Contacts of the helix formed by residues 498 - 508 (chain A) in PDB entry 1T9A
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 498 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497A VAL* 1.3 78.7 - - - +
499A GLN* 1.3 66.9 + - - -
500A HIS* 3.3 4.3 - - - -
501A GLN* 3.0 25.6 + - - +
502A MET* 3.2 5.9 + - - +
582A MET* 3.5 17.4 - - - +
701A FAD 4.3 0.9 - - - +
1698A P23 3.3 21.3 - - - -
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Residues in contact with GLN 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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498A GLY* 1.3 71.0 - - - -
500A HIS* 1.3 56.8 + - - +
502A MET* 3.1 3.1 + - - +
503A TRP* 2.9 49.7 + - + -
577A ASN* 3.8 12.5 + - - -
579A GLU* 4.7 3.5 - - - +
581A GLY* 3.0 32.4 + - - -
582A MET* 3.4 26.4 - - + +
584A THR* 5.3 0.2 + - - -
585A GLN* 2.8 27.1 + - - +
648A LYS* 5.9 0.4 - - - +
649A VAL 2.9 29.5 + - - +
650A PRO* 4.0 0.2 - - - +
651A VAL* 3.6 12.0 - - + +
1698A P23 2.8 13.1 + - - +
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Residues in contact with HIS 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A ILE* 4.7 1.0 - - - +
495A THR* 4.4 0.2 - - - -
496A GLY* 3.1 39.7 - - - -
497A VAL 3.5 21.7 + - - -
498A GLY 4.2 1.6 - - - -
499A GLN* 1.3 79.0 - - - +
501A GLN* 1.3 66.1 + - - +
503A TRP* 3.5 12.8 + - + +
504A ALA* 2.9 30.0 + - - +
547A ILE* 3.1 20.6 + - + +
548A ASP 3.4 6.4 - - - +
549A GLY* 3.2 27.4 + - - -
552A SER* 3.9 0.4 + - - -
575A LEU* 3.8 26.0 - - + -
1698A P23 3.1 36.9 + - - +
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Residues in contact with GLN 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A LEU* 4.1 9.2 - - + +
495A THR* 3.6 15.5 - - + +
496A GLY 3.5 20.8 + - - +
497A VAL* 3.3 4.5 - - - +
498A GLY 3.0 28.5 + - - +
500A HIS* 1.3 86.1 - - + +
502A MET* 1.3 69.8 + - + +
504A ALA* 3.3 4.4 + - - +
505A ALA* 3.0 26.0 + - - +
516A PHE* 4.4 3.4 - - + -
518A THR* 2.8 23.9 + - - +
519A SER 2.9 24.7 + - - +
701A FAD 3.4 20.2 - - - +
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Residues in contact with MET 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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335A LEU* 4.0 17.7 - - + -
351A MET* 4.8 4.7 - - - -
355A HIS* 3.9 18.8 - - + -
498A GLY 3.7 0.7 - - - +
499A GLN 3.1 6.3 + - - +
501A GLN* 1.3 104.0 - - + +
503A TRP* 1.3 60.5 + - - +
505A ALA* 3.0 4.6 + - - +
506A GLN* 2.8 35.8 + - + +
582A MET* 3.4 29.2 - - + -
651A VAL* 3.8 19.7 - - + -
701A FAD 3.3 48.7 - - + +
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Residues in contact with TRP 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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473A PRO* 3.4 35.2 - - + -
474A GLN* 3.4 44.9 - - + +
477A ILE* 3.6 15.1 - - + +
499A GLN* 2.9 45.4 + - + +
500A HIS* 3.8 11.2 - - + +
502A MET* 1.3 76.9 - - - +
504A ALA* 1.3 58.1 + - - +
506A GLN* 3.6 18.1 + - - -
507A HIS* 2.8 41.0 + + + +
575A LEU* 4.9 1.6 - - + -
577A ASN* 5.1 7.0 - - - -
645A VAL* 6.0 0.4 - - + -
646A ASP 6.2 0.2 - - - -
649A VAL* 3.4 31.6 - - + -
650A PRO 4.1 3.1 + - - -
651A VAL* 3.5 29.6 - - + +
652A LEU 5.0 0.6 - - - +
1698A P23 5.0 2.2 - - - -
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Residues in contact with ALA 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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477A ILE* 3.8 12.5 - - - +
493A VAL* 5.2 1.3 - - + -
495A THR* 4.3 14.1 - - + -
500A HIS 2.9 19.1 + - - +
501A GLN 3.5 5.8 - - - +
503A TRP* 1.3 76.4 - - - +
505A ALA* 1.3 60.9 + - - +
508A TRP* 3.0 31.6 + - - +
510A TRP* 3.4 4.8 - - - -
516A PHE* 4.7 4.7 - - + -
547A ILE* 4.1 29.4 - - + -
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Residues in contact with ALA 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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335A LEU* 3.5 32.5 - - + -
338A LEU* 3.8 14.1 - - + +
350A ASP* 4.7 2.3 - - - +
351A MET* 4.1 12.9 - - + +
501A GLN 3.0 11.2 + - - +
502A MET* 3.3 10.1 - - - +
504A ALA* 1.3 79.1 - - - +
506A GLN* 1.3 59.1 + - - +
510A TRP* 3.0 28.0 + - - +
516A PHE* 4.3 4.9 - - + -
1696A K 4.0 1.9 - - - -
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Residues in contact with GLN 506 (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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350A ASP* 4.7 0.2 - - - -
351A MET* 4.7 5.2 - - + -
355A HIS 2.8 28.1 + - - +
460A TYR* 3.4 52.8 - - + +
502A MET* 2.8 22.8 + - + +
503A TRP* 3.6 22.9 - - - -
505A ALA* 1.3 73.6 - - - +
507A HIS* 1.3 71.2 + - + +
651A VAL* 4.1 13.3 - - - +
652A LEU 3.3 27.0 + - - +
1696A K 2.8 20.7 - - - -
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Residues in contact with HIS 507 (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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460A TYR* 3.5 40.4 + - + +
462A TYR* 4.1 15.4 - + - -
474A GLN* 3.6 35.3 - - + +
477A ILE* 3.7 16.4 - - + -
478A LYS* 3.9 40.5 - - + +
481A SER* 4.4 2.3 - - - -
503A TRP* 2.8 27.6 + + - +
506A GLN* 1.3 90.1 + - - +
508A TRP* 1.3 62.5 + - - +
509A THR* 3.9 3.8 + - - -
1696A K 4.6 0.2 - - - -
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Residues in contact with TRP 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A GLN* 3.4 2.3 - - - +
477A ILE* 3.8 9.9 - - + +
480A LEU* 3.8 14.4 - - + -
481A SER* 3.6 38.9 + - - -
484A ALA* 3.7 24.5 - - + -
485A ASN* 5.4 1.1 - - + -
491A VAL* 4.0 16.7 - - + +
493A VAL* 3.7 19.9 - - + +
504A ALA 3.0 23.1 + - - +
506A GLN 3.5 0.2 - - - -
507A HIS* 1.3 77.6 - - - +
509A THR* 1.3 85.0 + - - +
510A TRP* 3.4 40.9 + + + -
545A ILE* 4.2 9.0 - - + -
547A ILE* 3.9 26.2 - - + -
1696A K 2.7 26.0 - - - -
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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