Contacts of the helix formed by residues 414 - 428 (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 ALA 414 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412A PRO 4.2 0.8 + - - -
413A MET* 1.3 73.7 - - - +
415A TRP* 1.3 66.7 + - - +
416A GLU* 3.2 10.5 - - + +
417A ASP* 3.1 25.0 + - - +
418A ARG* 2.9 19.6 + - - +
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Residues in contact with TRP 415 (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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414A ALA* 1.3 70.4 - - - +
416A GLU* 1.3 56.5 + - - +
418A ARG* 3.3 6.1 + - + +
419A ASN* 2.9 59.3 + - - +
668A ARG* 3.5 42.2 - - + -
1C T 3.5 45.1 + + - -
12D C 3.5 37.4 + - - -
13D T 3.6 29.8 + - - -
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Residues in contact with GLU 416 (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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414A ALA* 4.7 9.9 - - + -
415A TRP* 1.3 76.6 - - - +
417A ASP* 1.3 68.0 + - - +
419A ASN* 3.2 8.0 + - - +
420A ARG* 2.8 32.2 + - - +
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Residues in contact with ASP 417 (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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413A MET* 3.6 17.8 - - + +
414A ALA* 3.1 28.5 + - - +
416A GLU* 1.3 80.5 - - - +
418A ARG* 1.3 66.8 + - - +
420A ARG* 3.8 10.0 + - - +
421A LEU* 2.9 27.2 + - - +
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Residues in contact with ARG 418 (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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413A MET* 4.0 15.8 - - + +
414A ALA 2.9 15.8 + - - +
415A TRP* 3.7 9.1 - - + +
417A ASP* 1.3 78.0 - - - +
419A ASN* 1.3 97.9 + - - +
421A LEU* 3.2 1.9 + - - +
422A LYS* 2.9 55.1 + - - +
434A ILE* 3.8 22.2 - - + -
665A GLU* 2.9 39.8 + - - -
668A ARG* 3.6 14.3 - - - +
669A LEU* 4.0 4.4 - - - +
684A PHE 5.9 0.2 + - - -
1C T 3.7 54.7 - - + +
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Residues in contact with ASN 419 (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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415A TRP* 2.9 40.5 + - - +
416A GLU* 3.6 7.3 - - - +
418A ARG* 1.3 108.4 + - - +
420A ARG* 1.3 64.0 + - - +
423A ALA* 2.9 27.3 + - - +
668A ARG* 4.1 22.4 + - - +
669A LEU* 3.6 21.5 - - + +
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Residues in contact with ARG 420 (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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385A PRO* 3.8 36.0 + - - +
388A GLY* 6.1 0.6 - - - -
416A GLU 2.8 21.0 + - - +
417A ASP* 3.8 10.3 - - - +
419A ASN* 1.3 75.1 - - - +
421A LEU* 1.3 60.5 + - - +
423A ALA* 3.7 5.3 - - - +
424A LEU* 2.9 44.9 + - + +
563B ARG* 5.5 7.1 - - - +
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Residues in contact with LEU 421 (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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349A LEU* 4.7 9.2 - - + -
351A LEU* 3.9 14.8 - - + -
385A PRO* 4.6 23.6 - - + -
391A PHE* 4.7 2.0 - - + -
408A VAL* 4.0 18.8 - - + -
413A MET* 3.5 32.3 - - + -
417A ASP 2.9 18.8 + - - +
418A ARG 3.5 2.9 - - - +
420A ARG* 1.3 79.8 - - - +
422A LYS* 1.3 67.9 + - + +
424A LEU* 3.2 7.0 + - + +
425A LEU* 3.0 55.0 + - + +
432A SER* 5.9 1.1 - - - +
434A ILE* 5.1 5.4 - - + -
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Residues in contact with LYS 422 (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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418A ARG* 2.9 57.9 + - - +
419A ASN 3.7 4.5 - - - +
