Contacts of the helix formed by residues 568 - 585 (chain I) in PDB entry 3RWR
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 PRO 568 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F ASP* 3.0 29.2 - - + +
104F VAL* 4.2 0.2 - - + -
566I THR 3.4 6.1 - - - +
567I ALA* 1.3 89.1 - - + +
569I PRO* 1.3 80.1 - - + +
570I ALA 4.8 0.2 - - - +
571I ALA* 4.0 21.5 - - + +
572I PHE* 3.3 17.3 + - - +
56S GLN* 4.6 14.1 - - + -
60S GLU* 5.9 2.7 - - - +
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Residues in contact with PRO 569 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551I THR* 4.4 26.5 - - + +
554I VAL* 3.9 16.7 - - + +
555I SER* 5.1 7.2 - - - +
567I ALA 4.6 0.4 - - - +
568I PRO* 1.3 90.1 - - + +
570I ALA* 1.3 64.5 + - + +
572I PHE* 3.2 14.8 - - + +
573I LEU* 4.0 2.0 + - - +
122S HIS* 5.7 11.2 - - + -
124S MET* 4.3 23.8 - - + -
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Residues in contact with ALA 570 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531I LYS* 4.0 44.4 + - + +
551I THR* 5.8 2.6 - - + +
568I PRO* 4.8 0.8 - - + +
569I PRO* 1.3 75.4 - - - +
571I ALA* 1.3 58.2 + - - +
572I PHE 2.9 2.0 - - - -
573I LEU* 2.7 38.1 + - - +
574I CYS 3.8 1.7 + - - -
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Residues in contact with ALA 571 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F LYS* 3.3 46.9 - - - +
103F ASP* 4.5 5.8 - - + +
104F VAL* 4.7 3.4 - - + -
531I LYS* 5.0 2.7 - - - +
568I PRO* 4.0 31.8 + - + +
569I PRO 3.5 0.2 - - - -
570I ALA* 1.3 77.7 - - - +
572I PHE* 1.3 62.9 + - - +
574I CYS* 3.1 13.1 + - - +
575I HIS* 3.4 4.3 + - - +
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Residues in contact with PHE 572 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F VAL* 5.5 1.1 - - - -
554I VAL* 4.0 16.8 - - + -
558I ALA* 3.8 19.7 - - + -
559I LYS* 6.2 0.2 - - - -
562I ASN* 3.9 10.8 - - - -
565I LEU* 4.5 6.7 - - + -
567I ALA* 4.4 20.8 - - + +
568I PRO 3.3 13.0 + - - +
569I PRO* 3.2 15.0 - - + +
570I ALA 2.8 3.8 + - - -
571I ALA* 1.3 75.6 - - - +
573I LEU* 1.3 67.1 + - + +
575I HIS* 3.5 8.3 + - + +
576I LEU* 3.3 24.8 + - + +
617I PHE* 3.2 43.5 - + - -
619I TRP* 3.3 42.2 - + - -
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Residues in contact with LEU 573 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529I ILE* 3.7 15.4 - - + +
530I THR 3.5 12.8 - - - +
531I LYS* 3.3 15.3 - - - +
533I GLY* 3.2 43.3 - - - +
534I TYR* 3.9 28.0 - - + -
554I VAL* 4.4 21.1 - - + -
569I PRO 4.5 5.8 - - - +
570I ALA* 2.7 19.4 + - - +
572I PHE* 1.3 71.7 - - + +
574I CYS* 1.3 62.0 + - - +
576I LEU* 2.9 30.7 - - + +
577I ASP* 3.5 10.2 + - - +
619I TRP* 5.8 0.2 - - + -
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Residues in contact with CYS 574 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F LYS* 3.7 24.5 - - - +
530I THR 5.7 0.2 - - - -
531I LYS* 3.9 20.0 - - - +
570I ALA 3.8 1.6 + - - -
571I ALA 3.1 9.0 + - - +
573I LEU* 1.3 73.7 - - - +
575I HIS* 1.3 60.3 + - - +
576I LEU 2.9 10.6 + - - -
577I ASP* 3.2 19.1 + - - +
578I ASN* 3.8 15.6 + - - +
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Residues in contact with HIS 575 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F LEU* 4.1 14.3 - - + +
102F LYS* 3.3 47.2 + - + +
104F VAL* 4.1 20.2 - - + +
571I ALA 3.4 5.7 + - - +
572I PHE* 3.8 10.8 - - + +
573I LEU 3.4 0.2 - - - -
574I CYS* 1.3 78.2 - - - +
576I LEU* 1.3 60.3 + - - +
577I ASP 3.6 0.2 - - - -
578I ASN* 3.7 23.4 + - - +
579I LEU* 3.4 20.6 - - - +
612I LEU* 3.1 46.0 - - + +
617I PHE* 4.5 3.4 - - + -
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Residues in contact with LEU 576 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529I ILE* 4.2 11.9 - - + -
534I TYR* 4.4 7.4 - - + -
572I PHE* 3.3 23.7 + - + +
573I LEU* 2.9 36.1 + - + +
574I CYS 2.9 2.4 - - - -
575I HIS* 1.3 77.7 - - - +
577I ASP* 1.3 57.7 + - - +
