Contacts of the helix formed by residues 517 - 527 (chain C) in PDB entry 1HHS
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79C GLY 5.2 0.5 - - - +
81C ARG* 3.6 34.6 - - - +
498C GLY* 3.4 20.6 + - - +
500C ILE* 3.7 24.6 - - + +
515C VAL 3.6 1.2 + - - -
516C GLY* 1.3 70.9 - - - -
518C ILE* 1.3 58.4 + - - +
519C ASN* 2.9 24.4 + - - +
520C SER* 2.9 41.8 + - - +
558C TYR* 3.2 20.4 - - - -
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Residues in contact with ILE 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C GLY 5.4 4.1 + - - +
80C VAL* 4.9 5.2 - - + -
84C PHE* 4.2 15.0 - - + -
500C ILE* 5.5 0.4 - - - +
516C GLY 3.4 5.5 + - - -
517C ASN* 1.3 73.9 + - - +
519C ASN* 1.3 66.0 + - + +
521C MET* 3.1 45.4 + - + +
522C LEU* 3.1 13.7 + - + +
558C TYR* 4.2 9.0 - - + -
561C CYS* 3.6 27.2 - - + -
563C ILE* 4.1 16.6 - - + -
564C TYR* 4.0 28.0 - - + -
567C VAL* 3.7 26.5 - - + -
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Residues in contact with ASN 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ARG* 6.5 0.7 - - + -
82C THR* 5.5 1.7 - - - +
83C ASN 4.2 11.1 + - - +
84C PHE* 3.6 28.9 - - + -
86C GLY* 6.1 2.6 - - - -
87C MET* 6.1 0.3 - - - +
208C THR* 6.0 0.2 - - - -
517C ASN* 2.9 17.7 + - - +
518C ILE* 1.3 83.5 - - + +
520C SER* 1.3 56.9 + - - +
522C LEU* 3.3 11.3 + - - +
523C ASN* 2.9 51.9 + - - +
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Residues in contact with SER 520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C GLY* 4.8 6.0 + - - -
517C ASN* 2.9 34.1 + - - +
519C ASN* 1.3 76.2 - - - +
521C MET* 1.3 65.9 + - - +
523C ASN* 3.5 13.8 + - - +
524C ASN* 2.9 31.4 + - - -
558C TYR* 3.8 11.9 - - - -
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Residues in contact with MET 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517C ASN 3.3 2.8 + - - -
518C ILE* 3.1 35.4 + - + +
520C SER* 1.3 80.7 - - - +
522C LEU* 1.3 61.5 + - + +
524C ASN* 3.7 2.6 - - - +
525C GLN* 2.9 52.1 + - + +
554C MET* 3.7 28.7 - - + +
558C TYR* 3.5 41.4 - - + -
564C TYR* 4.3 2.7 - - - -
567C VAL* 4.1 18.6 - - + -
568C LEU* 4.4 12.8 - - + -
571C ILE* 4.1 16.4 - - + -
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Residues in contact with LEU 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C LEU* 4.2 9.4 - - + -
61C LEU* 3.7 13.2 - - + -
84C PHE* 3.5 36.3 - - + -
87C MET* 4.2 19.3 - - + +
518C ILE 3.1 12.9 + - - +
519C ASN* 3.5 10.8 - - - +
521C MET* 1.3 76.9 - - + +
523C ASN* 1.3 67.9 + - - +
526C PHE* 2.9 55.3 + - + +
527C SER* 3.8 1.0 + - - -
567C VAL* 4.0 13.5 - - + -
571C ILE* 3.9 17.3 - - + -
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Residues in contact with ASN 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C GLY* 5.4 1.7 - - - -
87C MET* 5.4 2.4 + - - +
207C SER* 5.4 1.6 - - - +
208C THR* 3.3 41.9 + - + +
519C ASN* 2.9 38.9 + - - +
520C SER* 3.3 16.3 + - - +
522C LEU* 1.3 74.4 - - - +
524C ASN* 1.3 67.0 + - - +
527C SER* 2.7 38.5 + - - +
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Residues in contact with ASN 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C TYR* 4.1 3.3 + - - -
520C SER* 2.9 22.3 + - - +
521C MET* 3.7 4.9 - - - +
523C ASN* 1.3 88.1 - - - +
525C GLN* 1.3 63.9 + - + +
528C PRO* 4.1 19.7 - - - +
544C ARG* 5.4 1.0 + - - -
558C TYR* 3.9 11.0 + - - +
620C GLU* 4.9 1.9 - - - +
624C ASP* 5.0 3.9 + - - -
627C LYS* 2.8 34.1 + - - +
630C TYR* 5.7 1.6 + - - -
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Residues in contact with GLN 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C TYR* 2.6 35.1 + - - +
521C MET* 2.9 44.0 + - + +
522C LEU* 6.0 0.2 - - - -
524C ASN* 1.3 77.0 - - + +
526C PHE* 1.3 79.0 + - + +
528C PRO* 4.4 2.0 - - - +
550C ALA* 5.5 8.7 - - + +
551C TRP* 3.8 10.7 - - - -
554C MET* 3.5 20.2 - - - +
571C ILE* 4.9 5.1 - - - +
583C TYR* 2.6 43.6 + - - +
587C ARG* 3.9 12.8 - - - +
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Residues in contact with PHE 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C THR* 4.3 0.5 - - - +
40C TYR* 5.1 2.2 - + - -
50C PHE* 3.3 30.3 - + + -
53C PHE* 3.7 38.6 - + + -
54C LYS* 3.2 29.3 + - + -
57C LEU* 4.4 3.6 - - + -
87C MET* 5.2 7.6 - - + -
91C ASN* 3.9 1.6 + - - -
522C LEU* 2.9 42.6 + - + +
525C GLN* 1.3 91.6 - - + +
527C SER* 1.3 61.5 + - - +
528C PRO* 3.5 7.9 - - - +
571C ILE* 3.9 13.7 - - + -
575C TRP* 3.9 4.0 - + - -
583C TYR* 3.4 48.2 - + - -
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Residues in contact with SER 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C LYS* 3.2 22.7 + - - -
87C MET* 4.0 9.5 + - - +
89C HIS* 6.0 0.2 - - - +
91C ASN* 3.8 11.7 + - - +
207C SER* 2.6 34.8 + - - -
208C THR* 3.5 28.9 - - - +
522C LEU 3.8 0.2 + - - -
523C ASN* 2.7 25.2 + - - +
524C ASN* 5.2 0.2 - - - -
526C PHE* 1.3 71.5 + - - +
528C PRO* 1.3 63.2 - - - +
529C GLU 3.6 0.2 + - - -
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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