Contacts of the helix formed by residues 424 - 436 (chain C) in PDB entry 1Y9D
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 424 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C MET* 3.9 19.7 - - + +
71C LYS* 5.6 0.7 - - - +
96C ASP* 4.6 8.5 - - - +
391C SER* 3.3 4.3 + - - -
392C ILE 3.6 21.5 - - - +
393C ASP* 3.1 7.1 + - - -
394C VAL* 4.4 0.9 - - + -
415C THR* 4.3 4.0 - - - +
416C SER* 3.8 23.3 - - - +
421C THR* 3.7 38.6 - - + +
423C GLY* 1.3 77.6 - - - +
425C GLY* 1.3 60.0 + - - +
426C ILE 3.4 0.2 - - - -
427C PRO* 3.5 5.8 - - - -
428C GLY* 2.8 29.7 + - - +
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Residues in contact with GLY 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C SER* 2.7 27.2 + - - -
392C ILE 4.3 0.2 - - - -
393C ASP* 3.0 27.2 + - - -
423C GLY 3.3 0.2 - - - -
424C VAL* 1.3 78.5 - - - +
426C ILE* 1.3 61.8 + - - +
429C ALA* 3.1 11.4 + - - +
443C ASN* 3.2 22.3 - - - +
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Residues in contact with ILE 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C ASP* 4.7 0.8 + - - -
423C GLY 4.0 1.2 + - - -
425C GLY* 1.3 73.2 - - - +
427C PRO* 1.3 66.2 - - + +
429C ALA* 3.3 4.2 + - - +
430C ILE* 3.0 44.8 + - + +
443C ASN* 3.5 22.7 + - - +
450C ALA* 4.0 15.3 - - + +
453C THR* 3.3 34.5 + - - +
454C MET* 3.8 8.1 - - + -
456C ASP* 3.8 24.9 - - + +
457C LEU* 3.8 26.7 - - + -
460C GLN* 4.0 7.8 + - - +
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Residues in contact with PRO 427 (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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61C VAL* 3.6 32.3 - - + +
64C MET* 3.6 29.8 - - + -
65C ALA* 3.7 12.6 - - + +
423C GLY 3.0 29.2 - - - +
424C VAL* 3.3 8.7 - - - +
426C ILE* 1.3 88.1 - - + +
428C GLY* 1.3 64.6 + - - +
430C ILE* 3.2 11.8 + - + +
431C ALA* 2.9 19.9 + - - +
453C THR* 4.1 3.8 - - - +
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Residues in contact with GLY 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C MET 5.2 0.2 + - - -
68C ALA* 3.7 22.5 - - - +
72C LEU* 4.6 0.2 - - - +
391C SER* 3.2 18.2 - - - -
414C ILE* 4.3 8.3 - - - +
424C VAL* 2.8 17.8 + - - -
427C PRO* 1.3 72.9 - - - +
429C ALA* 1.3 57.1 + - - +
431C ALA* 3.3 3.3 + - - +
432C ALA* 2.8 29.1 + - - +
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Residues in contact with ALA 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C SER* 3.3 6.8 + - - -
425C GLY 3.1 17.8 + - - +
426C ILE* 3.6 4.5 - - - +
428C GLY* 1.3 74.9 - - - +
430C ILE* 1.3 64.4 + - - +
433C LYS* 3.1 26.5 + - - +
441C VAL* 3.7 17.6 - - + +
442C PHE 4.2 0.2 - - - +
443C ASN* 3.8 9.6 - - + -
460C GLN* 4.7 0.9 - - - +
467C VAL* 3.5 33.9 - - + +
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Residues in contact with ILE 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TYR* 4.3 13.2 - - + -
54C ILE* 4.9 1.8 - - + -
56C VAL* 6.1 0.7 - - + -
61C VAL* 4.5 5.8 - - + -
65C ALA* 4.9 1.3 - - + -
426C ILE* 3.0 31.0 + - + +
427C PRO* 3.6 11.7 - - + +
429C ALA* 1.3 76.5 - - - +
431C ALA* 1.3 64.1 + - - +
433C LYS* 4.0 1.9 - - - +
