Contacts of the helix formed by residues 561 - 576 (chain B) 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 SER 561 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501B LYS* 3.3 11.9 - - - +
560B ILE* 1.3 77.3 - - - +
562B LEU* 1.3 69.9 + - - +
563B ASP* 2.8 11.3 + - - +
564B LEU* 3.1 4.7 + - - -
565B PHE* 3.1 17.5 + - - -
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Residues in contact with LEU 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B LEU* 6.3 2.0 - - + -
394B LEU* 4.1 34.5 - - + +
395B LYS* 4.0 27.8 - - + +
492B MET* 5.1 8.5 - - + -
493B LYS* 6.1 6.7 - - + -
501B LYS* 3.1 13.3 - - - +
561B SER* 1.3 76.2 - - - +
563B ASP* 1.3 89.6 + - - +
565B PHE* 3.7 15.0 - - + -
566B GLN* 2.7 38.6 + - + +
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Residues in contact with ASP 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395B LYS* 2.7 34.5 + - - +
561B SER* 2.8 12.6 + - - +
562B LEU* 1.3 84.8 - - - +
564B LEU* 1.3 56.9 + - + +
566B GLN* 4.4 2.6 - - - +
567B GLN* 2.9 36.2 + - - +
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Residues in contact with LEU 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ARG* 4.1 27.8 - - + +
101B GLU* 4.5 17.5 - - + +
555B MET* 6.6 0.2 - - - -
560B ILE* 3.5 31.4 - - + -
561B SER 3.1 2.2 + - - -
563B ASP* 1.3 76.9 - - - +
565B PHE* 1.3 67.8 + - - +
566B GLN 3.2 0.4 - - - -
567B GLN* 3.1 30.9 + - + +
568B MET* 3.1 28.0 + - + +
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Residues in contact with PHE 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B LEU* 4.4 17.3 - - + -
492B MET* 3.9 21.8 - - + -
498B VAL* 4.5 4.5 - - + -
501B LYS* 3.9 38.8 - - + -
502B ALA* 3.9 15.0 - - + -
505B LEU* 4.7 7.4 - - + -
551B PHE* 3.7 34.4 - + - -
560B ILE* 3.9 20.6 - - + +
561B SER 3.1 18.4 + - - +
562B LEU* 3.8 9.4 - - + +
564B LEU* 1.3 79.5 - - - +
566B GLN* 1.3 68.4 + - + +
568B MET* 3.3 4.2 + - - +
569B ILE* 3.2 41.2 + - + +
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Residues in contact with GLN 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B LEU* 4.0 28.1 - - + +
392B ASP* 3.0 28.1 + - - +
395B LYS* 3.0 36.6 - - - +
562B LEU* 2.7 25.5 + - + +
563B ASP 4.4 2.8 - - - +
565B PHE* 1.3 77.8 - - + +
567B GLN* 1.3 57.0 + - - +
569B ILE* 3.0 6.6 + - - +
570B GLU* 2.7 52.0 + - + +
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Residues in contact with GLN 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A GLU* 4.9 9.7 + - - -
117B SER* 5.3 9.6 - - - -
563B ASP* 2.9 33.7 + - - +
564B LEU* 3.1 27.0 + - + +
566B GLN* 1.3 79.6 - - + +
568B MET* 1.3 57.5 + - - +
570B GLU* 3.4 8.3 + - - +
571B ALA* 3.0 27.4 + - - +
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Residues in contact with MET 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B MET* 3.8 34.6 - - + +
97B ARG* 3.4 43.7 - - + +
551B PHE* 4.0 17.3 - - + -
555B MET* 3.5 37.5 - - + +
560B ILE* 4.8 5.2 - - - -
564B LEU* 3.1 32.0 + - + +
565B PHE 3.8 5.4 - - - +
566B GLN 3.1 0.2 - - - -
567B GLN* 1.3 74.0 - - + +
569B ILE* 1.3 61.8 + - - +
571B ALA* 3.4 7.2 + - - +
572B GLY* 2.9 23.9 + - - -
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Residues in contact with ILE 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B MET* 6.1 0.2 - - + -
