Contacts of the helix formed by residues 81 - 92 (chain C) in PDB entry 4UQJ
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 81 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C VAL* 2.8 28.8 + - - +
53C ALA 4.1 6.7 + - - -
55C SER* 3.8 11.4 - - - -
58C VAL* 3.9 19.4 - - - +
77C TYR* 3.7 6.8 - - - +
78C ASP* 3.0 18.3 + - - +
80C LYS* 1.3 74.8 - - - +
82C VAL* 1.3 65.5 + - - +
83C ASN 3.2 2.7 - - - -
84C THR* 3.0 18.8 + - - -
85C ILE* 3.3 12.5 + - - +
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Residues in contact with VAL 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C TYR* 3.5 42.2 - - + -
78C ASP 2.9 19.3 + - - +
79C LYS* 3.6 20.0 - - - +
81C SER* 1.3 77.6 + - - +
83C ASN* 1.3 75.7 + - - +
85C ILE* 3.3 3.2 + - - +
86C THR* 3.1 34.0 + - + +
101C PHE* 4.3 10.8 - - + -
103C THR* 4.3 8.5 - - + -
107C HIS* 6.5 0.2 - - + -
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Residues in contact with ASN 83 (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 LYS 4.9 1.8 + - - -
80C LYS 4.4 4.4 + - - +
81C SER 3.2 0.8 - - - -
82C VAL* 1.3 88.0 - - - +
84C THR* 1.3 65.3 + - - +
86C THR* 3.1 9.2 + - - -
87C SER* 3.1 27.4 + - - -
107C HIS* 5.4 5.5 + - - -
55D SER* 3.5 12.0 + - - +
79D LYS 4.1 4.8 + - - -
80D LYS* 2.9 50.3 + - - +
83D ASN* 4.6 10.1 - - - +
84D THR* 5.8 0.7 - - - +
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Residues in contact with THR 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C SER* 4.1 20.5 + - - +
58C VAL* 4.6 8.7 - - + -
59C THR* 3.5 31.3 + - - +
62C PHE* 6.2 1.6 - - + -
80C LYS 4.8 1.2 + - - -
81C SER* 3.0 14.2 + - - -
83C ASN* 1.3 79.0 - - - +
85C ILE* 1.3 63.7 + - + +
87C SER* 3.7 1.7 - - - -
88C PHE* 3.0 50.3 + - + +
55D SER* 4.6 5.6 - - - -
59D THR* 5.7 0.9 - - - +
84D THR* 4.0 17.1 + - + +
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Residues in contact with ILE 85 (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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17C LEU* 4.6 7.4 - - + -
58C VAL* 3.5 28.3 - - + -
62C PHE* 4.6 15.9 - - + -
76C PHE 5.2 1.1 - - - +
77C TYR* 4.3 22.2 - - + -
81C SER 3.3 11.5 + - - +
82C VAL 3.8 5.6 - - - +
84C THR* 1.3 77.5 - - + +
86C THR* 1.3 67.7 + - + +
87C SER 3.1 0.2 + - - -
88C PHE* 4.0 1.5 - - - -
89C CYS* 2.9 35.3 + - + +
96C PHE* 3.5 55.9 - - + -
110C VAL* 5.3 2.0 - - + -
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Residues in contact with THR 86 (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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77C TYR* 5.3 2.0 - - + -
82C VAL* 3.2 20.1 + - + +
83C ASN* 3.1 17.2 + - - -
85C ILE* 1.3 77.8 - - + +
87C SER* 1.3 63.0 + - - +
89C CYS* 4.3 0.5 - - - +
90C GLY* 3.3 16.9 + - - -
103C THR* 3.8 28.7 - - + -
107C HIS* 3.8 37.5 + - + +
108C PRO* 4.7 5.4 - - - +
110C VAL* 4.4 15.9 - - + -
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Residues in contact with SER 87 (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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83C ASN 3.1 17.2 + - - -
84C THR* 3.7 2.7 - - - -
85C ILE 3.1 0.6 - - - -
86C THR* 1.3 81.5 + - - +
88C PHE* 1.3 66.3 + - - +
90C GLY* 3.1 2.9 + - - -
91C THR* 3.0 26.4 + - - -
54D ASN* 3.0 9.7 + - - -
55D SER* 3.9 6.7 - - - -
56D PHE* 2.9 38.4 + - - +
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Residues in contact with PHE 88 (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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59C THR* 3.8 17.9 - - + -
62C PHE* 3.4 37.2 - + + -
63C CYS* 4.2 18.2 - - - -
84C THR* 3.0 47.1 + - + +
85C ILE* 4.1 1.6 - - - +
87C SER* 1.3 76.2 - - - +
89C CYS* 1.3 54.8 + - - +
91C THR 3.1 1.3 + - - +
92C LEU* 2.8 43.4 + - + +
315C CYS* 4.3 5.4 - - - -
316C LEU* 4.5 5.4 - - + -
55D SER 5.3 0.4 - - - -
56D PHE* 3.7 43.3 - + + -
59D THR* 3.9 29.8 - - + -
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Residues in contact with CYS 89 (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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62C PHE* 3.5 26.7 - - - -
85C ILE* 2.9 29.2 + - - +
86C THR 4.5 2.2 - - - +
88C PHE* 1.3 76.3 - - - +
90C GLY* 1.3 56.8 + - - +
93C HIS* 3.2 4.7 + - - -
94C VAL* 3.0 46.9 + - - +
96C PHE* 3.5 30.7 - - + -
109C PHE* 3.3 19.0 - - + +
110C VAL* 4.8 3.1 - - + -
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Residues in contact with GLY 90 (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 THR 3.3 11.7 + - - -
87C SER 3.1 7.2 + - - -
88C PHE 3.1 0.6 - - - -
89C CYS* 1.3 78.8 - - - +
91C THR* 1.3 60.9 + - - +
93C HIS* 3.5 18.7 + - - -
108C PRO* 4.5 10.1 - - - -
109C PHE* 4.3 13.5 - - - -
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Residues in contact with THR 91 (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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87C SER* 3.0 16.4 + - - -
88C PHE 3.8 2.2 - - - -
90C GLY* 1.3 78.2 - - - +
92C LEU* 1.3 60.1 + - + +
93C HIS* 3.2 5.1 + - - -
320C ALA* 4.2 16.6 - - + +
322C PRO* 3.4 26.6 - - + +
54D ASN* 5.2 4.2 + - - -
56D PHE* 3.8 49.9 - - + +
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Residues in contact with LEU 92 (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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62C PHE* 3.4 29.8 - - + -
66C PHE* 4.1 24.6 - - + -
88C PHE* 2.8 24.3 + - + +
91C THR* 1.3 86.2 - - + +
93C HIS* 1.3 71.5 + - - +
94C VAL* 3.0 13.8 + - + +
315C CYS* 3.6 37.5 - - + +
320C ALA* 4.6 11.0 - - + -
321C VAL 5.4 6.3 - - - +
322C PRO* 4.6 4.7 - - - -
323C TRP* 3.3 21.1 + - - -
56D PHE* 4.8 1.1 - - + -
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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