Contacts of the helix formed by residues 494 - 505 (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 THR 494 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492A GLY 4.9 3.6 - - - +
493A LEU* 1.3 74.1 - - - +
495A PRO* 1.4 73.3 - - - +
496A ASP* 3.9 7.8 + - - +
497A GLN* 2.7 60.2 + - - +
498A VAL* 3.0 13.3 + - - +
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Residues in contact with PRO 495 (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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458A GLY 4.7 7.9 - - - +
459A LEU* 4.6 12.8 - - + -
484A LEU* 4.0 20.8 - - + +
488A CYS* 4.4 11.7 - - + -
493A LEU 3.9 4.2 - - - +
494A THR* 1.4 84.7 - - - +
496A ASP* 1.3 61.8 + - - +
498A VAL* 4.0 0.7 - - - +
499A VAL* 3.0 34.5 + - - +
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Residues in contact with ASP 496 (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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463A GLN* 3.4 29.1 + - - +
494A THR* 3.1 6.7 + - - +
495A PRO* 1.3 82.4 - - - +
497A GLN* 1.3 56.1 + - + +
499A VAL* 3.8 4.8 - - - +
500A ALA* 2.7 35.3 + - - +
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Residues in contact with GLN 497 (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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493A LEU* 3.6 15.9 - - + +
494A THR* 2.7 53.5 + - - +
496A ASP* 1.3 73.6 - - - +
498A VAL* 1.3 69.6 + - - +
499A VAL 3.0 1.5 + - - -
500A ALA* 3.0 7.8 + - - +
501A ILE* 2.8 27.8 + - - +
529A ASP* 2.6 30.6 + - - -
532A VAL* 3.5 35.3 - - + +
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Residues in contact with VAL 498 (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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480A VAL* 4.5 6.3 - - + -
483A LEU 4.7 0.7 - - - +
484A LEU* 3.5 44.2 - - + +
487A LEU* 3.8 31.4 - - + -
488A CYS* 4.3 3.8 - - - -
493A LEU* 3.8 19.0 - - + +
494A THR 3.0 12.7 + - - +
495A PRO 4.1 0.2 - - - +
497A GLN* 1.3 75.9 - - - +
499A VAL* 1.3 58.2 + - - +
501A ILE* 3.2 10.7 + - - +
502A ALA* 2.8 25.8 + - - +
510A LEU* 3.7 17.9 - - + +
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Residues in contact with VAL 499 (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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459A LEU* 3.9 29.4 - - + -
463A GLN* 4.3 27.6 - - + +
466A ALA* 6.0 0.7 - - + -
467A ILE* 3.9 24.7 - - + -
480A VAL* 5.3 2.7 - - + -
484A LEU* 5.2 4.3 - - + -
495A PRO 3.0 23.0 + - - +
496A ASP* 3.8 4.7 - - - +
498A VAL* 1.3 73.9 - - - +
500A ALA* 1.3 70.8 + - - +
502A ALA* 2.5 20.5 + - - +
503A SER* 2.8 22.1 + - - +
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Residues in contact with ALA 500 (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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496A ASP 2.7 24.2 + - - +
497A GLN* 3.0 8.5 + - - +
499A VAL* 1.3 76.6 - - - +
501A ILE* 1.3 56.5 + - - +
503A SER* 3.4 13.1 + - - -
504A ASN* 3.1 23.0 + - - +
532A VAL* 5.4 2.0 - - + -
536A SER* 4.0 10.7 - - - +
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Residues in contact with ILE 501 (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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487A LEU* 5.4 1.6 - - + -
493A LEU* 4.9 4.7 - - + -
497A GLN 2.8 13.4 + - - +
498A VAL* 3.4 13.9 - - - +
499A VAL 2.6 3.6 + - - -
500A ALA* 1.3 68.3 - - - +
502A ALA* 1.3 58.8 + - - +
503A SER 3.1 1.8 - - - -
505A GLY* 2.9 27.9 + - - -
506A GLY 3.4 0.7 + - - -
509A ALA* 3.8 15.7 - - + -
510A LEU* 3.9 19.5 - - + +
513A VAL* 4.4 18.4 - - + -
532A VAL* 3.5 40.6 - - + -
535A ALA* 3.3 31.4 - - + +
536A SER* 3.7 8.3 - - - +
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Residues in contact with ALA 502 (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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467A ILE* 3.8 38.0 - - + +
476A ALA* 4.3 5.0 - - + +
480A VAL* 4.3 9.4 - - + -
498A VAL 2.8 12.9 + - - +
499A VAL* 2.5 15.1 + - - +
501A ILE* 1.3 70.0 - - - +
503A SER* 1.3 66.1 + - - +
504A ASN 3.5 0.2 + - - -
506A GLY* 3.6 17.7 + - - +
510A LEU* 4.0 20.6 - - + +
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Residues in contact with SER 503 (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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466A ALA* 4.4 10.0 - - - +
467A ILE* 3.7 24.2 + - - +
470A ASN* 2.4 36.0 + - - +
499A VAL* 2.8 17.4 + - - +
500A ALA* 3.5 15.2 - - - -
501A ILE 3.1 0.6 - - - -
502A ALA* 1.3 82.4 - - - +
504A ASN* 1.3 64.5 + - - +
506A GLY* 4.9 0.7 + - - -
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Residues in contact with ASN 504 (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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470A ASN* 4.6 5.4 - - - +
500A ALA 3.1 16.9 + - - +
503A SER* 1.3 82.3 - - - +
505A GLY* 1.3 62.2 + - - +
506A GLY 3.5 0.4 - - - -
536A SER* 3.0 37.3 + - - +
537A HIS* 3.6 4.0 - - - -
538A ASP* 2.8 51.3 + - - +
572A ASP* 5.7 0.2 - - - +
19C G 5.4 3.6 + - - -
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Residues in contact with GLY 505 (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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501A ILE 2.9 9.3 + - - -
504A ASN* 1.3 82.9 - - - +
506A GLY* 1.4 58.8 + - - +
508A GLN* 4.5 1.7 + - - +
509A ALA* 3.2 36.7 + - - +
535A ALA 3.7 4.7 - - - -
537A HIS 3.4 12.8 - - - -
538A ASP 4.1 7.9 - - - +
540A GLY* 4.5 1.0 - - - -
7B C 4.6 7.4 + - - -
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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