Contacts of the helix formed by residues 435 - 451 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390O TYR* 3.7 6.3 - - - -
433O PRO* 3.4 6.2 - - + +
434O ASP* 1.3 77.6 - - - +
436O MET* 1.3 66.0 + - - +
437O ASP* 3.5 15.3 + - - +
438O LYS* 2.9 39.2 + - + +
439O PHE 3.6 13.2 + - - -
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Residues in contact with MET 436 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194O ILE* 5.6 1.6 - - + -
388O ASN* 3.8 24.7 - - - +
389O ILE* 3.7 34.5 - - + -
390O TYR* 3.6 37.2 - - + -
434O ASP 3.6 2.2 + - - -
435O ASP* 1.3 71.1 + - - +
437O ASP* 1.3 68.1 + - - +
438O LYS 3.1 2.2 - - - -
439O PHE* 3.1 4.9 + - - +
440O MET* 2.8 57.0 + - + +
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Residues in contact with ASP 437 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435O ASP* 3.5 12.9 + - - +
436O MET* 1.3 83.2 - - - +
438O LYS* 1.3 55.9 + - - +
440O MET* 3.9 7.2 - - - +
441O ASP* 3.0 31.7 + - - +
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Residues in contact with LYS 438 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433O PRO* 4.0 22.0 - - + -
435O ASP* 2.9 26.7 + - + +
436O MET 3.1 0.2 - - - -
437O ASP* 1.3 74.6 - - - +
439O PHE* 1.3 65.5 + - - +
441O ASP* 4.0 3.3 - - - +
442O ASP* 3.1 64.7 + - - +
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Residues in contact with PHE 439 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182O PRO* 3.5 25.1 - - + -
185O LEU* 4.0 9.4 - - + -
186O TYR* 3.9 22.9 - + + -
190O CYS* 4.1 7.2 - - - -
390O TYR* 3.2 49.6 - + + +
432O LEU* 3.9 33.2 - - + -
433O PRO* 3.9 10.6 - - + +
435O ASP 3.6 4.5 + - - +
436O MET 3.1 7.6 + - - +
438O LYS* 1.3 78.8 - - - +
440O MET* 1.3 66.5 + - - +
442O ASP* 3.3 5.1 + - + +
443O CYS* 3.0 51.6 + - - -
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Residues in contact with MET 440 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186O TYR* 3.9 23.0 + - + +
190O CYS* 3.7 32.8 - - + -
191O LEU* 5.2 0.7 - - + -
194O ILE* 4.0 16.4 - - + -
436O MET* 2.8 46.1 + - + +
437O ASP* 3.9 7.6 - - - +
439O PHE* 1.3 78.4 - - + +
441O ASP* 1.3 56.4 + - - +
443O CYS* 4.0 1.4 - - - +
444O LEU* 3.1 29.5 + - - +
461O PHE* 3.8 31.2 - - + -
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Residues in contact with ASP 441 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437O ASP 3.0 17.9 + - - +
438O LYS* 4.1 3.6 - - - +
440O MET* 1.3 73.8 - - - +
442O ASP* 1.3 75.6 + - - +
444O LEU* 3.3 12.4 + - - +
445O THR* 3.3 36.2 + - - +
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Residues in contact with ASP 442 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433O PRO* 4.8 4.5 - - - +
438O LYS* 3.1 53.7 + - - +
439O PHE* 3.6 7.9 - - + +
441O ASP* 1.3 84.6 - - - +
443O CYS* 1.3 62.2 + - - +
445O THR* 3.5 6.6 + - - -
446O LYS* 3.2 24.9 + - - +
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Residues in contact with CYS 443 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182O PRO* 4.9 2.7 - - - -
186O TYR* 3.5 36.8 - - + -
439O PHE* 3.0 57.0 + - - +
442O ASP* 1.3 76.3 - - - +
444O LEU* 1.3 58.9 + - - +
446O LYS* 4.2 3.8 - - - -
