Contacts of the helix formed by residues 455 - 467 (chain B) in PDB entry 2CXO
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 SER 455 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453B GLY 3.6 3.4 + - - -
454B LYS* 1.3 75.2 - - - +
456B PRO* 1.3 70.6 - - - +
457B GLU* 3.7 6.7 + - - +
458B ASP* 3.1 33.0 + - - +
459B LEU* 2.8 27.2 + - - +
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Residues in contact with PRO 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B GLN* 5.7 6.7 - - - +
454B LYS 3.8 1.5 - - - +
455B SER* 1.3 87.6 - - - +
457B GLU* 1.3 59.8 - - - +
459B LEU* 3.7 8.9 + - + +
460B GLU* 3.2 26.0 + - - +
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Residues in contact with GLU 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455B SER* 3.2 6.8 + - - +
456B PRO* 1.3 75.5 - - - +
458B ASP* 1.3 73.6 + - - +
460B GLU* 3.5 11.1 + - - +
461B LYS* 3.2 51.2 + - + +
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Residues in contact with ASP 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B LYS* 4.3 17.1 + - + +
455B SER* 3.1 30.7 + - - +
457B GLU* 1.3 81.6 - - - +
459B LEU* 1.3 60.5 + - - +
461B LYS* 3.3 7.6 + - - +
462B LEU* 2.9 37.9 + - + +
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Residues in contact with LEU 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446B ARG* 3.7 45.3 - - + +
449B LEU* 3.8 32.3 - - + +
450B GLN* 3.7 42.0 - - + +
454B LYS* 4.2 10.9 - - + +
455B SER 2.8 17.3 + - - +
456B PRO* 3.9 7.4 - - + +
458B ASP* 1.3 77.3 - - - +
460B GLU* 1.3 62.6 + - + +
462B LEU 3.3 0.2 + - - -
463B LEU* 2.9 40.3 + - + +
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Residues in contact with GLU 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446B ARG* 5.9 3.4 - - - +
456B PRO 3.2 16.7 + - - +
457B GLU* 3.5 10.6 - - - +
459B LEU* 1.3 86.5 - - + +
461B LYS* 1.3 64.1 + - + +
463B LEU* 3.8 4.3 + - - +
464B PRO* 3.6 15.8 - - - +
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Residues in contact with LYS 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A GLY* 5.8 1.4 - - - -
457B GLU* 3.2 42.1 + - + +
458B ASP* 3.8 8.3 - - - +
459B LEU 3.2 0.6 - - - -
460B GLU* 1.3 84.8 - - + +
462B LEU* 1.3 62.2 + - + +
463B LEU 3.6 0.5 + - - -
464B PRO* 3.7 7.5 - - - +
465B HIS* 3.4 19.4 + - - -
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Residues in contact with LEU 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A THR* 3.3 48.9 - - + +
513A TRP* 4.7 7.4 - - + +
449B LEU* 4.1 14.4 - - + -
454B LYS* 3.8 38.1 - - + +
458B ASP* 2.9 19.5 + - + +
459B LEU 3.9 2.2 - - - +
461B LYS* 1.3 80.1 - - + +
463B LEU* 1.3 67.1 + - - +
465B HIS* 3.0 22.7 + - + +
466B LYS* 3.3 23.5 + - + +
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Residues in contact with LEU 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442B PRO* 3.7 17.7 - - + +
445B ALA* 3.8 11.2 - - + -
446B ARG* 3.6 60.6 - - + +
449B LEU* 3.8 9.4 - - + -
459B LEU* 2.9 20.4 + - + +
460B GLU* 4.0 5.6 - - - +
462B LEU* 1.3 74.5 - - - +
464B PRO* 1.3 67.3 - - + +
466B LYS* 2.9 20.1 + - - +
467B VAL* 3.3 21.6 + - + +
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Residues in contact with PRO 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A TYR* 4.9 0.9 - - - -
364A ILE* 3.4 38.4 - - + +
368A GLY* 4.3 20.9 - - - +
397B GLN* 4.6 0.2 - - - +
460B GLU 3.6 13.5 - - - +
461B LYS 3.7 8.5 - - - +
462B LEU 3.6 2.0 - - - -
463B LEU* 1.3 96.0 - - + +
465B HIS* 1.3 60.4 + - - +
466B LYS 3.4 0.5 + - - -
467B VAL* 3.5 24.0 + - + +
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Residues in contact with HIS 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A TYR* 4.3 12.0 + + - -
93A THR* 3.6 30.4 - - + +
364A ILE* 3.5 42.6 + - + +
365A THR 4.0 11.7 + - - -
366A LYS 5.5 1.8 - - - -
368A GLY* 5.2 2.7 - - - -
508A ASN* 5.5 2.1 - - + +
511A ASP* 4.4 7.0 - - - -
513A TRP* 3.5 30.6 - + + +
397B GLN* 2.9 21.6 - - - +
461B LYS 3.4 21.5 + - - -
462B LEU* 3.0 12.4 + - + +
464B PRO* 1.3 77.5 - - + +
466B LYS* 1.3 58.2 + - + +
467B VAL 3.4 0.2 - - - -
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Residues in contact with LYS 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513A TRP* 3.3 55.7 - - + -
440B LYS* 3.8 19.9 + - + +
445B ALA* 3.9 14.8 - - + +
448B GLU* 5.6 6.3 - - - -
449B LEU* 3.8 32.8 - - + +
454B LYS* 5.8 2.2 - - - +
462B LEU* 3.5 24.3 - - + +
463B LEU 2.9 7.8 + - - +
465B HIS* 1.3 76.1 - - + +
467B VAL* 1.3 61.8 + - - +
468B PHE* 3.3 23.0 - - - -
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Residues in contact with VAL 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A TYR* 3.5 11.8 + - + +
397B GLN* 3.3 18.2 - - - +
440B LYS 3.3 13.2 - - - +
442B PRO* 3.7 43.1 - - + -
445B ALA* 4.2 7.6 - - + -
463B LEU* 3.3 21.1 - - + +
464B PRO* 3.5 15.1 + - + +
465B HIS 3.4 1.0 - - - -
466B LYS* 1.3 81.0 - - - +
468B PHE* 1.3 68.8 + - - +
469B GLU* 4.8 2.0 - - - +
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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