Contacts of the strand formed by residues 609 - 618 (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 TYR 609 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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587Z GLU 3.5 1.2 - - - +
588Z VAL* 3.3 4.7 - - - -
589Z VAL* 2.9 37.8 + - + +
590Z ASP 5.0 0.7 - - - -
591Z GLN* 3.4 28.9 - - - +
592Z LYS* 3.8 22.8 - - + +
593Z PRO* 4.8 0.4 - - + -
600Z PHE* 3.6 38.4 - + + -
601Z PHE 3.5 4.0 - - - +
602Z PRO* 4.0 19.7 - - + -
603Z ILE* 3.6 5.8 - - - +
607Z GLU 3.7 18.3 + - - -
608Z LEU* 1.3 80.0 - - - +
610Z ALA* 1.3 60.4 + - - +
611Z VAL* 3.8 4.5 - - + -
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Residues in contact with ALA 610 (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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586Z PHE* 3.1 15.4 - - + -
587Z GLU 3.4 7.0 - - - +
600Z PHE* 3.3 1.6 - - - -
601Z PHE* 2.8 35.0 + - + +
603Z ILE* 3.8 5.4 - - + +
609Z TYR* 1.3 71.4 - - - +
611Z VAL* 1.3 60.9 + - - +
964Z TRP* 3.5 52.9 - - + +
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Residues in contact with VAL 611 (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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586Z PHE* 3.4 1.7 - - - -
587Z GLU* 2.8 38.5 + - + +
589Z VAL* 3.6 31.0 - - + -
593Z PRO* 4.1 18.2 - - + -
598Z LYS* 3.5 34.3 - - + -
599Z LEU 4.0 3.6 - - - +
600Z PHE* 4.0 12.6 - - + -
609Z TYR* 4.4 2.9 - - + -
610Z ALA* 1.3 73.2 - - - +
612Z HIS* 1.3 67.9 + - - +
613Z ARG* 3.3 2.1 + - + +
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Residues in contact with HIS 612 (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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14B U 3.7 23.1 + - - -
15B U 2.7 27.5 + - - +
16B U 5.0 3.8 - + - -
584Z SER* 3.4 14.6 - - - -
585Z ILE 3.7 3.1 - - - -
586Z PHE* 3.5 21.6 - + + -
598Z LYS* 3.2 24.3 + - - -
599Z LEU* 2.9 26.5 + - + +
611Z VAL* 1.3 71.5 - - - +
613Z ARG* 1.3 60.3 + - - +
614Z ALA* 3.1 23.3 + - - -
615Z SER* 2.4 32.2 + - - -
957Z GLN* 3.6 15.3 + - - -
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Residues in contact with ARG 613 (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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16B U 3.3 8.2 + - - +
17B G 2.5 85.4 + - - +
557Z LEU* 4.8 5.1 - - - +
569Z ARG* 4.6 6.4 - - - +
585Z ILE* 3.0 28.2 + - + +
587Z GLU* 3.2 38.6 + - + +
598Z LYS* 5.1 1.8 - - - +
611Z VAL* 3.3 5.8 + - + +
612Z HIS* 1.3 78.0 - - - +
614Z ALA* 1.3 62.1 + - - +
819Z ASN* 4.6 1.0 - - - +
820Z PRO* 3.6 24.6 - - - +
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Residues in contact with ALA 614 (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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16B U 4.1 6.1 - - - -
17B G 3.4 46.2 - - + +
585Z ILE* 2.8 33.0 + - + +
612Z HIS* 3.1 10.2 + - - -
613Z ARG* 1.3 84.1 - - + +
615Z SER* 1.3 70.8 + - - +
616Z PHE* 4.6 2.0 - - + -
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Residues in contact with SER 615 (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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14B U 3.6 14.0 + - - -
16B U 5.3 0.8 + - - -
17B G 4.5 0.6 + - - -
18B G 2.3 34.2 + - - +
583Z ALA 3.2 11.2 - - - -
584Z SER* 3.0 13.9 + - - -
612Z HIS* 2.4 32.2 + - - -
614Z ALA* 1.3 74.5 + - - +
616Z PHE* 1.3 65.0 + - - +
953Z ILE* 3.7 18.8 - - - -
957Z GLN* 3.6 3.5 + - - -
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Residues in contact with PHE 616 (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 3.9 29.2 - - - -
18B G 3.6 23.3 - - - +
19B U 4.2 1.8 - - - +
571Z MET* 3.9 20.9 - - + -
583Z ALA* 2.8 36.0 + - + +
585Z ILE* 4.1 21.8 - - + -
614Z ALA* 4.6 1.1 - - + -
615Z SER* 1.3 81.7 - - - +
617Z ASN* 1.3 83.0 + - - +
618Z ILE* 3.6 17.5 - - + -
802Z HIS* 3.4 36.3 - + + -
953Z ILE* 4.3 6.3 - - - +
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Residues in contact with ASN 617 (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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19B U 3.4 22.9 + - - +
20B C 3.2 24.7 + - - -
579Z GLN* 3.1 38.0 + - - +
581Z ALA 3.6 3.1 - - - +
582Z ALA* 3.6 1.3 - - - +
616Z PHE* 1.3 89.5 - - - +
618Z ILE* 1.3 59.7 + - - +
619Z LYS* 3.8 13.7 + - + +
802Z HIS* 5.5 0.9 + - - -
950Z HIS* 3.3 15.3 + - - -
953Z ILE* 3.4 21.9 - - - +
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Residues in contact with ILE 618 (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* 5.1 0.7 - - + -
573Z ILE* 4.3 13.2 - - + -
580Z ALA* 3.1 15.6 + - + +
581Z ALA* 2.6 41.7 + - + +
583Z ALA* 4.1 17.7 - - + -
616Z PHE* 3.6 28.7 - - + -
617Z ASN* 1.3 70.2 - - - +
619Z LYS* 1.3 61.7 + - - +
620Z LEU* 5.1 1.3 - - + -
795Z MET* 5.6 0.7 - - + +
798Z THR* 3.5 29.2 - - + -
799Z ILE* 4.5 16.6 - - + -
802Z HIS* 3.9 28.0 - - + +
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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