Contacts of the helix formed by residues 105 - 112 (chain C) in PDB entry 4HYY
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 105 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102C THR* 4.5 0.2 + - - -
103C THR* 3.1 4.9 + - - -
104C GLY* 1.3 78.5 - - - +
106C GLN* 1.3 58.6 + - - +
107C GLU* 3.6 4.2 + - - +
108C PHE* 3.2 28.4 + - - +
109C ASP* 2.8 32.6 + - - -
327C THR 4.4 0.3 + - - -
328C PHE* 3.6 13.9 - - - +
335C ILE* 3.9 11.0 - - - -
336C GLY 3.7 15.0 - - - -
337C ASP* 3.2 14.7 + - - -
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Residues in contact with GLN 106 (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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104C GLY 5.8 0.7 - - - +
105C SER* 1.3 69.1 - - - +
107C GLU* 1.3 58.2 + - + +
109C ASP* 3.2 11.9 + - - +
110C LYS* 2.8 34.2 + - - +
337C ASP* 2.9 27.4 + - - +
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Residues in contact with GLU 107 (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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105C SER* 3.8 4.0 - - - +
106C GLN* 1.3 76.7 - - - +
108C PHE* 1.3 62.5 + - - +
110C LYS* 3.2 29.9 + - - +
111C LEU* 3.1 16.8 + - - +
325C GLU 4.9 3.5 - - - +
326C ALA* 3.6 19.8 - - + +
327C THR* 3.6 26.7 + - - +
337C ASP* 3.7 8.8 + - + +
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Residues in contact with PHE 108 (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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103C THR* 3.2 27.4 - - + +
105C SER* 3.2 12.4 + - - +
107C GLU* 1.3 76.3 - - - +
109C ASP* 1.3 66.5 + - - +
111C LEU* 3.1 20.3 + - + +
112C LEU* 3.2 33.1 + - + +
116C ILE* 6.3 0.7 - - + -
135C LEU* 3.9 30.1 - - + -
301C ILE* 4.0 20.9 - - + -
303C LEU* 4.4 3.4 - - + -
313C ALA* 4.0 22.2 - - + -
326C ALA* 3.8 8.0 - - + +
327C THR 5.2 0.2 + - - -
328C PHE* 4.1 36.8 - + + +
335C ILE* 4.5 5.8 - - + -
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Residues in contact with ASP 109 (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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102C THR* 2.9 24.3 + - - -
103C THR* 2.9 35.5 + - - +
105C SER 2.8 22.2 + - - +
106C GLN* 3.2 13.5 + - - +
108C PHE* 1.3 72.6 - - - +
110C LYS* 1.3 63.5 + - - +
112C LEU* 3.0 2.8 + - - -
113C GLY 2.9 4.3 + - - -
114C GLY* 2.8 47.2 + - - +
115C GLY* 3.9 7.8 - - - +
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Residues in contact with LYS 110 (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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106C GLN 2.8 13.0 + - - +
107C GLU* 3.2 32.8 + - - +
109C ASP* 1.3 74.3 - - - +
111C LEU* 1.3 64.4 + - - +
112C LEU 2.8 2.1 + - - -
113C GLY* 3.1 12.6 + - - -
114C GLY 5.1 0.2 - - - +
322C PRO 5.3 5.5 + - - -
323C GLU* 5.2 15.3 - - - +
325C GLU 5.7 4.5 - - - +
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Residues in contact with LEU 111 (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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107C GLU 3.1 7.6 + - - +
108C PHE* 3.1 20.7 + - + +
110C LYS* 1.3 81.0 - - - +
112C LEU* 1.3 60.2 + - + +
113C GLY 3.5 0.6 + - - -
301C ILE* 5.0 2.5 - - + -
313C ALA* 3.8 36.3 - - + +
314C LYS 4.4 0.9 - - - +
315C ILE* 3.0 48.5 - - + +
323C GLU 3.3 26.5 - - - +
324C ASN* 3.4 13.2 - - - -
325C GLU 3.5 2.9 - - - +
326C ALA* 3.8 17.5 - - + +
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Residues in contact with LEU 112 (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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100C HIS* 4.5 5.2 - - - -
103C THR* 4.2 11.4 - - + -
108C PHE* 3.5 40.2 - - + +
109C ASP 3.7 3.1 - - - +
110C LYS 2.9 1.0 - - - -
111C LEU* 1.3 83.3 - - + +
113C GLY* 1.3 63.0 + - - +
115C GLY 3.2 37.1 - - - +
116C ILE* 4.2 9.4 - - + -
117C GLU* 5.5 1.2 - - - +
122C THR* 5.0 1.6 - - + -
299C THR* 3.8 19.3 - - + -
301C ILE* 3.5 29.4 - - + -
315C ILE* 5.0 3.8 - - + -
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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