.5 1.3 - - - -
429C PRO* 3.3 2.7 - - - +
430C SER* 2.9 32.3 + - - +
468C HIS* 3.6 23.1 - + - -
4003C SMB 5.8 2.7 - - + -
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Residues in contact with GLY 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C ILE* 4.0 25.8 - - - +
354C GLU* 5.5 0.6 - - - +
422C ALA 3.3 8.8 + - - -
423C ASP* 3.7 6.5 - - - -
426C PHE* 1.3 80.7 - - - +
428C VAL* 1.3 64.7 + - - +
430C SER* 3.5 2.1 - - - -
431C VAL* 3.1 22.3 + - - +
540C LYS* 4.3 14.5 - - - +
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Residues in contact with VAL 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C ASP* 2.9 23.4 + - + +
424C VAL* 5.0 2.2 - - - -
427C GLY* 1.3 70.7 - - - -
429C PRO* 1.3 71.4 - - + +
431C VAL* 3.0 13.0 + - - +
432C ILE* 3.1 28.6 + - + +
540C LYS* 5.6 0.2 - - + -
543C GLU* 4.1 20.2 - - + +
544C VAL* 3.8 28.5 - - + +
547C TRP* 3.6 39.9 - - + -
548C THR* 5.3 0.7 - - - +
551C PHE* 6.3 0.9 - - + -
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Residues in contact with PRO 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C VAL* 3.9 17.9 - - + -
251C LEU* 3.7 21.4 - - + +
252C THR* 4.3 12.1 - - - +
423C ASP 3.4 9.6 - - - +
424C VAL 3.3 19.7 - - - +
425C MET 4.1 8.1 - - - +
426C PHE 3.3 11.2 - - - +
428C VAL* 1.3 97.7 - - + +
430C SER* 1.3 61.3 + - - +
432C ILE* 3.3 6.8 + - + +
433C VAL* 3.1 26.5 + - - +
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Residues in contact with SER 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C GLY* 4.4 10.4 + - - -
249C VAL* 3.8 23.5 - - - +
252C THR* 5.7 0.2 + - - -
348C VAL* 3.7 20.4 - - - +
349C GLY 4.4 0.9 + - - -
350C ILE* 3.7 21.7 - - - +
426C PHE* 2.9 23.5 + - - -
427C GLY 3.5 3.4 - - - -
429C PRO* 1.3 76.9 - - - +
431C VAL* 1.3 62.7 + - - +
433C VAL* 3.3 4.9 + - - +
434C ALA 3.2 16.8 + - - -
446C MET* 3.9 6.0 - - - +
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Residues in contact with VAL 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C ILE* 6.1 0.4 - - + -
427C GLY 3.1 10.8 + - - +
428C VAL 3.0 7.4 + - - +
430C SER* 1.3 77.9 - - - +
432C ILE* 1.3 65.9 + - - +
434C ALA* 3.1 3.8 + - - +
435C ARG* 2.9 45.1 + - - +
446C MET* 3.4 28.0 - - + -
520C TYR* 3.4 17.3 - - - +
539C LEU* 3.5 28.9 - - + +
540C LYS* 4.1 7.4 - - + -
544C VAL* 4.0 14.1 - - + -
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Residues in contact with ILE 432 (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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251C LEU* 3.7 18.4 - - + -
336C GLN* 4.4 0.7 - - - +
428C VAL* 3.1 30.2 + - + +
429C PRO* 3.6 9.9 - - + +
431C VAL* 1.3 76.6 - - - +
433C VAL* 1.3 63.0 + - - +
435C ARG* 3.3 8.7 + - - +
436C ASN* 2.7 45.2 + - - +
544C VAL* 3.8 23.1 - - + -
548C THR* 4.3 9.4 - - - +
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Residues in contact with VAL 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C SER* 4.8 6.1 - - - +
249C VAL* 3.7 26.9 - - + -
250C ALA* 5.0 0.7 - - + +
251C LEU* 3.5 21.8 - - + +
336C GLN* 3.6 22.7 + - - +
346C TYR* 3.9 29.6 - - + +
348C VAL* 4.4 5.2 - - + -
429C PRO 3.1 18.2 + - - +
430C SER 3.5 8.3 - - - +
432C ILE* 1.3 74.6 - - - +
