Contacts of the helix formed by residues 582 - 600 (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 SER 582 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572R GLU* 3.0 17.5 + - - -
575R TRP* 4.2 0.9 - - - -
576R TRP* 3.6 9.8 - - - +
581R GLU* 1.3 73.3 - - - +
583R TYR* 1.3 64.3 + - - +
584R ARG* 3.2 10.4 + - - +
585R ALA* 2.9 32.9 + - - +
586R TYR* 3.0 20.6 + - - +
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Residues in contact with TYR 583 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40R TYR* 4.2 4.0 + + - -
525R GLN* 2.7 37.0 + - - +
526R PHE* 3.4 24.0 - + - -
551R TRP* 3.7 12.6 - + - -
568R LEU* 5.8 1.6 - - + -
571R ILE* 3.4 26.2 - - + -
572R GLU* 3.1 12.8 + - - +
575R TRP* 3.5 51.1 - + + +
581R GLU 3.5 4.9 + - - -
582R SER* 1.3 72.1 - - - +
584R ARG* 1.3 65.3 + - - +
586R TYR* 3.0 13.4 + + - +
587R ARG* 2.9 61.9 + - + +
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Residues in contact with ARG 584 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551R TRP* 4.2 22.5 - - + -
568R LEU* 5.4 8.5 + - - +
569R GLU* 6.1 1.8 - - - +
572R GLU* 2.9 48.6 + - - +
582R SER* 3.1 5.5 + - - +
583R TYR* 1.3 77.9 - - - +
585R ALA* 1.3 56.9 + - - +
587R ARG* 3.3 2.8 + - - +
588R GLU* 2.9 54.7 + - - +
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Residues in contact with ALA 585 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582R SER* 2.9 27.5 + - - +
584R ARG* 1.3 75.4 - - - +
586R TYR* 1.3 65.7 + - - +
588R GLU* 3.1 12.2 + - - +
589R ASP* 2.9 34.2 + - - +
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Residues in contact with TYR 586 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40R TYR* 3.2 32.6 - + - +
41R GLU 4.0 12.2 + - - -
43R LEU* 4.4 9.0 - - + +
575R TRP* 3.9 36.8 - + - +
581R GLU* 5.7 7.6 - - + +
582R SER 3.0 12.2 + - - +
583R TYR* 3.2 13.9 - + - +
585R ALA* 1.3 77.4 - - - +
587R ARG* 1.3 77.0 + - - +
589R ASP* 3.2 8.5 + - + +
590R MET* 3.0 47.2 + - + +
593R ARG* 4.6 9.9 + - - -
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Residues in contact with ARG 587 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40R TYR* 3.3 28.6 + - - -
525R GLN* 4.4 8.9 - - - +
547R PRO 4.0 11.3 + - - -
548R GLY 4.0 5.1 + - - -
550R ALA* 4.8 5.3 - - - +
551R TRP* 3.4 51.4 - - + +
583R TYR* 2.9 62.9 + - + +
584R ARG 3.9 0.2 - - - +
586R TYR* 1.3 86.5 - - - +
588R GLU* 1.3 57.7 + - - +
590R MET* 3.4 25.9 + - - +
591R LEU* 2.8 29.8 + - - +
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Residues in contact with GLU 588 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551R TRP* 3.6 17.8 + - + +
584R ARG* 2.9 43.9 + - - +
585R ALA* 3.1 11.1 + - - +
587R ARG* 1.3 76.5 - - - +
589R ASP* 1.3 63.3 + - - +
591R LEU* 3.2 11.3 - - + +
592R LYS* 2.9 37.6 + - + +
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Residues in contact with ASP 589 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585R ALA* 2.9 24.3 + - - +
586R TYR* 3.6 9.1 - - + +
588R GLU* 1.3 74.2 - - - +
590R MET* 1.3 69.1 + - - +
592R LYS* 3.0 26.0 + - - +
593R ARG* 2.8 41.5 + - - +
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Residues in contact with MET 590 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40R TYR* 3.7 31.4 - - + -
41R GLU* 5.6 1.8 - - - +
547R PRO* 4.3 3.1 - - - -
548R GLY* 3.7 22.4 - - - +
586R TYR* 3.0 49.1 + - + +
587R ARG* 3.6 33.9 - - - +
589R ASP* 1.3 76.4 - - - +
591R LEU* 1.3 57.7 + - - +
593R ARG* 3.3 29.2 + - - +
594R ASP* 2.9 37.2 + - - +
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Residues in contact with LEU 591 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548R GLY 3.5 21.7 + - - +
549R LEU* 4.2 9.9 - - + -
551R TRP* 3.9 22.0 - - + -
552R ALA* 4.1 18.8 - - + +
