Contacts of the helix formed by residues 563 - 580 (chain R) in PDB entry 1HI0
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 ILE 563 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65R PHE* 3.3 46.7 - - + -
78R ASN* 4.0 23.8 - - + +
80R VAL* 3.4 29.2 - - + -
84R PHE* 4.3 5.6 - - + -
518R ILE* 4.4 13.9 - - + -
561R CYS* 3.3 1.1 - - - -
562R PRO* 1.3 79.7 - - + +
564R TYR* 1.3 70.1 + - - +
565R SER 3.5 1.6 - - - -
566R ASP* 3.2 12.8 + - + +
567R VAL* 3.0 36.3 + - + +
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Residues in contact with TYR 564 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518R ILE* 4.3 10.8 - - + -
521R MET* 4.0 13.5 - - + -
554R MET* 3.3 29.9 - - + +
555R LYS* 3.0 60.5 + - + +
558R TYR* 3.7 25.4 - - + +
559R GLY* 3.7 16.8 - - - +
561R CYS* 3.1 18.6 + - - +
562R PRO 3.5 1.4 + - - -
563R ILE* 1.3 78.2 - - - +
565R SER* 1.3 77.8 + - - +
567R VAL* 2.8 11.1 + - - +
568R LEU* 3.1 34.9 + - + +
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Residues in contact with SER 565 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555R LYS* 5.7 1.4 + - - -
564R TYR* 1.3 87.5 - - - +
566R ASP* 1.3 70.0 + - - +
568R LEU* 3.4 8.5 + - - +
569R GLU* 3.1 34.4 + - - +
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Residues in contact with ASP 566 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65R PHE* 3.6 36.3 - - + -
562R PRO 4.4 2.8 - - - +
563R ILE* 3.4 22.0 - - - +
564R TYR 2.9 0.4 + - - -
565R SER* 1.3 79.2 - - - +
567R VAL* 1.3 59.8 + - - +
569R GLU* 3.2 9.7 + - - +
570R ALA* 2.8 29.3 + - - +
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Residues in contact with VAL 567 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61R LEU* 4.0 22.4 - - + -
84R PHE* 5.1 0.7 - - + -
518R ILE* 3.9 22.2 - - + -
521R MET* 3.6 25.6 - - + -
522R LEU* 4.1 15.7 - - + -
563R ILE* 3.0 29.0 + - + +
564R TYR 2.8 12.6 + - - +
566R ASP* 1.3 72.0 - - + +
568R LEU* 1.3 54.3 + - - +
570R ALA* 2.9 9.0 + - - +
571R ILE* 2.7 46.4 + - + +
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Residues in contact with LEU 568 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521R MET* 4.9 5.2 - - + -
525R GLN* 5.6 0.4 - - - +
551R TRP* 4.1 13.5 - - + -
554R MET* 3.8 29.8 - - + -
564R TYR* 3.1 57.9 + - + +
565R SER* 3.8 8.7 - - - +
567R VAL* 1.3 75.6 - - - +
569R GLU* 1.3 57.8 + - + +
571R ILE* 3.3 16.9 + - + +
572R GLU* 2.8 30.2 + - - +
583R TYR* 5.8 1.3 - - + -
584R ARG* 5.4 8.0 + - - +
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Residues in contact with GLU 569 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565R SER* 3.1 22.8 + - - +
566R ASP* 3.4 10.7 - - - +
568R LEU* 1.3 74.7 - - + +
570R ALA* 1.3 66.3 + - - +
572R GLU* 3.3 8.8 + - + +
573R ARG* 2.9 24.9 + - - +
584R ARG* 6.1 2.5 - - - +
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Residues in contact with ALA 570 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57R LEU* 3.9 17.5 - - + -
60R TYR* 3.9 26.0 - - + -
61R LEU* 4.0 10.8 - - + -
566R ASP 2.8 17.4 + - - +
567R VAL 3.4 6.7 - - - +
569R GLU* 1.3 71.7 - - - +
571R ILE* 1.3 58.0 + - - +
573R ARG* 3.3 14.6 + - - +
574R CYS* 2.9 33.6 + - - -
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Residues in contact with ILE 571 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53R PHE* 3.8 7.7 - - + -
57R LEU* 3.7 26.0 - - + +
521R MET* 4.9 3.6 - - + -
522R LEU* 4.0 10.3 - - + -
525R GLN* 4.5 9.9 - - - +
526R PHE* 3.6 29.2 - - + -
567R VAL* 2.7 31.0 + - + +
568R LEU* 3.4 18.8 - - + +
570R ALA* 1.3 70.1 - - - +
572R GLU* 1.3 68.9 + - - +
