Contacts of the strand formed by residues 498 - 506 (chain A) in PDB entry 6TX0
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 PHE 498 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457A VAL* 5.4 0.4 - - + -
477A PRO* 3.9 23.7 - - + +
480A VAL* 3.9 25.1 - - + -
481A ALA* 4.1 27.1 - - + -
493A LEU* 3.8 35.2 - - + -
494A LYS 3.5 23.6 - - - -
495A ALA 3.2 13.1 + - - +
496A GLU 4.3 4.4 - - - +
497A ASP* 1.3 81.9 - - + +
499A ILE* 1.3 68.4 - - - +
500A VAL* 5.1 1.1 - - + -
552A VAL* 4.1 11.9 - - + -
553A TYR 3.4 12.8 - - - -
554A CYS* 4.8 3.4 - - + -
555A LYS* 4.9 0.5 - - - -
565A ALA* 3.8 26.2 - - + -
568A TYR* 4.2 10.5 - + + -
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Residues in contact with ILE 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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381A ILE* 4.1 10.8 - - + -
384A THR* 4.4 18.8 - - + +
388A ASP* 6.0 0.4 - - - +
454A PHE* 3.4 38.4 - - + -
477A PRO* 5.2 1.3 - - - -
497A ASP 4.4 0.2 + - - -
498A PHE* 1.3 78.1 - - - +
500A VAL* 1.3 76.3 + - - +
501A ASP* 4.5 6.5 - - + +
551A ARG 3.6 0.7 - - - +
552A VAL* 3.3 6.6 - - - +
553A TYR* 3.0 50.0 + - + +
555A LYS* 4.0 19.1 - - + -
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Residues in contact with VAL 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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473A TYR* 5.5 4.1 - - - +
476A LEU* 3.7 44.6 - - + +
477A PRO* 4.1 23.1 - - + +
480A VAL* 4.3 15.3 - - + -
498A PHE* 5.1 1.1 - - + -
499A ILE* 1.3 84.4 - - - +
501A ASP* 1.4 57.9 + - - +
502A VAL* 4.0 6.6 + - + +
550A ILE* 3.6 29.8 - - + -
551A ARG 3.3 3.8 - - - +
552A VAL* 4.3 9.6 - - + -
572A TRP* 4.5 3.1 - - + -
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Residues in contact with ASP 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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220A ARG* 3.0 41.7 + - - -
380A ASN* 3.7 18.9 - - - +
384A THR* 5.3 3.1 - - - -
499A ILE* 4.8 6.5 - - + -
500A VAL* 1.4 71.0 - - - +
502A VAL* 1.3 65.6 + - - +
503A ILE* 3.9 12.9 + - - +
549A LEU 3.6 1.2 - - - +
550A ILE* 3.6 3.3 - - - -
551A ARG* 2.9 39.6 + - + +
553A TYR* 4.2 19.8 + - + -
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Residues in contact with VAL 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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468A ILE* 4.9 4.0 - - + -
473A TYR* 3.4 59.3 + - + +
476A LEU* 4.0 21.8 - - + -
500A VAL* 4.0 9.8 + - + +
501A ASP* 1.3 78.6 + - - +
503A ILE* 1.3 63.8 + - - +
504A ASN* 4.2 3.1 + - - +
548A GLN* 3.6 24.9 - - + +
549A LEU 3.6 6.1 - - - +
550A ILE* 4.7 11.7 - - + -
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Residues in contact with ILE 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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220A ARG* 5.7 0.7 - - - +
375A GLN* 3.8 24.0 - - + +
380A ASN* 3.7 11.0 - - - +
501A ASP* 3.9 16.6 - - - +
502A VAL* 1.3 77.8 - - - +
504A ASN* 1.3 66.9 + - - +
505A MET* 3.6 29.0 + - + +
548A GLN* 3.3 4.6 - - - -
549A LEU* 2.9 42.4 + - + +
551A ARG* 3.2 50.9 - - - +
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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 ARG* 4.6 12.5 - - - +
473A TYR* 3.8 14.5 + - - -
502A VAL* 4.2 1.5 + - - +
503A ILE* 1.3 76.9 - - - +
505A MET* 1.3 61.2 + - - +
506A ASP* 4.2 9.8 + - + +
547A GLU 3.8 5.6 - - - +
548A GLN* 3.2 33.3 + - - +
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Residues in contact with MET 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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367A ASN* 3.8 17.9 - - - +
370A HIS* 3.7 28.3 - - + -
371A ARG* 3.6 38.8 - - + +
375A GLN* 4.0 14.1 - - + +
503A ILE* 3.8 22.4 - - + +
504A ASN* 1.3 73.0 - - - +
506A ASP* 1.3 62.0 + - - +
546A ALA* 3.3 1.9 - - - +
547A GLU* 3.0 48.7 + - + +
549A LEU* 4.0 25.8 - - + -
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Residues in contact with ASP 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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366A ARG* 3.0 22.2 + - - -
367A ASN* 4.7 8.5 + - - +
504A ASN* 4.2 10.0 + - + +
505A MET* 1.3 77.4 - - - +
507A TYR* 1.3 68.4 + - - +
508A GLY* 2.8 20.7 + - - -
510A GLN* 3.4 31.3 + - - +
545A PHE 3.3 14.8 - - - +
546A ALA* 3.8 5.8 - - + -
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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