Contacts of the helix formed by residues 413 - 424 (chain A) in PDB entry 3U44
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 ASN 413 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A SER* 5.0 10.5 - - - +
372A GLU* 3.7 21.4 + - - -
411A ASP 3.7 0.6 + - - +
412A THR* 1.3 76.7 - - - +
414A LEU* 1.3 62.3 + - - +
415A VAL* 3.0 10.5 + - - +
416A GLN* 2.6 54.9 + - - +
417A GLU* 3.1 25.1 + - - +
447A ARG 5.9 0.4 + - - +
448A LEU 3.6 22.9 - - - +
449A ALA* 4.7 1.6 - - - -
450A GLU* 4.4 4.0 - - - +
453A LEU* 3.9 2.9 - - - +
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Residues in contact with LEU 414 (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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190A SER* 3.5 20.5 + - - +
191A HIS* 4.5 13.5 - - + -
192A PRO* 3.6 23.6 - - + +
413A ASN* 1.3 75.8 - - - +
415A VAL* 1.3 65.5 + - - +
417A GLU* 3.7 3.9 - - + +
418A SER* 3.0 25.3 + - - -
450A GLU* 5.0 17.7 - - + -
453A LEU* 4.9 17.9 - - + -
826A LYS* 6.1 5.4 - - + -
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Residues in contact with VAL 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ARG 3.4 25.6 - - - +
190A SER* 3.8 15.5 - - - +
191A HIS 4.0 5.8 - - - -
192A PRO* 4.5 2.9 - - - -
372A GLU* 3.9 42.0 - - + +
373A HIS* 3.9 17.7 - - + +
376A LEU* 4.1 15.5 - - + -
413A ASN* 3.0 9.1 + - - +
414A LEU* 1.3 74.6 - - - +
416A GLN* 1.3 64.5 + - - +
418A SER* 2.7 21.9 + - - -
419A ILE* 3.0 15.2 + - + +
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Residues in contact with GLN 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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109A LEU* 3.5 35.0 - - + +
110A HIS* 4.9 4.8 + - - -
372A GLU* 3.5 24.8 + - + +
411A ASP 4.2 3.1 - - - +
412A THR* 3.4 18.8 - - + +
413A ASN* 2.6 48.0 + - - +
415A VAL* 1.3 72.4 - - - +
417A GLU* 1.3 51.0 + - - +
419A ILE* 2.9 9.7 + - - +
420A LEU* 2.7 38.5 + - + +
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Residues in contact with GLU 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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409A TYR* 2.6 33.1 + - - -
412A THR* 3.8 3.1 - - + +
413A ASN 3.1 17.2 + - - +
414A LEU* 3.7 6.7 - - + +
415A VAL 3.3 0.2 - - - -
416A GLN* 1.3 78.5 - - - +
418A SER* 1.3 54.3 + - - +
420A LEU* 3.0 11.8 + - - +
421A GLN* 2.7 45.7 + - + +
433A LEU* 4.7 2.5 - - - +
453A LEU* 3.4 27.9 - - + +
457A LYS* 2.9 25.9 + - - -
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Residues in contact with SER 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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192A PRO* 4.2 11.9 - - - +
376A LEU* 3.5 26.6 - - - +
414A LEU 3.0 14.8 + - - -
415A VAL* 2.7 21.3 + - - -
417A GLU* 1.3 77.7 - - - +
419A ILE* 1.3 57.1 + - - +
421A GLN* 4.2 6.6 - - - +
422A LEU* 3.2 28.6 + - - +
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Residues in contact with ILE 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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109A LEU* 4.8 18.6 - - + -
112A PHE* 5.0 3.8 - - + -
113A CYS* 4.1 17.9 - - - -
372A GLU* 3.3 34.5 - - + +
375A CYS* 4.2 10.1 - - - -
376A LEU* 4.1 20.6 - - + +
379A LEU* 3.6 18.4 - - + -
415A VAL* 3.0 17.0 + - + +
416A GLN* 2.9 11.3 + - - +
418A SER* 1.3 76.0 - - - +
420A LEU* 1.3 64.6 - - + +
422A LEU* 3.2 6.5 + - - +
423A VAL* 3.1 27.7 + - + +
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Residues in contact with LEU 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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61A LEU* 5.7 0.9 - - + -
63A VAL* 4.7 4.5 - - + -
109A LEU* 4.4 25.4 - - + -
404A VAL* 4.7 12.1 - - + -
406A VAL* 3.7 39.0 - - + -
409A TYR* 4.1 13.7 - - + -
412A THR* 4.6 7.9 - - + -
416A GLN 2.7 20.1 + - - +
417A GLU* 3.0 25.5 + - - +
419A ILE* 1.3 69.2 - - - +
421A GLN* 1.3 63.4 + - - +
422A LEU 2.9 6.0 + - - -
423A VAL* 3.1 9.2 + - + +
424A THR* 2.9 29.4 + - - +
433A LEU* 5.0 11.0 - - + -
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Residues in contact with GLN 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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25A ASP* 5.0 5.3 + - - +
398A GLN* 5.0 0.9 + - - -
417A GLU* 2.7 30.5 + - + +
418A SER* 4.2 7.2 - - - +
420A LEU* 1.3 73.2 - - - +
422A LEU* 1.3 55.8 + - - +
424A THR* 3.0 29.2 + - - +
426A GLY 4.1 17.6 + - - -
427A PRO* 5.4 3.8 - - - +
428A GLU* 5.4 4.1 - - - +
433A LEU* 4.5 13.9 - - - +
457A LYS* 5.0 2.3 + - - -
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Residues in contact with LEU 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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376A LEU* 4.3 3.4 - - + -
379A LEU* 2.9 45.3 - - + +
380A THR* 3.2 35.7 - - + -
390A PRO* 4.9 10.8 - - + -
394A ALA* 3.1 28.8 - - + +
398A GLN* 2.8 29.5 + - - +
418A SER 3.2 18.7 + - - +
419A ILE* 3.2 6.0 + - - +
420A LEU 2.9 0.8 - - - -
421A GLN* 1.3 80.1 - - - +
423A VAL* 1.3 59.6 + - + +
424A THR 3.3 0.4 - - - -
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Residues in contact with VAL 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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61A LEU* 4.0 25.8 - - + -
109A LEU* 6.5 0.4 - - + -
112A PHE* 4.1 20.9 - - + -
379A LEU* 4.0 23.8 - - + -
394A ALA 5.0 0.4 - - - +
397A TYR* 3.9 25.2 - - + +
398A GLN* 3.6 22.7 + - - -
401A PHE* 4.6 2.8 - - + +
404A VAL* 4.5 7.1 - - + +
419A ILE* 3.1 15.1 + - + +
420A LEU* 3.4 21.5 - - + +
422A LEU* 1.3 75.4 - - - +
424A THR* 1.3 66.4 + - + +
425A SER 3.7 0.3 + - - -
432A ASN* 5.2 0.7 + - - -
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Residues in contact with THR 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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398A GLN* 3.8 10.3 + - - -
404A VAL* 4.0 22.0 - - + -
420A LEU 2.9 21.7 + - - +
421A GLN* 3.0 34.0 + - - +
423A VAL* 1.3 80.2 - - + +
425A SER* 1.3 61.7 + - - +
426A GLY 3.9 4.5 + - - +
432A ASN* 3.5 11.4 - - - +
433A LEU* 3.7 40.4 - - + +
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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