Contacts of the helix formed by residues 517 - 527 (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 ASN 517 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79R GLY 5.4 0.3 - - - +
81R ARG* 3.8 33.3 + - - +
498R GLY* 3.5 20.0 + - - +
500R ILE* 4.0 23.8 - - + +
516R GLY* 1.3 71.4 - - - -
518R ILE* 1.3 62.8 + - - +
519R ASN* 2.7 25.0 + - - +
520R SER* 3.1 32.1 + - - +
558R TYR* 3.2 20.1 - - - -
666R GTP 4.1 9.3 + - - +
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Residues in contact with ILE 518 (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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79R GLY 5.0 3.2 + - - +
80R VAL* 4.3 23.6 - - + -
84R PHE* 4.1 16.8 - - + -
516R GLY 3.5 5.1 + - - -
517R ASN* 1.3 71.7 + - - +
519R ASN* 1.3 74.7 + - + +
521R MET* 2.9 47.3 + - + +
522R LEU* 3.1 12.8 + - + +
558R TYR* 4.5 4.3 - - + -
561R CYS* 3.2 33.9 - - + -
563R ILE* 4.4 6.3 - - + -
564R TYR* 4.3 19.3 - - + -
567R VAL* 3.9 21.5 - - + -
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Residues in contact with ASN 519 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80R VAL* 5.8 0.2 - - - +
81R ARG* 6.3 1.6 - - + -
82R THR* 4.4 14.6 - - + +
83R ASN 3.4 19.1 + - - +
84R PHE* 3.1 32.4 - - - +
86R GLY* 5.4 6.3 - - - -
517R ASN* 2.7 21.6 + - - +
518R ILE* 1.3 79.2 - - + +
520R SER* 1.3 50.2 + - - +
522R LEU* 3.1 10.9 + - - +
523R ASN* 2.7 63.5 + - - +
666R GTP 5.7 1.5 + - - +
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Residues in contact with SER 520 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498R GLY* 5.0 2.7 + - - -
517R ASN* 3.1 33.2 + - - +
518R ILE 3.1 0.6 - - - -
519R ASN* 1.3 76.0 - - - +
521R MET* 1.3 65.0 + - - +
523R ASN* 3.9 10.0 - - - +
524R ASN* 2.9 33.9 + - - +
558R TYR* 3.8 11.4 - - - -
666R GTP 3.9 23.5 + - - -
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Residues in contact with MET 521 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518R ILE* 2.9 30.2 + - + +
520R SER* 1.3 79.1 - - - +
522R LEU* 1.3 70.1 + - + +
524R ASN* 3.8 2.3 - - - +
525R GLN* 3.0 39.8 + - + +
554R MET* 3.6 32.3 - - - +
558R TYR* 3.4 44.9 - - + -
564R TYR* 4.0 13.5 - - + -
567R VAL* 3.6 24.5 - - + -
568R LEU* 4.9 3.6 - - + -
571R ILE* 4.9 6.7 - - + -
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Residues in contact with LEU 522 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57R LEU* 4.1 13.7 - - + -
61R LEU* 3.6 14.6 - - + -
84R PHE* 3.3 37.7 - - + -
87R MET* 4.2 15.7 - - + +
518R ILE 3.1 9.8 + - - +
519R ASN* 3.1 10.0 + - - +
521R MET* 1.3 80.6 - - + +
523R ASN* 1.3 64.9 + - - +
525R GLN 3.3 0.2 + - - -
526R PHE* 3.0 54.3 + - + +
567R VAL* 4.1 15.7 - - + -
571R ILE* 4.0 15.0 - - + -
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Residues in contact with ASN 523 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R GLY* 4.8 4.2 - - - -
87R MET* 4.9 2.9 + - - +
207R SER* 5.7 0.7 - - - +
208R THR* 3.0 42.9 + - + +
519R ASN* 2.7 47.0 + - - +
520R SER* 3.7 9.7 - - - +
522R LEU* 1.3 71.2 - - - +
524R ASN* 1.3 64.4 + - - +
527R SER* 2.8 38.6 + - - +
666R GTP 4.4 23.6 + - - +
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Residues in contact with ASN 524 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40R TYR* 4.4 2.6 + - - -
520R SER* 2.9 27.7 + - - +
521R MET* 3.8 3.1 - - - +
523R ASN* 1.3 82.9 - - - +
525R GLN* 1.3 64.7 + - + +
527R SER 5.1 0.9 - - - -
528R PRO* 3.9 21.0 - - - +
544R ARG* 5.3 1.7 + - - -
558R TYR* 3.6 15.7 + - + +
620R GLU* 5.1 1.9 - - - +
627R LYS* 3.2 28.7 + - - +
666R GTP 4.8 12.5 + - - -
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Residues in contact with GLN 525 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39R THR* 4.5 1.2 - - - +
40R TYR* 2.9 38.3 + - - +
521R MET* 3.0 32.8 + - + +
522R LEU* 6.0 0.2 - - - -
524R ASN* 1.3 79.4 - - + +
526R PHE* 1.3 77.5 + - + +
528R PRO* 4.6 0.9 - - - -
550R ALA* 5.7 5.1 - - + +
551R TRP* 4.0 10.4 - - - -
554R MET* 3.4 28.1 - - - +
568R LEU* 5.7 0.4 - - - +
571R ILE* 4.5 6.2 - - - +
583R TYR* 2.7 42.1 + - - +
587R ARG* 4.4 6.5 - - - +
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Residues in contact with PHE 526 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39R THR* 4.9 0.2 - - - -
40R TYR* 5.0 1.6 - + - -
50R PHE* 3.7 23.9 - + + -
53R PHE* 3.6 37.5 - + + -
54R LYS* 3.1 35.4 + - + -
57R LEU* 4.4 2.2 - - + -
87R MET* 5.0 7.9 - - + -
91R ASN* 3.5 4.0 + - - -
522R LEU* 3.0 32.0 + - + +
525R GLN* 1.3 93.1 - - + +
527R SER* 1.3 61.9 + - - +
528R PRO* 3.4 7.2 - - - +
571R ILE* 3.6 27.6 - - + -
575R TRP* 3.9 3.8 - + - -
583R TYR* 3.4 43.7 - + - -
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Residues in contact with SER 527 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54R LYS* 3.4 17.7 + - - -
87R MET* 3.8 9.9 + - - +
91R ASN* 3.6 10.7 + - - +
207R SER* 2.5 35.7 + - - -
208R THR* 3.5 29.1 - - - +
522R LEU 4.2 0.4 + - - -
523R ASN* 2.8 20.0 + - - +
526R PHE* 1.3 81.5 + - - +
528R PRO* 1.3 62.0 - - - +
529R GLU* 3.6 0.3 + - - +
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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
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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