447O TYR* 2.7 53.9 + - + +
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Residues in contact with LEU 444 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186O TYR* 4.0 9.5 + - - +
440O MET 3.1 18.6 + - - +
441O ASP* 3.3 11.4 + - - +
443O CYS* 1.3 76.4 - - - +
445O THR* 1.3 63.9 + - + +
448O LYS* 3.0 48.2 + - + +
454O PHE* 4.1 11.8 - - + -
456O PRO* 3.7 34.5 - - + -
461O PHE* 4.5 23.6 - - + +
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Residues in contact with THR 445 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441O ASP* 3.3 26.1 + - - +
442O ASP* 3.5 10.0 + - - -
443O CYS 3.2 0.4 - - - -
444O LEU* 1.3 82.9 - - + +
446O LYS* 1.3 65.7 + - - +
448O LYS* 3.7 10.8 - - + +
449O SER* 3.3 23.0 + - - -
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Residues in contact with LYS 446 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180O ASP* 4.0 9.1 + - - -
182O PRO* 6.1 1.3 - - - -
442O ASP 3.2 19.8 + - - +
443O CYS* 3.6 4.9 - - - +
445O THR* 1.3 78.3 + - - +
447O TYR* 1.3 98.5 + - + +
449O SER* 3.2 5.8 + - - -
450O GLU* 2.8 62.6 + - - +
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Residues in contact with TYR 447 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171O VAL* 4.1 17.3 - - + -
174O TYR* 4.2 14.1 - + - -
175O ALA* 5.3 0.2 - - + -
180O ASP* 2.4 34.7 + - - -
182O PRO* 4.0 2.4 - - - +
183O GLY* 3.0 26.2 + - - -
186O TYR* 3.7 17.9 - + + -
443O CYS* 2.7 49.0 + - + +
446O LYS* 1.3 98.8 - - + +
448O LYS* 1.3 59.2 + - - +
449O SER 3.1 1.6 - - - -
450O GLU* 4.2 2.5 - - + +
451O VAL* 2.8 53.9 + - + +
454O PHE* 3.6 19.4 - - + -
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Residues in contact with LYS 448 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444O LEU* 3.0 45.3 + - + +
445O THR* 3.7 11.9 - - + +
447O TYR* 1.3 75.4 - - - +
449O SER* 1.3 60.2 + - - +
451O VAL 3.6 10.9 - - - +
452O LYS* 4.5 9.9 - - - +
454O PHE* 3.6 11.2 - - - +
456O PRO* 4.1 23.2 - - + +
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Residues in contact with SER 449 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445O THR 3.3 14.5 + - - -
446O LYS* 3.2 5.9 + - - -
447O TYR 3.1 0.4 - - - -
448O LYS* 1.3 79.6 - - - +
450O GLU* 1.3 67.3 + - - +
451O VAL 3.4 0.4 + - - -
452O LYS* 3.6 21.6 + - - +
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Residues in contact with GLU 450 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174O TYR* 2.5 56.9 + - + +
180O ASP* 4.8 0.9 - - - +
446O LYS* 2.8 63.1 + - + +
447O TYR* 4.7 1.3 - - + -
449O SER* 1.3 77.8 - - - +
451O VAL* 1.3 60.9 + - + +
452O LYS* 4.1 3.0 + - - +
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Residues in contact with VAL 451 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170O GLU* 4.4 14.4 - - + +
171O VAL* 4.6 7.9 - - + -
174O TYR* 3.7 36.1 - - + -
447O TYR* 2.8 38.0 + - + +
448O LYS 3.6 7.9 - - - +
449O SER 3.4 0.4 - - - -
450O GLU* 1.3 81.0 - - - +
452O LYS* 1.3 64.2 + - - +
453O VAL* 4.0 15.0 - - + -
454O PHE* 3.3 32.6 - - + +
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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