Contacts of the helix formed by residues 440 - 451 (chain A) in PDB entry 1XTB
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 440 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ARG* 4.5 4.3 - - - +
439A LYS* 1.3 76.6 - - - +
441A THR* 1.3 59.5 + - - +
442A GLU* 3.7 8.0 + - - +
443A GLU* 2.8 43.5 + - - +
444A ALA* 2.9 28.2 + - - +
466A VAL* 4.3 3.8 - - - -
467A PHE 5.1 0.2 - - - -
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Residues in contact with THR 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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440A SER* 1.3 73.4 - - - +
442A GLU* 1.3 54.9 + - - +
444A ALA* 3.3 2.1 + - - +
445A ARG* 2.8 45.5 + - - +
462A LEU* 3.7 24.6 - - + +
466A VAL* 3.7 28.0 - - + +
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Residues in contact with GLU 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 SER* 3.2 8.8 + - - +
441A THR* 1.3 78.4 - - - +
443A GLU* 1.3 65.8 + - + +
445A ARG* 3.2 26.8 + - - +
446A LYS* 3.1 49.3 + - - +
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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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26A ARG* 2.9 36.5 + - - -
437A LYS* 4.9 5.7 - - - -
438A GLY 4.5 1.1 - - - +
439A LYS* 3.6 17.9 - - + +
440A SER* 2.8 41.7 + - - +
442A GLU* 1.3 78.5 - - + +
444A ALA* 1.3 62.5 + - - +
446A LYS* 3.4 9.1 + - - +
447A GLU* 3.3 28.2 + - - +
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Residues in contact with ALA 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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439A LYS* 4.1 18.6 - - + +
440A SER 2.9 17.3 + - - +
441A THR 3.7 4.9 - - - +
443A GLU* 1.3 75.8 - - - +
445A ARG* 1.3 64.3 + - - +
447A GLU* 3.5 6.9 + - - +
448A LEU* 3.1 27.4 + - - +
462A LEU* 3.8 12.6 - - + -
465A LYS* 4.2 22.6 - - + +
466A VAL* 4.3 5.8 - - + -
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Residues in contact with ARG 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 THR* 2.8 32.1 + - - +
442A GLU* 3.2 28.2 + - - +
444A ALA* 1.3 71.4 - - - +
446A LYS* 1.3 66.1 + - - +
448A LEU* 3.2 4.7 + - - +
449A GLN* 2.9 24.7 + - + +
458A LEU* 3.8 22.0 - - + +
462A LEU* 3.5 35.7 - - + +
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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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442A GLU* 3.1 41.4 + - - +
443A GLU* 3.7 11.0 - - - +
445A ARG* 1.3 77.5 - - + +
447A GLU* 1.3 63.4 + - + +
449A GLN* 3.4 6.3 + - - +
450A ALA* 3.0 23.9 + - - +
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Residues in contact with GLU 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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439A LYS* 2.8 43.2 + - - +
443A GLU* 3.3 15.9 + - - +
444A ALA* 3.7 7.6 - - - +
445A ARG 3.2 0.4 - - - -
446A LYS* 1.3 78.8 - - + +
448A LEU* 1.3 62.9 + - + +
450A ALA* 3.3 9.4 + - - +
451A ALA* 3.2 19.2 + - - +
465A LYS* 5.4 6.1 + - - +
1519B GLN* 4.0 12.1 + - - -
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Residues in contact with LEU 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 ALA 3.1 18.0 + - - +
445A ARG 3.2 3.8 + - - +
447A GLU* 1.3 78.9 - - + +
449A GLN* 1.3 59.3 + - - +
451A ALA* 2.9 26.8 + - + +
453A LYS* 3.6 28.1 + - + +
458A LEU* 3.8 26.0 - - + +
461A LEU* 3.9 25.4 - - + -
462A LEU* 3.5 42.0 - - + +
465A LYS* 4.2 20.9 - - + +
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Residues in contact with GLN 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 ARG* 2.9 18.7 + - + +
446A LYS* 3.8 7.0 - - - +
447A GLU 3.3 0.2 - - - -
448A LEU* 1.3 76.4 - - - +
450A ALA* 1.3 60.8 + - - +
451A ALA 3.0 0.2 - - - -
452A GLY* 3.2 13.6 + - - +
453A LYS 4.0 12.6 + - - +
455A PRO* 6.3 0.6 - - - +
458A LEU* 3.5 21.3 - - + +
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Residues in contact with ALA 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 LYS 3.0 17.1 + - - +
447A GLU* 3.5 9.2 - - - +
448A LEU 3.2 0.2 - - - -
449A GLN* 1.3 77.7 - - - +
451A ALA* 1.3 55.9 + - - +
452A GLY 3.2 4.0 + - - -
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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 GLU 3.2 10.5 + - - +
448A LEU* 2.9 19.0 + - + +
450A ALA* 1.3 78.0 - - - +
452A GLY* 1.3 62.0 + - - +
453A LYS* 3.3 13.3 + - + +
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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