Contacts of the helix formed by residues 76 - 90 (chain C) in PDB entry 4UHY
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 CYS 76 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72C THR* 3.7 25.8 - - - -
75C PHE* 1.4 75.4 + - + -
77C ALA* 1.4 51.9 + - - +
78C ALA* 3.2 3.0 - - - +
79C LEU* 3.4 26.6 + - - +
80C ARG* 2.9 43.4 + - - +
110C MET* 5.2 0.5 - - - +
113C HIS* 4.5 1.8 - - - -
115C CYS* 2.0 53.6 - - + +
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Residues in contact with ALA 77 (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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74C GLU* 4.5 5.8 - - - +
75C PHE* 2.9 35.2 - - + +
76C CYS* 1.4 70.4 - - - +
78C ALA* 1.4 51.3 + - - +
80C ARG* 4.0 15.8 - - - +
81C SER* 2.9 30.1 + - - -
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Residues in contact with ALA 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C PHE* 3.3 16.0 - - + +
60C ALA* 3.8 21.8 - - + -
61C THR* 3.6 23.6 - - - +
75C PHE 4.8 2.0 - - - +
76C CYS 4.2 2.7 - - - +
77C ALA* 1.4 78.4 - - - +
79C LEU* 1.4 58.8 + - + +
81C SER* 2.9 17.4 + - - -
82C TYR* 3.2 19.4 + - - +
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Residues in contact with LEU 79 (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 PHE* 4.2 23.6 - - + -
61C THR* 5.0 7.2 - - + +
75C PHE 4.8 1.1 - - - +
76C CYS* 3.4 30.5 + - - +
78C ALA* 1.4 79.9 - - + +
80C ARG* 1.4 58.8 + - - +
81C SER 3.4 0.4 - - - -
82C TYR* 4.3 4.0 - - + +
83C ALA* 3.2 28.6 + - - +
106C ILE* 4.1 9.2 - - + +
109C LEU* 3.6 46.7 - - + +
110C MET* 3.4 27.8 - - + +
113C HIS* 5.5 1.1 - - + -
115C CYS* 5.1 5.4 - - - -
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Residues in contact with ARG 80 (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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75C PHE* 5.9 1.6 - - - -
76C CYS* 2.9 32.4 + - + +
77C ALA* 4.0 13.0 - - - +
79C LEU* 1.4 77.3 - - - +
81C SER* 1.4 56.7 + - - +
83C ALA* 3.8 1.3 - - - +
84C LEU* 3.3 32.5 + - + +
87C ARG* 3.7 7.9 + - - +
110C MET* 4.4 11.7 - - + -
115C CYS* 6.2 2.0 - - + -
116C SER* 5.4 10.1 - - - -
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Residues in contact with SER 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ALA 2.9 20.0 + - - -
78C ALA* 2.9 18.0 + - - -
80C ARG* 1.4 76.7 - - - +
82C TYR* 1.4 56.8 + - - +
83C ALA 3.4 0.2 - - - -
84C LEU* 3.4 14.5 + - - +
85C CYS* 3.1 24.4 + - - +
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Residues in contact with TYR 82 (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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331B PHE* 4.1 10.9 - + - -
332B PRO* 4.3 11.0 - - + +
50C ILE* 5.1 1.0 - - + +
53C CYS* 3.3 44.9 - - + -
54C ASN* 3.5 22.1 - - - +
57C PHE* 3.7 37.5 - + + -
78C ALA 3.2 16.7 + - - +
79C LEU* 3.9 4.2 + - - +
81C SER* 1.4 75.2 + - - +
83C ALA* 1.4 58.9 + - - +
85C CYS* 3.0 21.4 + - + +
86C THR* 3.0 21.9 + - + -
102C ALA* 3.6 19.3 - - + +
106C ILE* 3.6 32.5 - - + -
109C LEU* 6.3 0.4 - - + -
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Residues in contact with ALA 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 LEU 3.2 21.7 + - - +
80C ARG 3.8 6.1 - - - +
82C TYR* 1.4 74.9 - - - +
84C LEU* 1.3 57.2 + - - +
86C THR* 2.6 22.5 + - - -
87C ARG* 2.9 35.5 + - - +
106C ILE* 4.0 20.4 - - + +
110C MET* 4.5 7.0 - - + -
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Residues in contact with LEU 84 (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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80C ARG* 3.3 19.6 + - + +
81C SER* 3.5 15.5 - - - +
82C TYR 3.2 0.4 - - - -
83C ALA* 1.3 77.2 - - - +
85C CYS* 1.4 58.4 + - - +
87C ARG* 3.3 33.8 + - + +
88C ARG* 2.9 30.7 + - - +
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Residues in contact with CYS 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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52C LYS* 5.7 0.7 - - - -
53C CYS* 2.0 56.7 - - + -
56C GLU* 4.7 11.2 - - - -
81C SER 3.1 12.8 + - - +
82C TYR* 3.0 14.0 + - - +
84C LEU* 1.4 72.1 - - - +
86C THR* 1.3 65.1 + - - +
88C ARG* 3.5 6.3 + - - +
89C THR* 3.2 21.7 + - - +
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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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50C ILE* 4.1 23.1 - - + -
53C CYS* 5.1 0.9 - - + -
82C TYR* 3.0 20.7 + - + +
83C ALA* 2.6 29.3 + - - -
85C CYS* 1.3 73.6 - - - +
87C ARG* 1.4 50.7 + - - +
88C ARG 2.9 4.7 + - - -
89C THR* 2.9 12.3 + - - +
90C ALA* 2.8 32.7 + - - -
99C TYR* 3.7 5.6 - - - -
102C ALA* 4.2 10.8 - - + -
103C VAL* 3.9 19.6 - - + +
106C ILE* 3.8 20.3 - - + +
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Residues in contact with ARG 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ARG* 3.7 11.7 + - - +
83C ALA* 2.9 32.7 + - - +
84C LEU* 3.3 44.5 + - + +
86C THR* 1.4 74.2 + - - +
88C ARG* 1.4 55.2 + - - +
90C ALA* 3.4 20.1 - - - +
99C TYR* 5.2 0.9 - - - -
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Residues in contact with ARG 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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84C LEU 2.9 15.4 + - - +
85C CYS* 3.7 6.5 - - - +
86C THR 2.9 1.0 + - - -
87C ARG* 1.4 76.5 - - - +
89C THR* 1.4 56.8 + - - +
90C ALA* 3.1 8.0 + - - +
91C ARG* 4.2 7.8 + - - +
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Residues in contact with THR 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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49C LYS* 3.0 45.8 + - + +
50C ILE* 4.2 4.0 - - + +
53C CYS* 4.5 0.4 - - - -
85C CYS 3.2 17.2 + - - +
86C THR* 2.9 14.1 + - - +
88C ARG* 1.4 74.7 - - - +
90C ALA* 1.4 55.0 + - - +
91C ARG 3.3 2.0 - - - -
92C THR* 2.7 44.8 + - - -
93C CYS* 3.1 23.3 + - - -
99C TYR* 4.4 5.2 - - + -
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Residues in contact with ALA 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 2.8 6.4 + - - +
87C ARG* 3.4 23.8 - - - +
88C ARG 3.1 1.0 - - - +
89C THR* 1.4 73.8 - - - +
91C ARG* 1.3 62.8 + - + +
93C CYS 3.2 12.0 + - - -
94C ARG* 3.7 15.0 + - - +
99C TYR* 3.4 31.2 + - - +
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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