421A LEU* 1.3 77.2 - - + +
423A ALA* 1.3 64.9 + - - +
425A LEU* 3.2 2.5 + - - +
426A LEU* 2.9 29.6 + - + +
430A LEU 4.9 0.3 - - - +
432A SER* 3.0 37.2 + - - +
434A ILE* 3.6 17.0 - - + -
457A LYS* 4.4 4.0 - - - +
665A GLU* 4.5 5.1 + - - +
669A LEU* 4.3 13.5 - - + -
683A PHE 4.6 8.4 + - - +
685A VAL* 5.3 0.4 + - - -
1C T 2.8 34.5 + - - -
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Residues in contact with ALA 423 (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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419A ASN 2.9 16.8 + - - +
420A ARG* 3.7 5.4 - - - +
422A LYS* 1.3 80.1 - - - +
424A LEU* 1.3 57.2 + - - +
426A LEU* 3.3 11.4 - - - +
427A ARG* 2.9 36.8 + - - +
669A LEU* 4.4 7.8 - - + +
673A HIS* 3.6 36.5 + - + +
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Residues in contact with LEU 424 (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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385A PRO* 5.0 1.6 - - + +
388A GLY 5.6 3.8 - - - +
391A PHE* 3.8 28.7 - - + -
392A ARG* 4.3 19.1 - - + +
395A LEU* 4.3 12.2 - - + +
420A ARG* 2.9 42.5 + - + +
421A LEU* 3.2 8.0 + - + +
423A ALA* 1.3 75.4 - - - +
425A LEU* 1.3 64.9 + - + +
427A ARG* 3.2 28.3 + - + +
428A GLU* 3.6 5.2 + - - +
524B GLU* 3.9 24.9 - - - +
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Residues in contact with LEU 425 (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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349A LEU* 5.0 3.8 - - + -
391A PHE* 4.2 9.6 - - + -
395A LEU* 4.0 28.0 - - + -
406A VAL* 3.8 32.3 - - + -
408A VAL* 4.6 4.9 - - + -
421A LEU* 3.0 53.6 + - + +
422A LYS 4.0 3.6 - - - +
424A LEU* 1.3 77.7 - - + +
426A LEU* 1.3 63.1 + - - +
428A GLU* 3.1 10.6 + - - +
429A GLY 3.3 0.2 + - - -
430A LEU* 2.9 36.7 + - + +
432A SER* 3.8 26.7 - - - -
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Residues in contact with LEU 426 (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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422A LYS* 2.9 17.7 + - + +
423A ALA* 3.3 9.2 - - - +
425A LEU* 1.3 77.1 - - - +
427A ARG* 1.3 54.2 + - - +
429A GLY* 2.7 24.4 + - - -
430A LEU 3.5 11.3 + - - +
431A PRO* 4.6 4.5 - - + -
669A LEU* 3.6 31.4 - - + -
673A HIS* 3.2 19.4 - - + +
674A LEU* 4.0 18.6 - - + -
676A GLU* 5.2 0.9 - - - +
677A VAL* 3.4 39.1 - - + +
683A PHE* 4.0 27.6 - - + -
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Residues in contact with ARG 427 (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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392A ARG* 3.5 24.5 + - - +
423A ALA* 2.9 20.1 + - - +
424A LEU* 3.5 23.9 - - + +
425A LEU 3.2 0.6 - - - -
426A LEU* 1.3 75.3 - - - +
428A GLU* 1.3 58.5 + - - +
429A GLY 3.3 1.1 + - - -
672A ARG* 4.5 7.0 - - - +
673A HIS* 3.2 46.2 + - - +
676A GLU* 4.3 16.8 - - - +
520B TRP* 5.2 0.6 - - - +
521B ASP* 3.3 38.4 + - - +
524B GLU* 2.8 37.2 + - - -
525B GLU* 4.0 20.0 + - - +
679B ARG* 6.3 0.4 - - - +
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Residues in contact with GLU 428 (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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392A ARG* 3.0 48.4 + - + +
395A LEU* 3.9 26.5 - - + -
396A ARG* 3.4 33.3 - - - +
399A LYS* 3.6 23.7 - - - +
424A LEU 3.6 3.9 + - - +
425A LEU 3.1 7.9 + - - +
426A LEU 3.0 0.8 - - - -
427A ARG* 1.3 78.4 - - - +
429A GLY* 1.3 58.3 + - - -
430A LEU* 3.3 6.7 + - + +
676A GLU* 5.0 12.0 - - - +
528B TRP* 3.3 14.6 + - - -
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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