Contacts of the helix formed by residues 435 - 451 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390G TYR* 3.7 9.1 - - - -
433G PRO* 3.3 6.2 - - + +
434G ASP* 1.3 78.4 - - - +
436G MET* 1.3 69.6 + - - +
437G ASP* 3.6 17.3 + - - +
438G LYS* 3.2 36.0 + - + +
439G PHE* 3.6 13.2 + - - +
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Residues in contact with MET 436 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194G ILE* 6.0 0.9 - - + -
388G ASN* 3.5 34.6 - - - +
389G ILE* 3.7 28.7 - - + -
390G TYR* 3.6 30.0 - - + -
434G ASP 3.9 2.2 + - - -
435G ASP* 1.3 76.4 + - - +
437G ASP* 1.3 64.8 + - - +
439G PHE* 3.2 4.9 + - - +
440G MET* 2.8 60.3 + - + +
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Residues in contact with ASP 437 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435G ASP* 3.6 15.4 + - - +
436G MET* 1.3 81.9 - - - +
438G LYS* 1.3 56.9 + - - +
440G MET* 3.7 6.9 - - - +
441G ASP* 2.8 36.2 + - - +
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Residues in contact with LYS 438 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433G PRO* 4.1 22.9 - - + +
435G ASP* 3.2 25.8 + - + +
437G ASP* 1.3 74.2 - - - +
439G PHE* 1.3 58.7 + - - +
441G ASP* 3.9 4.8 - - - +
442G ASP* 2.8 69.2 + - - +
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Residues in contact with PHE 439 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182G PRO* 3.6 24.7 - - + -
185G LEU* 4.1 6.5 - - + -
186G TYR* 3.8 22.4 - + + -
190G CYS* 4.2 6.3 - - - -
390G TYR* 3.2 53.4 - + + +
432G LEU* 4.1 31.6 - - + -
433G PRO* 4.3 11.1 - - + +
435G ASP 3.6 4.9 + - - +
436G MET 3.2 7.9 + - - +
438G LYS* 1.3 77.6 - - - +
440G MET* 1.3 68.5 + - - +
442G ASP* 3.6 6.1 - - + +
443G CYS* 3.0 54.6 + - - -
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Residues in contact with MET 440 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186G TYR* 3.8 20.6 - - + -
190G CYS* 3.7 31.9 - - + -
191G LEU* 5.4 0.2 - - + -
194G ILE* 3.9 17.0 - - + -
389G ILE* 5.8 0.2 - - + -
390G TYR* 5.5 0.4 - - + -
436G MET* 2.8 47.2 + - + +
437G ASP* 3.7 7.4 - - - +
439G PHE* 1.3 79.2 - - + +
441G ASP* 1.3 64.0 + - - +
443G CYS* 3.6 1.7 - - - +
444G LEU* 2.8 24.8 + - - +
461G PHE* 3.5 36.8 - - + -
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Residues in contact with ASP 441 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437G ASP 2.8 21.4 + - - +
438G LYS* 4.0 5.3 - - - +
440G MET* 1.3 69.7 - - - +
442G ASP* 1.3 78.3 + - - +
444G LEU* 3.0 20.6 + - - +
445G THR* 3.2 22.7 + - - +
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Residues in contact with ASP 442 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433G PRO* 5.1 3.3 - - - +
438G LYS* 2.8 61.7 + - - +
439G PHE* 3.6 7.9 - - + +
441G ASP* 1.3 82.7 - - - +
443G CYS* 1.3 59.9 + - - +
445G THR* 3.2 7.4 + - - -
446G LYS* 2.9 29.7 + - + +
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Residues in contact with CYS 443 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182G PRO* 4.9 3.1 - - - -
186G TYR* 3.4 35.2 - - + -
439G PHE* 3.0 56.5 + - - +
442G ASP* 1.3 77.7 - - - +
444G LEU* 1.3 66.7 + - - +
446G LYS* 3.9 11.4 - - - -
