Contacts of the helix formed by residues 435 - 451 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390A TYR* 4.2 1.3 - - - -
433A PRO* 3.3 5.8 - - + +
434A ASP* 1.3 76.4 - - - +
436A MET* 1.3 67.9 + - - +
437A ASP* 3.4 14.8 + - - +
438A LYS* 2.8 50.2 + - + +
439A PHE* 3.4 7.4 + - - +
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Residues in contact with MET 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A CYS* 5.7 0.2 - - - -
194A ILE* 5.3 2.2 - - + -
388A ASN* 4.1 18.8 - - - +
389A ILE* 3.7 35.2 - - + -
390A TYR* 3.5 40.8 - - + -
434A ASP 3.5 4.6 + - - -
435A ASP* 1.3 73.6 + - - +
437A ASP* 1.3 61.4 + - - +
439A PHE* 3.0 5.7 + - - +
440A MET* 2.7 64.2 + - + +
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Residues in contact with ASP 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A ASP* 3.4 13.1 + - - +
436A MET* 1.3 80.7 - - - +
438A LYS* 1.3 53.9 + - - +
440A MET* 3.6 7.8 - - - +
441A ASP* 2.8 38.3 + - - +
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Residues in contact with LYS 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433A PRO* 4.0 20.0 - - + -
435A ASP* 2.8 31.6 + - + +
437A ASP* 1.3 72.9 - - - +
439A PHE* 1.3 52.2 + - - +
441A ASP* 3.6 4.7 - - + +
442A ASP* 2.8 64.2 + - - +
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Residues in contact with PHE 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A PRO* 3.6 24.5 - - + -
185A LEU* 4.0 11.7 - - + -
186A TYR* 3.8 13.7 - + + -
190A CYS* 3.9 14.1 - - - -
390A TYR* 3.2 47.3 - + + +
432A LEU* 3.7 35.7 - - + -
433A PRO* 4.3 8.7 - - + +
435A ASP 3.4 3.3 + - - +
436A MET 3.0 7.9 + - - +
438A LYS* 1.3 74.9 - - - +
440A MET* 1.3 71.3 + - - +
442A ASP* 3.3 6.8 + - + -
443A CYS* 2.9 55.6 + - - -
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Residues in contact with MET 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A TYR* 3.8 20.7 + - + -
190A CYS* 3.5 37.2 - - + -
191A LEU* 5.0 0.4 - - + -
194A ILE* 3.8 17.0 - - + -
436A MET* 2.7 49.0 + - + +
437A ASP* 3.6 8.7 - - - +
439A PHE* 1.3 74.6 - - - +
441A ASP* 1.3 52.1 + - - +
443A CYS* 3.7 1.6 - - - +
444A LEU* 2.8 36.6 + - - +
461A PHE* 3.7 33.0 - - + -
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Residues in contact with ASP 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437A ASP 2.8 21.6 + - - +
438A LYS* 3.7 5.5 - - + +
440A MET* 1.3 70.8 - - - +
442A ASP* 1.3 69.9 + - - +
444A LEU* 3.5 11.8 + - - +
445A THR* 3.1 42.6 + - - +
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Residues in contact with ASP 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433A PRO* 5.1 5.9 - - - +
438A LYS* 2.8 58.4 + - - +
439A PHE* 3.7 9.5 - - + +
441A ASP* 1.3 76.6 - - - +
443A CYS* 1.3 59.7 + - - +
445A THR* 3.5 5.3 + - - -
446A LYS* 3.0 30.0 + - - +
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Residues in contact with CYS 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A PRO* 4.9 3.4 - - - -
186A TYR* 3.4 36.3 - - + -
439A PHE* 2.9 58.0 + - - +
442A ASP* 1.3 76.1 - - - +
444A LEU* 1.3 67.8 - - - +
446A LYS* 3.2 4.0 + - - -
447A TYR* 2.8 43.2 + - + +
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Residues in contact with LEU 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A TYR* 3.8 11.3 + - - +
440A MET 2.8 21.4 + - - +
441A ASP* 3.7 15.3 - - - +
443A CYS* 1.3 72.7 - - - +
445A THR* 1.3 62.6 + - + +
448A LYS* 3.0 51.3 + - + +
454A PHE* 3.9 13.1 - - + -
456A PRO* 3.8 34.1 - - + -
461A PHE* 4.7 23.8 - - + +
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Residues in contact with THR 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A ASP* 3.1 33.5 + - - +
442A ASP* 4.0 4.4 + - - -
443A CYS 3.2 0.4 - - - -
444A LEU* 1.3 79.3 - - + +
446A LYS* 1.3 65.1 + - - +
448A LYS* 3.5 10.7 + - + +
449A SER* 3.2 23.9 + - - -
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Residues in contact with LYS 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ASP* 3.9 12.6 - - - -
182A PRO* 6.2 1.3 - - + -
442A ASP 3.0 20.4 + - - +
443A CYS* 3.2 5.8 + - - +
445A THR* 1.3 80.5 + - - +
447A TYR* 1.3 92.2 + - + +
449A SER* 3.3 3.4 + - - -
450A GLU* 2.9 64.0 + - - +
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Residues in contact with TYR 447 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A VAL* 3.7 22.4 - - + -
174A TYR* 4.1 14.4 - + - -
175A ALA* 5.5 0.4 - - + -
180A ASP* 2.6 31.5 + - - -
182A PRO* 4.2 2.8 - - - +
183A GLY* 3.1 24.6 + - - -
186A TYR* 3.6 26.0 - + + -
443A CYS* 2.8 45.2 + - + +
446A LYS* 1.3 97.2 - - + +
448A LYS* 1.3 59.0 + - - +
449A SER 3.2 1.1 - - - -
450A GLU* 4.2 1.8 - - + +
451A VAL* 2.9 52.0 + - + +
454A PHE* 3.5 19.7 - - + -
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Residues in contact with LYS 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A LEU* 3.0 44.8 + - + +
445A THR* 3.7 10.3 - - + +
446A LYS 3.4 0.2 - - - -
447A TYR* 1.3 77.0 - - - +
449A SER* 1.3 61.0 + - - +
451A VAL 4.1 7.4 - - - +
452A LYS* 3.5 14.9 + - - +
454A PHE* 3.6 8.4 - - + +
456A PRO* 3.8 32.5 - - + +
461A PHE 5.7 2.6 + - - -
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Residues in contact with SER 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A THR 3.2 14.3 + - - -
446A LYS* 3.7 4.3 - - - -
448A LYS* 1.3 81.1 - - - +
450A GLU* 1.3 67.0 + - - +
452A LYS* 3.1 24.3 + - - +
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Residues in contact with GLU 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A TYR* 2.4 57.4 + - + +
180A ASP* 5.0 0.5 - - - +
446A LYS* 2.9 57.1 + - + +
447A TYR* 4.5 1.3 - - + -
449A SER* 1.3 84.5 - - - +
451A VAL* 1.3 62.0 + - + +
452A LYS* 4.0 2.3 + - - +
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Residues in contact with VAL 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A GLU 4.2 17.3 - - - +
171A VAL* 4.9 4.3 - - + -
174A TYR* 3.7 37.7 - - + -
447A TYR* 2.9 33.9 + - + +
448A LYS 4.1 4.4 - - - +
449A SER 3.5 0.6 - - - -
450A GLU* 1.3 82.9 - - - +
452A LYS* 1.3 63.5 + - - +
453A VAL* 3.8 23.1 - - + -
454A PHE* 3.0 28.2 + - + +
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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