573R ARG 3.0 0.5 + - - -
574R CYS* 3.0 1.9 + - - -
575R TRP* 2.7 26.9 + - - +
583R TYR* 3.4 34.8 - - + -
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Residues in contact with GLU 572 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568R LEU 2.8 21.3 + - - +
569R GLU* 3.5 8.7 - - - +
571R ILE* 1.3 76.5 - - - +
573R ARG* 1.3 57.8 + - - +
575R TRP* 3.8 1.7 - - - +
576R TRP* 3.1 38.3 + - + +
582R SER* 3.0 34.7 + - - -
583R TYR* 3.1 9.6 + - - +
584R ARG* 2.9 57.9 + - - +
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Residues in contact with ARG 573 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56R GLU* 3.7 21.8 + - - +
60R TYR* 3.1 55.2 + - - +
569R GLU 2.9 16.2 + - - +
570R ALA* 3.3 9.5 - - - +
572R GLU* 1.3 77.3 - - - +
574R CYS* 1.3 70.6 + - - +
576R TRP* 2.8 24.2 + - - +
577R ASN* 3.1 22.3 + - - +
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Residues in contact with CYS 574 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53R PHE* 3.5 21.5 - - + +
56R GLU* 3.4 41.5 - - - +
57R LEU* 3.9 25.4 - - + +
60R TYR* 5.2 0.4 - - - -
570R ALA 2.9 22.3 + - - +
573R ARG* 1.3 86.9 - - - +
575R TRP* 1.3 61.6 + - - +
577R ASN* 3.4 6.0 + - - +
578R ALA* 3.0 28.4 + - - +
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Residues in contact with TRP 575 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40R TYR* 5.5 2.0 - + - -
43R LEU* 4.4 9.6 - - + -
50R PHE* 3.9 24.2 - + - -
53R PHE* 3.5 28.0 - + + -
526R PHE* 3.9 7.0 - + - -
571R ILE 2.7 20.5 + - - +
572R GLU 3.8 3.8 - - - +
574R CYS* 1.3 70.0 - - - +
576R TRP* 1.3 61.8 + - - +
578R ALA 4.4 0.2 - - - +
579R PHE* 2.8 75.4 + + + +
581R GLU* 3.4 25.4 + - - +
582R SER 4.7 0.4 + - - -
583R TYR* 3.5 50.8 - + + +
586R TYR* 3.9 31.6 - + - +
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Residues in contact with TRP 576 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572R GLU* 3.1 28.6 + - + +
573R ARG* 2.8 13.5 + - - +
575R TRP* 1.3 76.3 - - - +
577R ASN* 1.3 64.4 + - - +
580R GLY* 2.7 62.0 + - - +
581R GLU* 3.1 32.9 + - - -
582R SER* 3.6 8.8 - - - +
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Residues in contact with ASN 577 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56R GLU* 3.0 36.4 + - - +
573R ARG* 3.1 27.8 + - - +
574R CYS* 3.5 6.5 - - - +
575R TRP 3.3 0.2 - - - -
576R TRP* 1.3 79.3 - - - +
578R ALA* 1.3 61.3 + - - +
580R GLY 4.8 0.5 + - - -
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Residues in contact with ALA 578 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49R ARG* 3.3 49.2 - - - +
52R SER* 5.0 4.9 - - - +
53R PHE* 3.6 18.2 - - + +
574R CYS 3.0 18.2 + - - +
577R ASN* 1.3 79.6 - - + +
579R PHE* 1.3 67.9 + - + +
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Residues in contact with PHE 579 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43R LEU* 4.8 13.5 - - + -
47R ASP* 4.8 0.2 - - - -
49R ARG* 3.4 50.5 - - + +
50R PHE* 3.6 32.8 - + + -
53R PHE* 4.3 5.6 - - + -
575R TRP* 2.8 72.2 + + - +
578R ALA* 1.3 86.6 - - + +
580R GLY* 1.3 67.0 + - - +
581R GLU* 3.2 18.0 - - + +
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Residues in contact with GLY 580 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576R TRP* 2.7 53.9 + - - -
577R ASN 4.6 0.6 + - - -
578R ALA 3.8 0.4 - - - -
579R PHE* 1.3 73.2 - - - +
581R GLU* 1.3 64.3 + - - +
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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
------------------------------------------------------------
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