587R ARG 2.8 14.7 + - - +
588R GLU* 3.2 14.8 - - + +
590R MET* 1.3 77.8 - - - +
592R LYS* 1.3 57.0 + - + +
594R ASP* 3.3 1.2 + - - +
595R THR* 2.8 50.1 + - - +
611R LEU* 3.8 16.8 - - + -
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Residues in contact with LYS 592 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588R GLU* 2.9 21.1 + - + +
589R ASP* 3.0 29.8 + - - +
591R LEU* 1.3 75.8 - - + +
593R ARG* 1.3 65.0 + - - +
595R THR* 3.1 7.3 + - - -
596R LEU* 3.0 32.6 + - + +
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Residues in contact with ARG 593 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41R GLU* 3.3 32.9 + - - +
586R TYR* 4.6 9.7 + - - -
589R ASP* 2.8 29.2 + - - +
590R MET* 3.3 49.9 - - - +
592R LYS* 1.3 73.3 - - + +
594R ASP* 1.3 61.8 + - - +
596R LEU* 3.1 12.1 + - + +
597R GLU* 3.0 27.7 + - - +
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Residues in contact with ASP 594 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41R GLU* 5.4 2.6 - - - +
539R ARG* 2.8 28.7 + - - -
546R PHE* 3.1 20.8 - - + -
547R PRO* 3.1 4.5 - - - +
548R GLY* 2.6 31.2 + - - -
549R LEU* 4.0 16.2 - - + -
590R MET* 2.9 23.3 + - - +
591R LEU 3.9 2.2 - - - +
593R ARG* 1.3 74.3 - - - +
595R THR* 1.3 61.5 + - - +
597R GLU* 3.6 4.7 - - - +
598R LEU* 2.8 32.2 + - - +
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Residues in contact with THR 595 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549R LEU* 4.0 6.8 - - - +
591R LEU* 2.8 45.9 + - - +
592R LYS* 3.6 7.3 - - - -
594R ASP* 1.3 74.2 - - - +
596R LEU* 1.3 67.8 + - + +
598R LEU* 3.4 10.2 + - + +
599R SER* 3.5 11.3 + - - -
605R MET* 5.1 3.0 - - + +
608R GLN* 6.1 0.6 - - - -
609R ALA 4.7 4.3 - - - +
610R GLY* 4.6 9.4 - - - -
611R LEU* 3.5 38.7 - - + +
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Residues in contact with LEU 596 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592R LYS* 3.0 19.6 + - + +
593R ARG* 3.4 9.6 - - - +
595R THR* 1.3 82.3 - - + +
597R GLU* 1.3 61.6 + - - +
599R SER* 2.5 28.4 + - - +
600R ARG* 3.8 4.0 + - - +
608R GLN* 3.7 40.2 - - + +
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Residues in contact with GLU 597 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539R ARG* 3.5 43.1 + - - +
546R PHE* 4.1 3.4 - - + -
593R ARG 3.0 13.7 + - - +
594R ASP* 3.6 11.0 - - - +
596R LEU* 1.3 77.0 - - - +
598R LEU* 1.3 57.5 + - - +
600R ARG* 2.8 70.1 + - - +
601R TYR* 3.4 11.8 + - + -
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Residues in contact with LEU 598 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546R PHE* 3.4 41.5 - - + -
549R LEU* 4.0 9.4 - - + -
594R ASP 2.8 20.9 + - - +
595R THR* 3.6 6.1 - - - +
597R GLU* 1.3 72.9 - - - +
599R SER* 1.3 51.9 - - - +
601R TYR* 2.6 29.7 + - + +
602R VAL* 3.1 27.7 + - + -
605R MET* 3.6 12.3 - - + -
611R LEU* 4.4 6.3 - - + -
614R LEU* 3.6 31.4 - - + -
622R LEU* 3.8 20.4 - - + -
644R VAL* 5.4 1.3 - - + -
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Residues in contact with SER 599 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595R THR 3.5 7.6 + - - -
596R LEU* 2.5 24.2 + - - +
598R LEU* 1.3 78.2 - - - +
600R ARG* 1.3 59.6 + - - +
601R TYR 3.0 0.2 - - - -
602R VAL 2.9 21.3 - - - +
605R MET* 4.0 23.6 - - - +
606R ALA 3.6 24.5 - - - -
607R ARG* 3.9 17.7 + - - +
608R GLN* 4.0 7.3 + - - -
609R ALA 5.0 0.9 - - - -
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Residues in contact with ARG 600 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596R LEU 4.8 2.2 + - - +
597R GLU* 2.8 61.1 + - - +
599R SER* 1.3 80.3 + - - +
601R TYR* 1.3 71.4 + - + +
607R ARG* 6.5 0.9 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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