Contacts of the helix formed by residues 443 - 458 (chain A) in PDB entry 5XOU
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 GLU 443 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438A PRO 4.0 2.0 - - - +
439A LEU* 3.7 2.2 - - + +
440A ARG* 2.9 64.7 + - - +
442A GLU* 1.3 73.0 - - - +
444A ARG* 1.3 63.0 + - - +
445A HIS 3.3 3.3 + - - -
446A ARG* 2.8 47.2 + - + +
447A TRP* 2.9 26.3 + - + -
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Residues in contact with ARG 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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329A LYS* 5.6 2.8 - - - +
335A ARG* 3.4 31.5 - - - +
441A GLU 4.4 4.3 - - - +
442A GLU* 2.9 12.8 + - - +
443A GLU* 1.3 74.4 - - - +
445A HIS* 1.3 83.9 + - + +
447A TRP* 3.4 22.2 - - + +
448A GLU* 2.9 59.4 + - + +
647A PHE* 4.7 6.3 - - - -
19D G 5.1 5.5 + - - -
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Residues in contact with HIS 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A GLU 3.3 0.6 - - - -
444A ARG* 1.3 100.8 + - + +
446A ARG* 1.3 57.7 - - - +
449A ASN* 2.9 35.0 + - - +
647A PHE* 3.8 30.0 - + + -
2C G 3.7 13.2 - - + +
18D C 3.2 72.9 + + + +
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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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435A LEU* 3.9 5.3 - - + +
436A ASN* 2.8 22.4 + - - +
438A PRO 3.0 21.4 + - - -
439A LEU* 3.2 14.4 - - - +
443A GLU* 2.8 47.6 + - + +
444A ARG 3.4 0.2 - - - -
445A HIS* 1.3 78.3 - - - +
447A TRP* 1.3 58.8 + - - +
449A ASN 3.2 1.9 + - - -
450A ALA* 2.9 24.8 + - - +
2C G 2.7 101.1 + - + +
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Residues in contact with TRP 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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334A LEU* 5.6 0.7 - - + -
360A PHE* 3.7 35.9 - + + -
361A LEU* 3.6 18.8 - - + -
364A ALA* 3.9 28.9 - - + -
367A ARG* 6.2 0.7 - - - -
435A LEU* 4.0 27.6 - - + -
439A LEU* 4.1 11.9 - - + -
440A ARG 3.9 8.7 - - - -
441A GLU* 3.0 29.3 + - + -
443A GLU 2.9 22.9 + - - -
444A ARG* 3.4 20.2 - - + +
446A ARG* 1.3 76.6 - - - +
448A GLU* 1.3 81.0 + - + +
450A ALA* 3.3 0.3 + - - +
451A LEU* 2.9 38.4 + - + +
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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
----------------------------------------------------------
331A ALA* 3.9 6.1 - - + +
334A LEU* 3.7 23.4 - - + +
335A ARG* 2.9 38.0 + - - -
444A ARG* 2.9 46.5 + - + +
445A HIS 4.1 2.0 - - - +
447A TRP* 1.3 96.2 - - + +
449A ASN* 1.3 66.8 + - - +
451A LEU* 3.1 4.7 + - - +
452A LEU* 3.0 26.5 + - - +
647A PHE* 3.1 23.6 - - + -
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Residues in contact with ASN 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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433A GLN* 5.2 0.2 - - - +
445A HIS 2.9 16.9 + - - +
446A ARG 3.5 4.0 - - - +
448A GLU* 1.3 77.0 - - - +
450A ALA* 1.3 57.1 + - - +
452A LEU* 3.2 7.3 + - - +
453A GLY* 2.9 24.9 + - - -
644A ALA 3.7 11.9 - - - +
645A SER* 5.0 0.4 + - - -
646A GLY* 2.7 36.2 + - - +
647A PHE* 4.0 3.0 - - - +
2C G 2.9 38.7 + - - +
3C A 2.7 33.8 + - - +
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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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407A LEU* 4.9 1.1 - - + -
433A GLN* 3.3 30.1 - - + +
435A LEU* 3.6 37.9 - - + -
446A ARG 2.9 7.5 + - - +
447A TRP* 3.5 8.5 - - - +
448A GLU 3.2 0.2 - - - -
449A ASN* 1.3 76.3 - - - +
451A LEU* 1.3 59.9 + - + +
453A GLY 3.1 1.7 + - - -
454A LEU* 2.9 26.0 + - - +
2C G 4.1 9.6 + - - -
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Residues in contact with LEU 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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334A LEU* 4.7 14.6 - - + -
361A LEU* 3.8 29.8 - - + +
364A ALA* 4.2 20.4 - - + -
365A LEU* 3.8 36.6 - - + -
407A LEU* 4.6 19.3 - - + -