434C LEU* 3.1 35.3 + - + +
456C ASP* 3.6 28.3 - - + +
459C THR* 4.1 21.8 - - + -
460C GLN* 3.7 18.6 - - + -
465C LEU* 3.7 21.8 - - + +
467C VAL* 4.6 2.0 - - - +
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Residues in contact with ALA 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TYR* 3.7 12.8 - - - +
65C ALA* 3.4 20.8 - - - +
68C ALA* 3.8 11.7 - - + -
69C ASP* 3.4 20.6 - - - +
72C LEU* 4.6 0.9 - - + -
427C PRO 2.9 12.5 + - - +
428C GLY 3.7 7.0 - - - +
430C ILE* 1.3 78.1 - - - +
432C ALA* 1.3 53.8 + - - +
434C LEU* 3.1 2.2 + - - +
435C ASN* 2.6 39.5 + - - +
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Residues in contact with ALA 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LEU* 3.6 17.9 - - + +
389C ILE* 3.7 31.0 - - + -
391C SER* 5.8 0.2 - - - -
414C ILE* 4.9 1.3 - - + -
428C GLY 2.8 20.5 + - - +
429C ALA* 3.3 4.7 + - - +
431C ALA* 1.3 72.8 - - - +
433C LYS* 1.3 57.7 + - - +
435C ASN* 3.2 1.6 + - - +
436C TYR* 2.8 37.1 + - - +
441C VAL* 3.8 17.0 - - + -
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Residues in contact with LYS 433 (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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429C ALA 3.1 16.0 + - - +
430C ILE 4.0 2.5 - - - +
432C ALA* 1.3 77.4 - - - +
434C LEU* 1.3 62.7 + - - +
436C TYR 4.1 4.7 - - - -
437C PRO* 3.3 44.6 + - + +
439C ARG 2.7 29.8 + - - -
440C GLN* 3.9 3.6 - - - +
441C VAL* 3.9 22.2 - - + +
465C LEU* 4.1 23.4 - - + +
466C PRO* 3.4 54.7 + - + +
467C VAL* 4.4 2.5 - - + +
533C ALA 4.7 3.8 + - - -
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Residues in contact with LEU 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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27C ASP* 4.4 7.8 - - - +
28C HIS* 3.7 28.2 - - + +
30C TYR* 3.6 33.2 - - + +
52C HIS* 6.4 0.4 - - + -
54C ILE* 3.9 28.5 - - + -
430C ILE* 3.1 27.3 + - + +
431C ALA 3.1 4.9 + - - +
433C LYS* 1.3 78.0 - - - +
435C ASN* 1.3 63.5 + - - +
437C PRO* 4.3 8.5 - - - +
463C TYR* 5.3 2.5 - - + -
465C LEU* 3.7 26.7 - - + -
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Residues in contact with ASN 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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27C ASP* 5.9 0.3 - - - +
28C HIS* 3.4 15.2 - - - -
69C ASP* 2.8 32.1 + - - +
72C LEU* 4.2 5.7 - - - +
73C THR* 3.5 21.9 + - + +
431C ALA* 2.6 29.7 + - - +
434C LEU* 1.3 81.2 - - - +
436C TYR* 1.3 86.6 + - + +
437C PRO* 3.7 6.0 - - - +
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Residues in contact with TYR 436 (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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72C LEU* 3.6 34.8 + - + -
73C THR* 4.0 10.1 - - + +
389C ILE* 3.3 26.9 - - + -
412C ARG* 4.8 4.3 + - + -
432C ALA* 2.8 22.3 + - - +
433C LYS* 3.4 8.0 - - - +
435C ASN* 1.3 99.1 - - + +
437C PRO* 1.3 67.3 - - - +
438C GLU 3.1 2.7 - - - +
439C ARG* 3.1 58.4 + - + +
441C VAL* 4.9 0.6 - - + +
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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