434C ALA* 1.3 54.5 + - - +
436C ASN* 3.1 4.2 + - - +
437C HIS* 2.8 34.0 + - + +
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Residues in contact with ALA 434 (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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348C VAL* 4.4 8.5 - - + -
430C SER 3.2 5.5 + - - +
431C VAL 3.1 3.9 + - - +
433C VAL* 1.3 79.4 - - - +
435C ARG* 1.3 52.2 + - - +
437C HIS* 3.2 4.8 + - - +
438C ARG* 2.6 36.4 + - - +
444C THR* 3.5 28.1 - - + +
446C MET* 3.5 35.7 - - + -
520C TYR* 3.9 5.2 - - + -
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Residues in contact with ARG 435 (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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431C VAL* 2.9 30.8 + - - +
432C ILE* 3.5 11.1 - - - +
434C ALA* 1.3 72.5 - - - +
436C ASN* 1.3 58.0 + - - +
438C ARG* 2.9 23.0 + - - +
439C ASP* 2.7 41.7 + - - +
520C TYR* 3.3 25.2 + - + +
524C GLU* 2.7 35.3 + - - -
539C LEU 5.2 0.2 + - - -
541C ASP* 3.6 30.1 + - - +
544C VAL* 4.1 20.7 - - - +
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Residues in contact with ASN 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C GLN* 3.7 46.5 + - + +
337C ALA* 4.6 4.6 - - - +
339C ARG* 2.9 37.6 + - - +
432C ILE* 2.7 44.5 + - - +
433C VAL 3.5 3.4 - - - +
435C ARG* 1.3 76.5 - - - +
437C HIS* 1.3 61.6 + - - +
439C ASP* 3.4 2.4 + - - -
440C ALA* 3.1 6.9 + - - +
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Residues in contact with HIS 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C VAL* 4.9 12.6 - - + +
336C GLN* 4.7 2.2 - - - +
343C THR* 4.8 6.3 - - + +
344C VAL* 2.8 36.3 + - + -
346C TYR* 3.2 37.8 - + + +
433C VAL* 2.8 14.6 + - + +
434C ALA* 3.4 10.5 - - - +
436C ASN* 1.3 75.3 - - - +
438C ARG* 1.3 66.1 + - - +
440C ALA* 3.1 19.7 + - - +
442C ALA* 3.4 34.0 + - + +
443C PRO 3.6 3.1 + - - -
444C THR* 2.8 22.9 - - + +
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Residues in contact with ARG 438 (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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434C ALA 2.6 21.2 + - - +
435C ARG* 3.3 25.7 + - - +
437C HIS* 1.3 73.1 - - - +
439C ASP* 1.3 87.3 + - - +
441C GLY* 2.9 23.0 + - - -
442C ALA 3.8 6.5 + - - +
444C THR* 3.2 11.8 + - - +
519C GLU* 5.7 2.0 - - - +
520C TYR* 3.2 25.6 - - + +
521C ASN* 2.9 40.2 + - - -
522C GLN* 3.1 24.0 + - - +
524C GLU* 3.4 26.1 + - - +
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Residues in contact with ASP 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C ARG* 3.2 29.7 + - - +
435C ARG* 2.7 24.4 + - - +
436C ASN* 4.6 1.2 - - - -
438C ARG* 1.3 100.3 + - - +
440C ALA* 1.3 56.5 + - - +
441C GLY* 2.9 10.4 + - - -
522C GLN* 3.3 11.5 + - - +
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Residues in contact with ALA 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C ARG* 3.3 45.6 - - + +
343C THR* 4.3 23.7 + - + +
436C ASN 3.1 7.2 + - - +
437C HIS* 3.1 16.0 + - - +
439C ASP* 1.3 75.3 - - - +
441C GLY* 1.3 59.6 + - - +
442C ALA 3.7 0.2 - - - -
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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