Contacts of the helix formed by residues 441 - 452 (chain A) in PDB entry 2CXU
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 LEU 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ARG* 3.8 32.1 - - - +
440A LYS* 1.3 74.0 - - - +
442A PRO* 1.3 80.3 - - + +
443A GLU* 4.2 7.6 - - + +
444A GLU* 2.9 23.6 + - + +
445A ALA* 2.9 20.6 + - - +
467A VAL* 4.5 0.7 - - - -
468A PHE 6.1 0.2 - - - +
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Residues in contact with PRO 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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440A LYS 3.9 0.2 - - - -
441A LEU* 1.3 93.2 - - + +
443A GLU* 1.3 61.7 + - + +
445A ALA 3.3 0.3 + - - -
446A ARG* 2.8 32.6 + - - +
463A LEU* 3.4 14.8 - - + +
467A VAL* 3.7 34.7 - - + -
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Residues in contact with GLU 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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441A LEU* 3.2 6.5 - - + +
442A PRO* 1.3 82.2 - - + +
444A GLU* 1.3 62.7 + - + +
446A ARG* 3.0 39.6 + - - +
447A LYS* 3.2 44.9 + - - +
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Residues in contact with GLU 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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27A ARG* 2.8 44.8 + - - -
438A LYS* 5.1 5.7 + - - -
439A GLY 4.4 0.3 - - - +
440A LYS* 3.5 15.7 - - + +
441A LEU* 2.9 29.0 + - + +
443A GLU* 1.3 77.0 - - + +
445A ALA* 1.3 63.8 + - - +
447A LYS* 3.5 11.0 + - + +
448A GLU* 3.3 26.6 + - - +
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Residues in contact with ALA 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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440A LYS* 4.0 21.9 - - + +
441A LEU 2.9 11.2 + - - +
442A PRO 3.7 7.0 - - - +
444A GLU* 1.3 73.3 - - - +
446A ARG* 1.3 64.6 + - - +
448A GLU* 3.2 7.5 + - - +
449A LEU* 3.0 26.9 + - - +
463A LEU* 3.7 15.0 - - + -
466A LYS* 4.0 26.1 - - + +
467A VAL* 4.5 3.1 - - + -
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Residues in contact with ARG 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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442A PRO* 2.8 21.9 + - - +
443A GLU* 3.0 38.4 + - - +
444A GLU 3.3 0.2 - - - -
445A ALA* 1.3 72.7 - - - +
447A LYS* 1.3 56.6 + - + +
449A LEU* 3.2 7.0 + - - +
450A GLN* 2.9 52.3 + - - +
459A LEU* 3.5 15.8 - - + +
460A GLU* 3.4 28.9 + - - -
463A LEU* 3.3 32.7 - - + +
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Residues in contact with LYS 447 (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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443A GLU* 3.2 34.0 + - - +
444A GLU* 3.7 9.9 - - + +
445A ALA 3.3 0.2 - - - -
446A ARG* 1.3 78.6 - - + +
448A GLU* 1.3 58.0 + - + +
450A GLN* 3.4 16.2 - - - +
451A ALA* 3.0 29.8 + - - +
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Residues in contact with GLU 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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440A LYS* 2.7 38.9 + - - +
444A GLU* 3.3 13.8 + - - +
445A ALA* 3.2 10.2 + - - +
447A LYS* 1.3 77.8 - - + +
449A LEU* 1.3 58.3 + - + +
451A ALA* 3.4 7.1 + - - +
452A ALA* 3.1 27.4 + - - +
466A LYS* 5.1 8.2 - - - -
516B GLU* 4.9 4.0 - - - +
520B GLN* 3.2 24.3 + - - -
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Residues in contact with LEU 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 ALA 3.0 18.8 + - - +
446A ARG 3.7 5.2 - - - +
448A GLU* 1.3 72.5 - - + +
450A GLN* 1.3 66.4 + - - +
452A ALA* 3.2 13.7 + - + +
453A GLY 3.3 0.2 + - - -
454A LYS* 3.3 40.2 + - + +
459A LEU* 3.8 26.7 - - + +
462A LEU* 3.9 27.6 - - + -
463A LEU* 3.8 38.1 - - + +
466A LYS* 4.1 26.5 - - + +
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Residues in contact with GLN 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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446A ARG* 2.9 44.0 + - - +
447A LYS* 3.4 21.8 - - - +
449A LEU* 1.3 75.2 - - - +
451A ALA* 1.3 57.4 + - - +
453A GLY* 3.1 19.9 + - - -
454A LYS 4.3 3.7 + - - +
459A LEU* 3.7 16.7 - - + +
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Residues in contact with ALA 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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447A LYS 3.0 17.2 + - - +
448A GLU* 3.7 7.6 - - - +
449A LEU 3.3 0.2 - - - -
450A GLN* 1.3 75.4 - - - +
452A ALA* 1.3 60.2 + - - +
453A GLY* 3.1 2.2 + - - -
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Residues in contact with ALA 452 (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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448A GLU 3.1 13.5 + - - +
449A LEU* 3.2 15.4 + - + +
451A ALA* 1.3 75.4 - - - +
453A GLY* 1.3 59.8 + - - +
454A LYS* 3.5 15.1 - - + +
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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