Contacts of the strand formed by residues 546 - 554 (chain A) in PDB entry 6TXA
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 ALA 546 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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505A MET 3.2 11.2 - - - +
506A ASP* 3.8 5.2 - - + -
510A GLN* 3.5 22.0 - - - +
511A GLU* 4.1 15.0 - - + +
544A LYS* 3.7 22.3 - - - +
545A PHE* 1.3 80.3 - - - +
547A GLU* 1.3 67.2 + - - +
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Residues in contact with GLU 547 (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* 5.2 4.5 + - - -
371A ARG* 2.9 31.2 + - - -
461A GLN* 2.8 32.4 + - - +
504A ASN* 3.6 5.4 - - - +
505A MET* 2.8 46.7 + - + +
544A LYS* 6.1 1.3 - - + -
546A ALA* 1.3 78.2 - - - +
548A GLN* 1.3 66.0 + - - +
549A LEU* 4.7 0.7 - - + -
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Residues in contact with GLN 548 (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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461A GLN* 3.3 24.3 + - - +
462A PRO* 3.8 22.8 - - + +
466A ILE 4.1 3.6 - - - +
467A LYS* 3.6 11.4 - - - +
468A ILE* 2.9 53.3 + - - +
473A TYR* 3.9 2.0 + - - -
502A VAL* 3.6 20.7 - - + +
503A ILE 3.3 4.0 - - - +
504A ASN* 3.1 27.7 + - - +
547A GLU* 1.3 78.1 - - - +
549A LEU* 1.3 65.5 + - - +
550A ILE* 5.3 0.9 - - + -
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Residues in contact with LEU 549 (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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371A ARG* 3.5 37.7 - - + +
375A GLN* 5.9 0.7 - - + -
459A GLU* 3.4 30.7 - - + +
460A THR 3.8 1.6 - - - -
461A GLN* 3.7 19.7 - - + +
501A ASP 3.6 1.6 - - - +
502A VAL* 3.4 3.6 - - - +
503A ILE* 2.8 40.7 + - + +
505A MET* 3.8 31.4 - - + -
547A GLU* 4.7 2.0 - - - -
548A GLN* 1.3 83.5 - - - +
550A ILE* 1.3 63.5 + - - +
551A ARG* 4.0 18.2 - - - +
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Residues in contact with ILE 550 (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 3.9 0.5 - - - +
459A GLU* 3.3 2.8 - - - -
460A THR* 2.8 46.3 + - + +
462A PRO* 3.8 20.6 - - + -
468A ILE* 3.5 31.2 - - + -
476A LEU* 5.1 0.4 - - + -
500A VAL* 3.5 31.4 - - + -
501A ASP 3.5 3.8 - - - +
502A VAL* 4.4 11.2 - - + -
548A GLN* 5.2 0.9 - - + -
549A LEU* 1.3 77.2 - - - +
551A ARG* 1.3 61.9 + - - +
552A VAL* 4.1 2.7 + - + +
572A TRP* 3.9 17.7 - - + -
578A PHE* 3.7 24.0 - - + -
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Residues in contact with ARG 551 (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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371A ARG* 5.0 7.5 + - - +
375A GLN* 2.8 35.9 + - - +
376A HIS* 4.9 0.4 - - - +
377A LYS* 3.9 19.7 - - + +
380A ASN* 3.4 6.3 + - - -
456A TYR* 3.9 20.9 - - + -
458A GLY 3.5 3.8 - - - +
459A GLU* 2.8 32.0 + - + -
499A ILE 3.8 0.5 - - - +
500A VAL* 3.4 3.8 - - - +
501A ASP* 2.9 37.3 + - + +
503A ILE* 3.3 31.4 - - - +
549A LEU* 4.2 14.3 - - - +
550A ILE* 1.3 75.7 - - - +
552A VAL* 1.3 60.5 + - - +
553A TYR* 3.6 26.8 + - + +
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Residues in contact with VAL 552 (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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456A TYR* 3.9 2.1 - - - -
457A VAL* 2.9 32.2 + - + +
458A GLY 3.0 9.5 + - - +
480A VAL* 4.7 4.0 - - + -
498A PHE* 3.9 21.1 - - + -
499A ILE 3.4 6.3 - - - +
500A VAL* 4.1 16.4 - - + -
550A ILE* 4.5 2.0 - - + -
551A ARG* 1.3 77.0 - - - +
553A TYR* 1.3 74.8 + - - +
569A PHE* 3.4 42.4 - - + -
572A TRP* 4.0 17.9 - - + -
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Residues in contact with TYR 553 (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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377A LYS* 2.8 38.8 + - - -
378A VAL* 6.2 0.2 - - + -
380A ASN* 4.0 10.7 - - - +
381A ILE* 3.3 44.2 - - + -
384A THR* 6.2 0.7 - - + -
454A PHE* 4.4 7.0 - - + -
455A LYS 3.1 9.6 - - - +
456A TYR* 3.6 35.2 - + + -
457A VAL* 3.9 4.0 - - - -
498A PHE* 3.6 10.7 - - - -
499A ILE* 2.9 43.7 + - + +
501A ASP* 4.0 15.1 + - + -
551A ARG* 3.6 32.0 + - + +
552A VAL* 1.3 76.0 - - - +
554A CYS* 1.3 60.9 + - - +
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Residues in contact with CYS 554 (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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454A PHE* 3.7 3.1 - - - -
455A LYS* 2.8 34.4 + - + +
457A VAL* 4.0 5.8 - - + -
493A LEU* 4.4 14.4 - - - -
497A ASP* 3.5 9.6 - - - -
498A PHE* 4.7 3.6 - - + +
553A TYR* 1.3 75.0 - - - +
555A LYS* 1.3 63.2 + - - +
556A LYS* 3.3 38.2 + - - +
561A SER 4.5 4.5 - - - -
562A LEU* 5.1 2.5 - - + -
565A ALA* 3.9 29.8 - - + -
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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