579I LEU* 2.9 31.6 + - + +
580I LEU* 3.1 34.6 + - + -
608I VAL* 5.4 4.9 - - + -
617I PHE* 4.8 7.2 - - + -
619I TRP* 4.3 25.4 - - + +
621I PHE* 4.5 6.7 - - + -
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Residues in contact with ASP 577 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527I VAL* 5.1 4.7 - - - +
529I ILE* 3.2 45.4 + - - +
573I LEU 3.5 6.8 + - - +
574I CYS* 3.2 10.2 + - - +
576I LEU* 1.3 73.6 - - - +
578I ASN* 1.3 59.1 + - - +
579I LEU 2.8 5.6 - - - -
580I LEU* 2.6 17.5 + - - +
581I ARG* 2.5 48.7 + - + +
582I PRO* 3.0 3.4 - - - +
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Residues in contact with ASN 578 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F LYS* 5.8 2.2 - - - +
574I CYS* 3.9 12.1 + - - +
575I HIS* 3.7 38.9 + - - +
576I LEU 3.2 0.6 - - - -
577I ASP* 1.3 77.5 - - - +
579I LEU* 1.3 64.0 + - + +
582I PRO* 3.3 27.1 - - + +
589I HIS* 4.1 5.0 + - - -
612I LEU* 5.2 2.6 - - + +
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Residues in contact with LEU 579 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575I HIS 3.4 16.6 - - - +
576I LEU* 3.2 18.6 - - + +
577I ASP 2.8 0.4 - - - -
578I ASN* 1.3 82.1 - - + +
580I LEU* 1.3 62.5 + - + +
583I LEU* 3.1 31.7 - - - +
589I HIS* 3.4 11.0 + - - +
595I PHE* 4.4 1.1 - - + -
608I VAL* 5.7 6.7 - - + -
610I SER* 3.1 34.3 - - - +
611I GLU 3.4 19.3 - - - +
612I LEU* 3.4 14.6 - - + -
617I PHE* 3.5 30.1 - - + -
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Residues in contact with LEU 580 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527I VAL* 4.2 21.3 - - + -
529I ILE* 3.4 25.1 - - + -
576I LEU* 3.1 35.7 + - + +
577I ASP* 2.6 17.1 + - - +
579I LEU* 1.3 73.2 - - - +
581I ARG* 1.3 54.5 + - - +
582I PRO 3.4 0.2 - - - -
583I LEU* 2.7 9.2 + - - +
584I LEU* 2.5 40.2 + - + +
595I PHE* 3.5 34.3 - - + -
608I VAL* 5.0 3.1 - - + -
621I PHE* 4.2 18.6 - - + -
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Residues in contact with ARG 581 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577I ASP* 2.5 32.6 + - + +
580I LEU* 1.3 73.5 - - - +
582I PRO* 1.3 66.3 - - + +
583I LEU 2.6 11.6 + - - -
584I LEU* 3.1 20.7 + - + -
585I LYS* 3.1 45.7 + - - +
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Residues in contact with PRO 582 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577I ASP 3.0 17.9 - - - +
578I ASN* 3.3 23.6 - - - +
580I LEU 3.8 0.9 - - - -
581I ARG* 1.3 92.7 - - + +
583I LEU* 1.3 56.9 + - - -
585I LYS* 4.9 5.8 - - + -
586I ASP* 4.8 3.5 - - - +
588I ALA* 4.5 2.3 + - - +
589I HIS* 3.2 29.3 + - + +
590I PRO* 6.1 0.9 - - + -
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Residues in contact with LEU 583 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516I LEU* 3.4 33.2 - - + +
579I LEU 3.1 22.9 - - - +
580I LEU* 2.7 10.6 + - - +
581I ARG 2.6 6.1 + - - -
582I PRO* 1.3 76.0 - - - +
584I LEU* 1.3 56.5 + - - -
585I LYS 3.4 0.4 - - - -
586I ASP 2.5 26.9 - - - +
587I ALA* 5.9 2.2 - - - -
589I HIS* 3.4 32.1 - - + +
593I ALA* 4.0 10.3 - - + +
595I PHE* 3.4 30.5 - - + -
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Residues in contact with LEU 584 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511I GLN* 4.4 15.7 - - - +
512I PRO 5.5 1.1 - - - +
514I ALA* 3.3 36.6 - - + +
515I TRP 5.9 1.0 - - - -
516I LEU* 5.8 7.2 - - + +
525I ALA* 4.6 2.0 - - + +
526I LYS* 4.6 4.7 - - - -
527I VAL* 4.1 34.5 - - + +
580I LEU* 2.5 20.3 + - + +
581I ARG* 4.0 17.3 - - + +
583I LEU* 1.3 71.8 - - - +
585I LYS* 1.3 76.6 + - + +
586I ASP 3.2 2.6 + - - -
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Residues in contact with LYS 585 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581I ARG* 3.1 45.1 + - - +
582I PRO* 5.1 4.3 - - + -
584I LEU* 1.3 89.4 - - + +
586I ASP* 1.3 65.6 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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