Contacts of the helix formed by residues 472 - 489 (chain A) in PDB entry 3UGM
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 GLY 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437A ASP 4.3 8.8 + - - -
438A GLY 5.4 1.1 + - - -
470A ASN 2.7 4.2 + - - -
471A GLY* 1.3 71.6 - - - -
473A GLY* 1.3 49.6 + - - -
474A LYS* 2.6 3.4 + - - +
475A GLN* 2.5 42.3 + - - +
476A ALA* 3.7 0.6 + - - -
5B C 3.9 30.4 - - - +
6B T 4.0 14.7 - - - +
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Residues in contact with GLY 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A GLY 5.7 0.6 + - - -
442A ALA* 5.2 4.0 - - - +
467A ILE 3.7 10.3 - - - +
468A ALA* 3.5 23.1 - - - -
470A ASN* 2.8 13.5 + - - -
471A GLY 3.3 2.3 + - - -
472A GLY* 1.3 74.8 - - - +
474A LYS* 1.3 61.8 + - - +
475A GLN 3.0 0.2 - - - -
476A ALA* 2.8 25.2 + - - +
477A LEU* 2.8 13.4 + - - +
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Residues in contact with LYS 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A GLN* 2.8 67.2 + - + +
442A ALA* 4.6 4.6 - - - +
445A THR* 3.5 21.8 - - - +
448A ARG* 4.8 8.3 - - - +
472A GLY 2.6 7.5 + - - +
473A GLY* 1.3 72.2 - - - +
475A GLN* 1.3 85.3 + - - +
477A LEU* 4.4 1.8 - - - +
478A GLU* 2.8 37.5 + - + +
4B T 5.2 0.4 + - - -
5B C 3.6 11.7 + - - +
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Residues in contact with GLN 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A GLY 2.5 18.6 + - - +
474A LYS* 1.3 110.8 - - - +
476A ALA* 1.3 50.5 + - - +
478A GLU* 3.9 6.3 + - - +
479A THR* 2.2 40.5 + - - -
507A LYS* 3.7 37.3 + - + +
5B C 3.3 31.2 + - - +
6B T 3.5 24.2 + - - +
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Residues in contact with ALA 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A ILE* 3.3 28.9 - - + +
472A GLY 3.7 0.8 + - - -
473A GLY* 2.8 19.6 + - - +
475A GLN* 1.3 74.8 - - - +
477A LEU* 1.3 55.9 + - - +
478A GLU 3.1 1.1 - - - -
479A THR* 2.8 6.4 + - - -
480A VAL* 2.5 39.5 + - - +
502A ALA* 4.3 11.4 - - + +
506A GLY* 5.1 6.7 - - - -
507A LYS 4.7 6.8 - - - +
510A LEU* 5.0 2.9 - - - +
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Residues in contact with LEU 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A ALA* 4.2 7.2 - - - +
445A THR* 3.6 48.2 - - + +
446A VAL* 4.0 12.3 - - + +
449A LEU* 3.8 15.8 - - + +
453A LEU* 4.1 12.8 - - + -
464A VAL* 4.0 26.0 - - + +
467A ILE* 4.3 21.1 - - + +
468A ALA* 4.5 9.4 - - + +
473A GLY 2.8 18.1 + - - +
474A LYS* 4.0 2.2 - - - +
476A ALA* 1.3 72.7 - - + +
478A GLU* 1.3 68.4 + - - +
480A VAL* 3.0 16.7 + - + +
481A GLN 3.1 10.2 + - - -
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Residues in contact with GLU 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A THR* 4.4 0.6 - - + +
448A ARG* 2.6 33.0 + - - +
449A LEU* 4.1 7.8 - - - +
474A LYS* 2.8 37.4 + - + +
475A GLN* 3.9 8.2 + - - +
477A LEU* 1.3 78.7 - - - +
479A THR* 1.3 64.9 + - - +
480A VAL 3.0 0.2 + - - -
481A GLN* 3.2 17.1 + - - +
482A ARG* 3.0 33.9 + - - +
507A LYS* 5.2 5.5 + - - +
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Residues in contact with THR 479 (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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475A GLN 2.2 25.9 + - - -
476A ALA 2.8 6.0 + - - -
478A GLU* 1.3 74.3 - - - +
480A VAL* 1.3 64.2 + - - +
482A ARG* 3.1 24.7 + - - +
483A LEU* 3.0 27.3 + - + +
507A LYS* 3.1 23.1 + - + +
510A LEU* 3.8 24.7 - - + -
511A GLU* 4.0 26.2 - - + +
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Residues in contact with VAL 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A LEU* 3.8 21.1 - - + -
457A HIS* 5.5 0.2 - - - -
459A LEU* 5.5 4.0 - - + -
467A ILE* 4.4 14.8 - - + -
476A ALA 2.5 18.3 + - - +
477A LEU* 3.2 25.8 - - + +
479A THR* 1.3 71.2 - - - +
481A GLN* 1.3 57.7 + - - +
482A ARG 2.8 1.9 + - - -
483A LEU* 2.7 25.3 + - - +
484A LEU* 2.9 36.7 + - + +
498A VAL* 4.5 10.8 - - + -
499A VAL* 5.3 2.5 - - + -
