Contacts of the helix formed by residues 435 - 451 (chain C) in PDB entry 2I2X
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 ASP 435 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390C TYR* 3.9 1.8 - - - -
433C PRO* 3.2 5.4 - - + +
434C ASP* 1.3 78.9 - - - +
436C MET* 1.3 65.1 + - - +
437C ASP* 3.4 14.7 + - - +
438C LYS* 2.8 38.7 + - + +
439C PHE* 3.3 20.8 + - - +
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Residues in contact with MET 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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194C ILE* 5.7 0.7 - - + -
388C ASN* 3.7 29.4 - - - +
389C ILE* 3.7 33.7 - - + -
390C TYR* 3.5 32.3 - - + -
434C ASP 3.5 3.6 + - - -
435C ASP* 1.3 72.5 + - - +
437C ASP* 1.3 59.7 + - - +
439C PHE* 3.1 3.5 + - - +
440C MET* 2.7 65.5 + - + +
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Residues in contact with ASP 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C ASP* 3.4 12.9 + - - +
436C MET* 1.3 77.3 - - - +
438C LYS* 1.3 68.0 + - - +
440C MET* 4.4 7.2 - - - +
441C ASP* 2.9 41.7 + - - +
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Residues in contact with LYS 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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433C PRO* 4.1 18.8 - - + -
435C ASP* 2.8 30.6 + - + +
437C ASP* 1.3 78.6 - - - +
439C PHE* 1.4 56.5 + - - +
441C ASP* 3.9 4.1 - - + +
442C ASP* 3.0 52.8 + - - +
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Residues in contact with PHE 439 (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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182C PRO* 3.7 24.2 - - + -
185C LEU* 3.9 9.9 - - + -
186C TYR* 3.9 18.8 - + + -
190C CYS* 4.0 10.1 - - - -
390C TYR* 3.2 48.9 - + + +
432C LEU* 3.9 31.2 - - + -
433C PRO* 4.2 11.1 - - + +
435C ASP 3.3 5.4 + - - +
436C MET 3.1 7.4 + - - +
438C LYS* 1.4 74.9 - - - +
440C MET* 1.3 71.5 + - - +
442C ASP* 3.5 5.6 + - + +
443C CYS* 3.1 49.4 + - - -
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Residues in contact with MET 440 (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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186C TYR* 4.0 15.3 + - + -
190C CYS* 3.7 35.4 - - + -
194C ILE* 3.8 17.3 - - + -
436C MET* 2.7 53.0 + - + +
437C ASP* 3.8 8.5 - - - +
439C PHE* 1.3 74.5 - - + +
441C ASP* 1.3 62.3 + - - +
443C CYS* 3.4 1.7 + - - +
444C LEU* 2.9 30.8 + - - +
461C PHE* 3.7 34.8 - - + -
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Residues in contact with ASP 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C ASP* 2.9 33.9 + - - +
438C LYS* 3.9 5.5 - - + +
440C MET* 1.3 75.6 - - - +
442C ASP* 1.3 68.5 + - - +
444C LEU* 3.4 7.8 + - - +
445C THR* 2.9 30.3 + - + +
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Residues in contact with ASP 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433C PRO* 5.1 4.7 - - - +
438C LYS* 3.0 54.1 + - - +
439C PHE* 4.0 6.7 - - + +
441C ASP* 1.3 77.0 - - - +
443C CYS* 1.3 61.2 + - - +
445C THR* 3.5 4.9 + - - +
446C LYS* 2.9 30.5 + - - +
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Residues in contact with CYS 443 (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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182C PRO* 4.9 3.8 - - - -
186C TYR* 3.5 34.1 - - + -
439C PHE* 3.1 58.2 + - - +
442C ASP* 1.3 75.2 - - - +
444C LEU* 1.3 68.5 + - - +
446C LYS* 4.1 6.1 - - - -
447C TYR* 2.7 43.8 + - + +