447G TYR* 2.9 40.0 + - + +
454G PHE* 5.3 0.2 - - - -
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Residues in contact with LEU 444 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186G TYR* 3.8 13.8 + - - +
440G MET 2.8 14.0 + - - +
441G ASP* 3.0 16.8 + - - +
443G CYS* 1.3 76.4 - - - +
445G THR* 1.3 64.4 + - + +
448G LYS* 3.0 44.8 + - + +
454G PHE* 4.0 10.3 - - + -
456G PRO* 3.8 33.7 - - + -
461G PHE* 4.5 22.0 - - + -
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Residues in contact with THR 445 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441G ASP* 3.2 18.3 + - - +
442G ASP* 3.2 11.1 + - - -
444G LEU* 1.3 82.5 - - + +
446G LYS* 1.3 65.8 + - - +
447G TYR 3.5 0.2 - - - -
448G LYS* 4.0 16.4 - - + +
449G SER* 3.5 19.4 + - - -
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Residues in contact with LYS 446 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180G ASP* 4.3 8.8 + - - -
182G PRO* 5.9 3.1 - - - -
442G ASP* 2.9 17.6 + - + +
443G CYS* 3.2 12.3 + - - +
445G THR* 1.3 80.5 + - - +
447G TYR* 1.3 95.3 + - + +
449G SER* 3.4 2.3 + - - -
450G GLU* 3.0 57.1 + - - +
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Residues in contact with TYR 447 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171G VAL* 3.9 22.4 - - + -
174G TYR* 4.2 14.6 - + - -
175G ALA* 5.4 0.4 - - + -
180G ASP* 2.5 39.2 + - - -
182G PRO* 4.1 2.4 - - - +
183G GLY* 3.2 16.7 + - - -
186G TYR* 3.8 19.5 - + + -
443G CYS* 2.9 43.1 + - + +
446G LYS* 1.3 101.1 - - + +
448G LYS* 1.3 61.9 + - - +
449G SER 3.1 1.8 - - - -
450G GLU* 4.1 5.4 - - + +
451G VAL* 2.9 51.6 + - + +
454G PHE* 3.8 16.9 - - + -
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Residues in contact with LYS 448 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444G LEU* 3.0 43.4 + - + +
445G THR* 4.0 16.4 - - + +
447G TYR* 1.3 77.9 - - - +
449G SER* 1.3 61.2 + - - +
451G VAL 4.0 7.6 - - - +
452G LYS* 5.0 7.1 + - - +
454G PHE* 3.9 9.2 - - + +
456G PRO* 4.1 29.4 - - + +
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Residues in contact with SER 449 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445G THR 3.5 15.0 + - - -
446G LYS 3.4 4.1 + - - -
447G TYR 3.1 0.2 - - - -
448G LYS* 1.3 79.7 - - - +
450G GLU* 1.3 66.4 + - - +
451G VAL* 3.6 1.2 + - - -
452G LYS* 3.5 24.9 + - - +
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Residues in contact with GLU 450 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174G TYR* 3.0 48.8 + - + +
180G ASP* 4.9 0.5 - - - +
446G LYS* 3.0 51.9 + - + +
447G TYR* 4.2 8.9 - - + -
449G SER* 1.3 80.4 - - - +
451G VAL* 1.3 61.1 + - - +
452G LYS* 3.9 3.1 + - - +
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Residues in contact with VAL 451 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170G GLU* 4.4 16.2 - - + +
171G VAL* 4.8 5.2 - - + -
174G TYR* 3.6 39.5 - - + -
447G TYR* 2.9 37.3 + - + +
448G LYS 4.0 6.6 - - - +
450G GLU* 1.3 77.6 - - - +
452G LYS* 1.3 65.0 + - - +
453G VAL* 3.8 21.3 - - + -
454G PHE* 3.1 26.6 + - + +
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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