435A LEU* 5.2 0.9 - - + -
447A TRP* 2.9 23.7 + - + +
448A GLU* 3.1 10.7 + - - +
450A ALA* 1.3 83.6 - - + +
452A LEU* 1.3 56.6 + - - +
454A LEU* 3.3 9.5 + - + +
455A LEU* 3.0 36.0 + - - +
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Residues in contact with LEU 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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330A PRO 4.0 8.5 - - - +
331A ALA* 3.8 16.6 - - + +
333A ALA* 5.3 0.7 - - + -
334A LEU* 4.3 21.8 - - + -
338A PHE* 5.4 0.2 - - + -
448A GLU 3.0 17.9 + - - +
449A ASN* 3.2 12.8 + - - +
451A LEU* 1.3 72.1 - - - +
453A GLY* 1.3 65.3 + - - +
455A LEU* 3.3 7.1 + - + +
456A ALA* 3.0 24.8 + - - +
462A VAL* 3.8 34.3 - - + +
643A PRO 3.6 18.4 - - - +
644A ALA* 4.4 5.6 - - - -
646A GLY* 3.6 32.5 - - - +
647A PHE* 5.7 0.2 - - + -
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Residues in contact with GLY 453 (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 GLN* 3.6 17.0 - - - -
449A ASN 2.9 14.8 + - - -
450A ALA 3.1 4.4 + - - -
452A LEU* 1.3 75.1 - - - +
454A LEU* 1.3 62.4 + - - +
456A ALA* 3.1 4.3 + - - +
457A LYS* 2.9 28.8 + - - +
644A ALA* 4.4 6.6 - - - +
685A VAL* 4.2 15.3 - - - -
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Residues in contact with LEU 454 (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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346A LEU* 3.6 35.2 - - + -
357A TRP* 4.6 3.4 - - + -
365A LEU* 4.8 6.1 - - + -
405A ALA* 3.9 12.9 - - + +
406A VAL* 3.5 35.0 - - - +
407A LEU* 3.7 27.4 - - + +
432A SER 5.2 0.2 - - - -
433A GLN* 3.8 17.3 - - + +
450A ALA 2.9 13.3 + - - +
451A LEU* 3.4 14.6 - - + +
453A GLY* 1.3 74.3 - - - +
455A LEU* 1.3 57.9 + - + +
457A LYS* 3.3 6.1 + - + +
458A ALA* 3.0 27.4 + - - +
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Residues in contact with LEU 455 (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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334A LEU* 4.2 14.8 - - + -
338A PHE* 3.3 32.8 - - + -
346A LEU* 4.5 18.8 - - + -
365A LEU* 4.5 11.2 - - + -
369A PHE* 3.9 30.1 - - + -
451A LEU 3.0 18.6 + - - +
452A LEU* 3.8 6.3 - - + +
453A GLY 3.2 0.4 - - - -
454A LEU* 1.3 74.6 - - + +
456A ALA* 1.3 66.3 + - - +
458A ALA* 3.1 8.6 + - - +
460A LEU* 3.1 41.9 + - + +
462A VAL* 4.3 13.0 - - + -
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Residues in contact with ALA 456 (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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452A LEU 3.0 17.0 + - - +
453A GLY* 3.6 4.5 - - - +
455A LEU* 1.3 75.8 - - - +
457A LYS* 1.3 60.9 + - - +
459A GLY* 3.2 12.0 + - - -
460A LEU 4.2 10.7 - - - +
462A VAL* 4.7 2.1 - - + +
643A PRO* 4.1 27.1 - - + -
644A ALA* 5.0 1.3 - - + -
680A GLU 4.0 0.3 - - - +
682A LEU* 3.1 35.9 + - + +
685A VAL* 4.4 10.1 - - + -
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Residues in contact with LYS 457 (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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405A ALA* 4.1 6.5 - - + -
422A LYS* 4.4 0.9 - - - +
431A PRO* 3.2 22.8 - - + +
432A SER 3.0 38.8 - - - +
433A GLN* 3.3 27.8 - - + +
453A GLY 2.9 16.6 + - - +
454A LEU* 3.6 5.6 - - + +
456A ALA* 1.3 76.9 - - - +
458A ALA* 1.3 56.8 + - - +
459A GLY 3.2 1.1 - - - -
681A LYS* 3.1 23.3 - - - +
682A LEU 3.2 21.3 + - - +
683A PHE* 2.9 29.1 + - - +
685A VAL* 2.8 27.3 + - + +
1C T 3.9 3.4 - - - -
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Residues in contact with ALA 458 (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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344A THR* 4.4 2.5 - - + -
346A LEU* 4.0 15.3 - - + -
404A GLN* 4.0 33.3 + - + +
405A ALA* 3.8 15.7 - - + -
454A LEU 3.0 15.5 + - - +
455A LEU 3.1 5.9 + - - +
457A LYS* 1.3 78.0 - - - +
459A GLY* 1.3 59.8 + - - +
460A LEU* 3.5 13.7 + - + +
681A LYS* 4.0 7.6 - - - +
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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