502A ALA* 4.3 22.0 - - + -
510A LEU* 4.8 7.4 - - + -
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Residues in contact with GLN 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A ARG* 4.4 6.6 + - - -
449A LEU* 3.4 33.9 - - + +
453A LEU* 4.2 13.7 - - + -
457A HIS* 4.2 18.9 + - - +
477A LEU 3.1 5.7 + - - +
478A GLU* 3.2 11.7 + - - +
480A VAL* 1.3 81.8 - - - +
482A ARG* 1.3 87.0 + - - +
484A LEU 4.7 0.2 - - - -
485A PRO* 4.3 10.9 - - - +
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Residues in contact with ARG 482 (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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478A GLU* 3.0 50.9 + - - +
479A THR* 3.1 25.0 + - - +
480A VAL 2.8 2.6 + - - -
481A GLN* 1.3 95.8 - - - +
483A LEU* 1.3 71.5 + - + +
484A LEU 3.8 0.7 - - - -
485A PRO* 4.4 2.8 - - - +
486A VAL* 3.4 20.4 - - - +
507A LYS* 4.9 8.9 - - - +
511A GLU* 4.7 7.5 + - - -
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Residues in contact with LEU 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A THR* 3.0 19.8 + - + +
480A VAL* 2.7 12.6 + - - +
482A ARG* 1.3 87.8 - - + +
484A LEU* 1.3 65.2 + - - +
485A PRO* 3.5 2.0 - - - -
486A VAL* 4.1 7.6 - - + -
487A LEU* 3.2 34.2 + - + +
498A VAL* 5.0 1.3 - - - -
510A LEU* 3.9 17.0 - - + -
511A GLU* 3.9 37.9 - - + +
514A GLN* 3.8 34.1 - - + +
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Residues in contact with LEU 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A HIS* 3.8 31.9 - - + +
459A LEU* 3.6 32.5 - - + -
480A VAL* 2.9 27.6 + - + +
483A LEU* 1.3 74.6 - - - +
485A PRO* 1.3 69.1 - - + +
487A LEU* 3.8 1.2 - - - +
488A CYS* 2.8 37.8 + - - -
495A PRO* 4.0 18.4 - - + +
498A VAL* 3.5 36.2 - - + +
499A VAL* 5.1 1.3 - - + +
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Residues in contact with PRO 485 (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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457A HIS* 4.5 13.2 - - + -
481A GLN 4.3 14.6 - - - +
482A ARG 4.4 2.9 - - - +
483A LEU 3.7 1.3 - - - -
484A LEU* 1.3 96.3 - - + +
486A VAL* 1.3 64.7 + - + +
488A CYS* 3.4 7.3 + - + +
489A GLN* 3.0 37.0 + - + +
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Residues in contact with VAL 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ARG 3.4 24.7 - - - +
483A LEU* 4.1 10.8 - - + +
484A LEU 3.4 0.4 - - - -
485A PRO* 1.3 80.6 - - + +
487A LEU* 1.3 59.7 + - - +
489A GLN* 3.6 3.9 - - - +
490A ALA* 3.0 36.2 + - + +
514A GLN* 3.1 37.5 - - - +
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Residues in contact with LEU 487 (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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483A LEU* 3.2 29.4 + - + +
484A LEU 3.8 2.0 - - - +
486A VAL* 1.3 82.0 - - + +
488A CYS* 1.3 55.7 + - - +
491A HIS* 3.1 49.1 + - + +
492A GLY 3.4 4.0 + - - -
493A LEU* 3.4 17.1 + - + +
498A VAL* 3.8 31.0 - - + -
501A ILE* 5.4 2.7 - - + -
510A LEU* 4.7 16.2 - - + -
513A VAL* 4.5 12.3 - - + -
514A GLN* 3.4 39.3 - - + +
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Residues in contact with CYS 488 (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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484A LEU* 2.8 44.6 + - - +
485A PRO* 3.8 7.9 - - + +
487A LEU* 1.3 74.8 - - - +
489A GLN* 1.3 61.4 + - + +
490A ALA 3.6 0.4 - - - -
492A GLY* 3.1 20.6 - - - -
493A LEU 3.3 28.3 - - - +
495A PRO* 4.4 13.0 - - + -
498A VAL* 4.3 5.4 - - - -
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Residues in contact with GLN 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A PRO* 3.0 21.4 + - + +
486A VAL* 3.6 4.7 - - - +
488A CYS* 1.3 80.9 - - + +
490A ALA* 1.3 58.9 + - - +
492A GLY* 4.6 1.1 - - - -
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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
------------------------------------------------------------
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