Contacts of the strand formed by residues 581 - 589 (chain Z) in PDB entry 5WTI
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 581 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573Z ILE* 3.7 34.1 - - + -
574Z ASP 3.3 7.0 - - - +
575Z LEU* 4.2 4.3 - - + -
576Z GLY 4.3 1.6 - - - +
579Z GLN* 3.5 12.7 + - - -
580Z ALA* 1.3 80.7 - - + +
582Z ALA* 1.3 56.8 + - - +
617Z ASN 3.6 0.2 - - - -
618Z ILE* 2.6 48.6 + - + +
799Z ILE* 4.7 7.2 - - + -
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Residues in contact with ALA 582 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573Z ILE* 3.5 2.8 - - - -
574Z ASP 2.9 31.7 + - - +
579Z GLN* 3.4 19.5 - - - +
581Z ALA* 1.3 73.4 - - - +
583Z ALA* 1.3 60.9 + - - +
616Z PHE 3.7 4.9 - - - -
617Z ASN* 3.6 10.1 - - - +
952Z ASP* 3.6 31.6 - - + +
953Z ILE* 3.8 7.4 - - + +
956Z ALA* 3.5 5.9 - - - +
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Residues in contact with ALA 583 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571Z MET* 3.9 22.2 - - + -
572Z SER 3.2 12.3 - - - +
573Z ILE* 3.6 15.9 - - + -
581Z ALA 4.3 0.2 - - - -
582Z ALA* 1.3 74.6 - - - +
584Z SER* 1.3 60.6 + - - +
615Z SER* 3.2 4.2 - - - -
616Z PHE* 2.8 43.0 + - + +
618Z ILE* 4.1 11.4 - - + +
953Z ILE* 4.8 3.0 - - - +
956Z ALA* 4.5 2.2 - - - -
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Residues in contact with SER 584 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571Z MET* 3.3 1.9 - - - -
572Z SER* 2.8 42.5 + - - -
583Z ALA* 1.3 75.3 - - - +
585Z ILE* 1.3 64.7 + - - +
586Z PHE* 3.3 22.9 - - - -
612Z HIS* 3.4 2.6 - - - -
614Z ALA 3.5 4.5 - - - -
615Z SER* 3.0 18.7 + - - -
953Z ILE 4.9 0.7 - - - -
956Z ALA* 4.3 6.9 - - - +
957Z GLN* 3.5 17.2 - - - +
960Z GLN* 3.1 6.5 + - - -
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Residues in contact with ILE 585 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B G 3.1 40.4 - - + +
569Z ARG* 4.9 1.8 - - + -
570Z VAL 3.4 3.6 - - - +
571Z MET* 3.6 32.3 - - + -
584Z SER* 1.3 79.2 + - - +
586Z PHE* 1.3 73.1 + - - +
612Z HIS* 3.7 0.5 - - - -
613Z ARG* 3.0 50.5 + - + -
614Z ALA* 2.8 17.8 + - + +
616Z PHE* 4.1 9.4 - - + -
802Z HIS 4.7 0.4 - - - +
822Z CYS* 3.6 25.1 - - - -
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Residues in contact with PHE 586 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569Z ARG* 3.2 6.8 - - - +
570Z VAL* 2.9 31.9 + - - +
584Z SER* 3.3 20.6 - - - -
585Z ILE* 1.3 84.3 - - - +
587Z GLU* 1.3 58.8 + - - +
599Z LEU* 3.5 14.1 - - + -
601Z PHE* 3.4 33.7 - + - -
610Z ALA* 3.1 35.9 - - + -
611Z VAL 3.4 3.1 - - - -
612Z HIS* 3.5 33.0 - + + -
613Z ARG* 4.4 0.7 - - - +
957Z GLN* 4.6 2.9 - - + -
960Z GLN* 3.3 40.4 - - + +
964Z TRP* 4.0 10.2 - - + +
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Residues in contact with GLU 587 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557Z LEU* 3.4 22.6 - - - +
567Z GLY* 6.1 0.5 - - - -
568Z LEU 3.8 4.7 - - - +
569Z ARG* 3.8 24.7 + - + -
586Z PHE* 1.3 74.1 - - - +
588Z VAL* 1.3 74.6 + - - +
589Z VAL* 3.8 13.8 + - + +
609Z TYR 3.5 1.2 - - - +
610Z ALA* 3.4 3.0 - - - -
611Z VAL* 2.8 38.0 + - + +
613Z ARG* 3.2 33.5 + - + +
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Residues in contact with VAL 588 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545Z LEU* 4.5 3.6 - - + -
549Z ILE* 3.7 34.0 - - + +
567Z GLY* 5.9 0.5 - - - -
568Z LEU* 3.1 28.5 + - + +
587Z GLU* 1.3 80.1 - - - +
589Z VAL* 1.3 66.7 + - - +
603Z ILE* 3.6 20.2 - - + -
608Z LEU* 3.7 20.0 - - + -
609Z TYR 3.3 3.1 - - - +
610Z ALA* 5.0 0.4 - - - -
964Z TRP* 3.4 39.0 - - + -
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Residues in contact with VAL 589 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549Z ILE* 4.6 5.2 - - - -
587Z GLU* 4.3 18.8 - - + +
588Z VAL* 1.3 80.3 - - - +
590Z ASP* 1.3 59.8 + - - +
591Z GLN* 3.2 24.5 - - + +
608Z LEU* 3.4 8.5 - - - +
609Z TYR* 2.9 35.8 + - + +
611Z VAL* 3.6 28.3 - - + -
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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