Contacts of the helix formed by residues 435 - 451 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390K TYR* 4.2 1.6 - - - -
433K PRO* 3.2 11.1 - - + +
434K ASP* 1.3 75.8 - - - +
436K MET* 1.3 64.7 + - - +
437K ASP* 3.7 12.1 + - - +
438K LYS* 3.1 38.1 + - + +
439K PHE* 3.3 20.8 + - - +
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Residues in contact with MET 436 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194K ILE* 5.5 1.6 - - + -
388K ASN* 3.6 34.6 - - - +
389K ILE* 3.9 26.0 - - + -
390K TYR* 3.6 29.2 - - + -
434K ASP 3.3 4.9 + - - -
435K ASP* 1.3 72.1 + - - +
437K ASP* 1.3 60.9 + - - +
439K PHE* 3.2 2.3 + - - +
440K MET* 2.7 72.3 + - + +
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Residues in contact with ASP 437 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435K ASP* 3.4 13.5 + - - +
436K MET* 1.3 83.3 - - - +
438K LYS* 1.3 57.8 + - - +
440K MET* 3.3 6.8 + - - +
441K ASP* 2.8 32.6 + - - +
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Residues in contact with LYS 438 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433K PRO* 4.8 13.7 - - + -
435K ASP* 3.1 26.6 + - + +
437K ASP* 1.3 75.5 - - - +
439K PHE* 1.3 58.2 + - - +
441K ASP* 3.9 3.8 - - - +
442K ASP* 2.9 63.3 + - - +
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Residues in contact with PHE 439 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182K PRO* 3.8 23.1 - - + -
185K LEU* 3.9 7.0 - - + -
186K TYR* 4.0 10.3 - + + -
190K CYS* 4.0 17.7 - - - -
390K TYR* 3.2 55.9 - + + +
432K LEU* 4.1 29.4 - - + -
433K PRO* 4.7 7.5 - - + +
435K ASP 3.3 7.1 + - - +
436K MET 3.2 7.3 + - - +
438K LYS* 1.3 79.8 - - - +
440K MET* 1.3 65.6 + - - +
442K ASP* 3.3 5.8 + - + +
443K CYS* 3.0 55.3 + - - -
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Residues in contact with MET 440 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186K TYR* 4.0 20.2 + - + -
190K CYS* 3.6 42.0 - - + -
191K LEU 5.5 0.2 - - - +
194K ILE* 4.0 10.8 - - + -
436K MET* 2.7 56.7 + - + +
437K ASP* 3.7 8.1 - - - +
439K PHE* 1.3 74.8 - - + +
441K ASP* 1.3 58.4 + - - +
443K CYS* 4.0 0.7 - - - +
444K LEU* 2.9 31.2 + - - +
461K PHE* 3.9 29.4 - - + -
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Residues in contact with ASP 441 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437K ASP 2.8 21.0 + - - +
438K LYS* 4.0 4.5 - - - +
440K MET* 1.3 71.3 - - - +
442K ASP* 1.3 69.9 + - - +
444K LEU* 3.4 13.2 + - - +
445K THR* 3.2 34.7 + - - +
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Residues in contact with ASP 442 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438K LYS* 2.9 55.5 + - - +
439K PHE* 3.8 6.6 - - + +
441K ASP* 1.3 78.8 - - - +
443K CYS* 1.3 60.0 + - - +
445K THR* 3.0 8.4 + - - -
446K LYS* 2.9 31.5 + - - +
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Residues in contact with CYS 443 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182K PRO* 5.0 4.5 - - - -
186K TYR* 3.4 35.9 - - + -
439K PHE* 3.0 56.6 + - - +
442K ASP* 1.3 76.9 - - - +
444K LEU* 1.3 66.9 + - - +
446K LYS* 4.3 3.1 - - - -
447K TYR* 2.8 44.6 + - + +
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Residues in contact with LEU 444 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186K TYR* 3.6 13.4 + - - +
440K MET 2.9 20.2 + - - +
441K ASP* 3.7 16.4 - - - +
442K ASP 3.4 0.2 - - - -
443K CYS* 1.3 77.3 - - - +
445K THR* 1.3 63.6 + - + +
448K LYS* 3.0 46.0 + - + +
454K PHE* 4.1 10.4 - - + -
456K PRO* 3.6 33.7 - - + -
461K PHE* 4.7 18.8 - - + +
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Residues in contact with THR 445 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441K ASP* 3.2 26.1 + - - +
442K ASP* 3.0 16.1 + - - -
444K LEU* 1.3 80.2 - - + +
446K LYS* 1.3 68.8 + - - +
448K LYS* 3.5 8.5 + - + +
449K SER* 3.3 19.4 + - - -
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Residues in contact with LYS 446 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180K ASP* 4.1 7.0 - - - -
182K PRO* 6.1 2.2 - - + -
442K ASP 2.9 19.2 + - - +
443K CYS* 3.8 4.7 - - - +
445K THR* 1.3 76.9 + - - +
447K TYR* 1.3 101.0 + - + +
449K SER* 3.1 8.8 + - - -
450K GLU* 2.8 58.9 + - - +
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Residues in contact with TYR 447 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171K VAL* 3.9 23.1 - - + -
174K TYR* 4.3 14.4 - + - -
175K ALA* 5.5 0.4 - - + -
180K ASP* 2.5 31.6 + - - -
182K PRO* 4.0 3.3 - - - +
183K GLY* 3.1 25.3 + - - -
186K TYR* 3.6 20.9 - + - -
443K CYS* 2.8 44.2 + - + +
446K LYS* 1.3 100.6 - - + +
448K LYS* 1.3 60.6 + - - +
449K SER 3.1 1.3 - - - -
450K GLU* 4.2 3.1 - - + +
451K VAL* 2.8 48.2 + - + +
454K PHE* 3.6 18.7 - - + -
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Residues in contact with LYS 448 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444K LEU* 3.0 41.0 + - + +
445K THR* 3.6 9.6 - - + +
447K TYR* 1.3 76.7 - - - +
449K SER* 1.3 61.2 + - - +
451K VAL 3.8 10.1 - - - +
452K LYS* 4.5 8.0 + - - +
454K PHE* 3.5 13.8 - - + +
456K PRO* 3.9 37.1 - - + +
461K PHE 5.9 1.0 + - - -
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Residues in contact with SER 449 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445K THR 3.3 8.9 + - - -
446K LYS* 3.1 10.4 + - - -
447K TYR 3.1 0.2 - - - -
448K LYS* 1.3 79.5 - - - +
450K GLU* 1.3 67.5 + - - +
451K VAL 3.3 0.7 + - - -
452K LYS* 2.8 31.5 + - - +
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Residues in contact with GLU 450 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174K TYR* 2.6 54.9 + - + +
180K ASP* 5.3 0.3 - - - +
446K LYS* 2.8 61.3 + - - +
447K TYR* 4.6 1.3 - - + -
449K SER* 1.3 76.5 - - - +
451K VAL* 1.3 64.4 + - + +
452K LYS* 4.0 2.3 + - - +
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Residues in contact with VAL 451 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170K GLU 4.0 17.9 - - - +
171K VAL* 4.7 5.2 - - - -
174K TYR* 3.7 35.7 - - + -
447K TYR* 2.8 33.9 + - + +
448K LYS 3.8 6.6 - - - +
449K SER 3.3 1.0 - - - -
450K GLU* 1.3 82.6 - - - +
452K LYS* 1.3 59.6 + - - +
453K VAL* 4.0 15.5 - - + -
454K PHE* 2.9 39.8 + - + +
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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