Contacts of the helix formed by residues 549 - 559 (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 LEU 549 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546R PHE* 3.1 34.2 + - + +
548R GLY* 1.3 71.3 - - - +
550R ALA* 1.3 62.4 + - - +
551R TRP 2.9 5.6 - - - -
552R ALA* 2.8 23.0 + - - +
553R SER* 3.6 4.0 + - - -
591R LEU* 4.2 7.2 - - + -
594R ASP* 4.0 15.3 - - + +
595R THR* 4.0 24.7 - - - +
598R LEU* 4.0 11.7 - - + -
611R LEU* 4.2 14.1 - - + -
619R LEU* 4.1 24.9 - - + +
622R LEU* 3.6 33.7 - - + -
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Residues in contact with ALA 550 (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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525R GLN* 5.7 4.4 - - + +
547R PRO 3.4 13.5 + - - +
548R GLY 3.2 0.8 - - - -
549R LEU* 1.3 77.3 - - - +
551R TRP* 1.3 60.7 + - - +
552R ALA 3.2 0.2 - - - -
553R SER* 3.4 12.1 + - - +
554R MET* 3.0 23.9 + - - +
587R ARG* 4.8 6.7 - - - +
619R LEU 5.0 1.8 - - - -
620R GLU* 4.1 11.7 - - - +
623R ALA* 4.0 18.1 - - + +
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Residues in contact with TRP 551 (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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525R GLN* 4.0 8.3 - - - -
548R GLY 3.3 15.7 + - - +
549R LEU 2.8 0.6 + - - -
550R ALA* 1.3 78.8 - - - +
552R ALA* 1.3 62.5 + - - +
554R MET* 3.3 58.4 + - + +
555R LYS* 4.5 1.6 + - - +
568R LEU* 4.1 12.1 - - + -
583R TYR* 3.7 25.4 - + - -
584R ARG* 4.2 24.5 - - + -
587R ARG* 3.4 55.7 - - + +
588R GLU* 3.6 21.9 + - + -
591R LEU* 3.9 21.5 - - + -
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Residues in contact with ALA 552 (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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549R LEU 2.8 7.6 + - - +
551R TRP* 1.3 82.2 - - - +
553R SER* 1.3 57.8 + - - +
554R MET 3.6 0.2 + - - -
555R LYS* 4.6 6.2 + - - +
556R ASP* 5.0 3.3 + - - +
591R LEU* 4.1 14.6 - - + +
611R LEU* 4.1 20.6 - - + -
619R LEU* 3.3 24.5 - - + +
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Residues in contact with SER 553 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549R LEU 3.6 0.6 + - - -
550R ALA* 3.4 12.3 + - - -
551R TRP 3.3 0.2 - - - -
552R ALA* 1.3 78.8 - - - +
554R MET* 1.3 54.0 - - - +
555R LYS 3.5 0.9 - - - -
556R ASP* 3.2 9.2 + - - +
557R THR* 2.7 35.9 + - - -
616R PRO* 3.7 29.6 - - - -
619R LEU* 3.8 15.1 - - - +
620R GLU* 2.6 33.7 + - - +
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Residues in contact with MET 554 (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* 3.6 25.8 - - + +
525R GLN* 3.4 24.9 - - - +
550R ALA 3.0 13.2 + - - +
551R TRP* 3.3 55.6 - - + +
552R ALA 3.3 1.6 - - - -
553R SER* 1.3 77.5 - - - +
555R LYS* 1.3 56.0 + - + +
557R THR* 4.6 0.9 - - - -
558R TYR* 2.7 43.7 + - + -
559R GLY 3.8 0.3 + - - -
564R TYR* 3.3 18.1 + - + +
568R LEU* 3.8 15.9 - - + -
620R GLU* 4.7 1.6 - - - -
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Residues in contact with LYS 555 (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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551R TRP 4.5 2.6 + - - +
552R ALA 4.6 5.1 + - - +
553R SER 3.5 0.4 - - - -
554R MET* 1.3 77.5 - - + +
556R ASP* 1.3 58.2 + - - +
559R GLY* 2.6 40.4 + - - -
564R TYR* 3.0 45.2 + - + +
565R SER* 5.7 1.2 + - - -
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Residues in contact with ASP 556 (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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307R ARG* 5.0 12.0 + - - -
552R ALA 5.0 2.0 + - - +
553R SER* 3.2 12.9 + - - +
554R MET 3.1 0.8 - - - -
555R LYS* 1.3 84.2 - - - +
557R THR* 1.3 64.8 + - - +
558R TYR 3.5 0.2 + - - -
559R GLY 4.2 1.6 + - - -
560R ALA* 5.2 2.4 + - - +
616R PRO* 3.5 36.8 - - + +
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Residues in contact with THR 557 (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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307R ARG* 4.3 8.9 - - - +
499R ASP* 5.1 0.5 - - - +
516R GLY* 4.0 18.4 + - - -
553R SER* 2.7 18.5 + - - -
556R ASP* 1.3 78.4 + - - +
558R TYR* 1.3 96.0 + - + +
560R ALA 5.4 0.2 + - - -
616R PRO* 5.4 2.1 - - - +
620R GLU* 3.2 30.2 + - - +
631R LYS* 6.3 2.7 - - - -
632R TRP* 5.7 1.3 - - + -
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Residues in contact with TYR 558 (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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516R GLY* 4.7 3.8 - - - -
517R ASN 3.2 37.2 - - - -
518R ILE* 4.5 5.4 - - + -
520R SER* 3.7 7.7 + - - -
521R MET* 3.4 48.3 + - + -
524R ASN* 3.6 19.4 + - - +
554R MET* 2.7 27.3 + - + +
557R THR* 1.3 101.4 - - + +
559R GLY* 1.3 64.7 + - - +
560R ALA* 3.1 3.4 - - - -
561R CYS* 2.8 24.2 + - + +
564R TYR* 3.7 19.4 - - + -
620R GLU* 4.7 9.3 + - - -
627R LYS* 5.7 1.7 - - - -
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Residues in contact with GLY 559 (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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554R MET 3.8 0.6 + - - -
555R LYS* 2.6 40.4 + - - -
556R ASP 4.2 0.6 + - - -
557R THR 3.8 0.6 - - - -
558R TYR* 1.3 70.8 - - - +
560R ALA* 1.3 60.4 + - - +
561R CYS 3.1 9.0 + - - +
564R TYR* 3.7 28.5 - - - +
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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