387B ILE* 4.6 16.6 - - + -
388B ARG* 5.5 6.5 - - + -
391B LEU* 4.3 14.8 - - + -
505B LEU* 4.7 6.5 - - + -
547B LEU* 4.3 19.4 - - + +
548B LEU* 4.2 24.0 - - + -
551B PHE* 4.2 16.8 - - + -
565B PHE* 3.2 35.2 + - + +
566B GLN* 3.0 10.6 + - - +
568B MET* 1.3 74.3 - - - +
570B GLU* 1.3 62.8 + - - +
572B GLY* 2.9 3.4 + - - +
573B ALA* 2.9 29.1 + - + +
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Residues in contact with GLU 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756A ARG* 3.6 9.6 + - - -
379B LEU* 5.5 0.2 - - - +
388B ARG* 2.7 52.8 + - - +
391B LEU* 5.9 0.7 - - - +
392B ASP* 5.1 1.5 - - - +
566B GLN* 2.7 39.6 + - + +
567B GLN* 3.4 10.8 - - - +
569B ILE* 1.3 75.6 - - - +
571B ALA* 1.3 60.6 + - - +
572B GLY 3.4 0.2 + - - -
573B ALA* 3.4 7.2 + - - +
574B GLU* 3.3 20.6 + - - +
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Residues in contact with ALA 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B THR* 5.3 1.1 - - - +
93B GLN* 5.9 2.9 - - - +
97B ARG* 5.8 5.4 - - - +
117B SER* 6.3 2.9 - - - -
567B GLN 3.0 17.0 + - - +
568B MET* 3.8 7.4 - - - +
569B ILE 3.2 0.2 - - - -
570B GLU* 1.3 75.0 - - - +
572B GLY* 1.3 62.7 + - - +
574B GLU* 3.7 15.2 + - - +
575B SER* 3.4 20.6 + - - -
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Residues in contact with GLY 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B THR* 5.3 3.1 - - - -
94B MET* 5.6 0.9 - - - -
547B LEU* 4.0 24.4 - - - +
568B MET 2.9 14.9 + - - -
569B ILE 2.9 5.3 + - - -
571B ALA* 1.3 76.9 - - - +
573B ALA* 1.3 63.3 + - - +
575B SER* 2.7 22.4 + - - -
576B LEU* 3.1 17.0 + - - +
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Residues in contact with ALA 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B SER* 5.0 0.2 + - - -
378B MET* 5.3 0.2 - - - +
379B LEU* 3.6 25.0 + - + +
384B ILE* 3.8 20.2 - - + +
388B ARG* 4.4 14.6 - - + -
547B LEU* 4.5 1.5 - - + +
569B ILE* 2.9 12.5 + - + +
570B GLU 3.7 8.1 - - - +
571B ALA 3.4 0.2 - - - -
572B GLY* 1.3 73.9 - - - +
574B GLU* 1.3 65.6 + - - +
576B LEU* 2.9 31.5 + - + +
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Residues in contact with GLU 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B SER* 4.6 6.9 + - - -
379B LEU* 3.6 24.1 - - + +
570B GLU 3.3 10.0 + - - +
571B ALA* 3.9 17.3 - - - +
573B ALA* 1.3 79.3 - - - +
575B SER* 1.3 60.2 + - - +
576B LEU 3.6 4.5 + - - +
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Residues in contact with SER 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B THR* 3.2 33.5 - - - +
547B LEU* 5.6 0.3 - - - +
571B ALA 3.4 9.7 + - - -
572B GLY* 2.7 22.4 + - - -
574B GLU* 1.3 77.8 - - - +
576B LEU* 1.3 69.5 + - - +
577B THR* 3.5 8.0 + - - +
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Residues in contact with LEU 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B SER* 4.1 5.7 + - - -
378B MET* 3.6 28.1 + - + -
384B ILE* 3.4 31.6 - - + -
543B ALA* 3.8 42.6 - - + +
544B VAL* 4.4 5.2 - - + -
547B LEU* 4.9 12.1 - - + -
572B GLY 3.1 20.8 + - - +
573B ALA* 2.9 21.0 + - + +
574B GLU 4.0 4.3 - - - +
575B SER* 1.3 81.8 - - - +
577B THR* 1.3 59.7 + - - +
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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