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Residues in contact with LEU 444 (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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186C TYR* 3.7 12.0 + - - +
440C MET 2.9 18.4 + - - +
441C ASP* 3.8 9.4 - - - +
442C ASP 3.4 0.4 - - - -
443C CYS* 1.3 73.2 - - - +
445C THR* 1.3 62.1 + - + +
448C LYS* 3.0 47.7 + - + +
454C PHE* 3.8 15.7 - - + -
456C PRO* 3.6 32.8 - - + -
461C PHE* 4.5 24.9 - - + +
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Residues in contact with THR 445 (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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441C ASP* 2.9 22.0 + - + +
442C ASP* 4.2 5.2 + - - +
443C CYS 3.1 0.4 - - - -
444C LEU* 1.3 79.0 - - + +
446C LYS* 1.3 65.8 + - - +
448C LYS* 3.8 9.0 - - - +
449C SER* 3.3 22.0 + - - -
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Residues in contact with LYS 446 (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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180C ASP* 4.1 9.2 - - - -
182C PRO* 6.1 2.2 - - + -
442C ASP 2.9 19.1 + - - +
443C CYS* 3.7 7.2 - - - +
445C THR* 1.3 80.0 + - - +
447C TYR* 1.3 94.4 + - + +
449C SER* 3.3 5.3 + - - -
450C GLU* 2.8 59.4 + - - +
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Residues in contact with TYR 447 (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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171C VAL* 3.6 22.4 - - + -
174C TYR* 4.2 14.6 - + - -
175C ALA* 5.6 0.4 - - + -
180C ASP* 2.7 31.5 + - - -
182C PRO* 4.1 2.8 - - - +
183C GLY* 3.1 24.9 + - - -
186C TYR* 3.7 20.6 - + - -
443C CYS* 2.7 48.4 + - + +
446C LYS* 1.3 100.1 - - + +
448C LYS* 1.3 60.4 + - - +
449C SER 3.1 1.3 - - - -
450C GLU* 4.0 3.4 - - + +
451C VAL* 2.8 49.7 + - + +
454C PHE* 3.6 18.7 - - + -
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Residues in contact with LYS 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C LEU* 3.0 37.4 + - + +
445C THR* 3.8 9.2 - - - +
447C TYR* 1.3 75.8 - - - +
449C SER* 1.3 61.0 + - - +
451C VAL 3.6 10.8 - - - +
452C LYS* 3.9 12.3 + - - +
454C PHE* 3.6 11.7 - - + +
456C PRO* 4.0 37.0 - - + +
461C PHE 5.8 1.2 + - - -
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Residues in contact with SER 449 (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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445C THR 3.3 16.2 + - - -
446C LYS* 3.4 5.2 - - - -
447C TYR 3.1 0.2 - - - -
448C LYS* 1.3 81.0 - - - +
450C GLU* 1.3 65.4 + - - +
451C VAL 3.5 0.3 + - - -
452C LYS* 3.2 27.9 + - - +
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Residues in contact with GLU 450 (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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174C TYR* 2.3 58.6 + - + +
180C ASP* 4.8 1.2 - - - +
446C LYS* 2.8 59.7 + - - +
447C TYR* 3.3 2.9 + - + -
449C SER* 1.3 78.9 - - - +
451C VAL* 1.3 62.2 + - + +
452C LYS* 4.1 2.7 + - - +
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Residues in contact with VAL 451 (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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170C GLU 4.4 16.4 - - - +
171C VAL* 4.8 5.2 - - + +
174C TYR* 3.6 37.5 - - + -
447C TYR* 2.8 35.6 + - + +
448C LYS 3.6 5.8 - - - +
449C SER 3.4 0.2 - - - -
450C GLU* 1.3 83.0 - - - +
452C LYS* 1.3 59.3 + - - +
453C VAL* 3.9 24.5 - - + -
454C PHE* 3.2 29.6 + - + +
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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
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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