Contacts of the helix formed by residues 80 - 93 (chain C) in PDB entry 3UGV
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 ALA 80 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78C PRO* 3.0 14.1 + - + +
79C LEU* 1.3 73.4 - - - +
81C PRO* 1.3 69.3 - - + +
82C ALA* 3.3 2.5 - - + -
83C GLU* 2.9 39.7 + - + +
84C ILE* 3.0 16.4 + - - +
116C LEU* 5.7 0.2 - - - -
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Residues in contact with PRO 81 (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 3.9 6.1 - - - +
80C ALA* 1.3 83.5 - - + +
82C ALA* 1.3 58.8 + - - +
84C ILE* 3.4 2.8 + - + +
85C TYR* 2.8 30.7 + - - +
109C ASP* 4.0 5.4 - - - +
112C VAL* 3.6 30.5 - - + +
113C TRP* 3.2 51.8 - - + +
116C LEU* 4.0 24.9 - - + -
285C SER* 4.4 2.2 - - - -
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Residues in contact with ALA 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ALA* 3.3 1.2 - - + -
81C PRO* 1.3 80.4 - - - +
83C GLU* 1.3 64.7 + - + +
85C TYR* 3.5 7.7 + - - +
86C ASP* 3.2 20.4 + - - +
113C TRP* 5.1 6.0 - - + -
285C SER* 4.5 5.8 + - - +
289C ARG* 4.6 17.7 + - - +
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Residues in contact with GLU 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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78C PRO* 4.4 19.0 - - - +
80C ALA* 2.9 26.0 + - + +
82C ALA* 1.3 78.5 - - + +
84C ILE* 1.3 63.8 + - + +
86C ASP* 3.3 8.4 + - - +
87C LYS* 3.1 43.0 + - - +
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Residues in contact with ILE 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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7C PHE* 4.8 6.7 - - + -
74C LEU* 3.7 39.9 - - + -
77C GLN* 6.2 0.7 - - + -
78C PRO 3.7 23.3 - - - +
79C LEU* 4.1 9.9 - - + -
80C ALA 3.0 22.0 + - - +
81C PRO* 3.8 4.7 - - + +
83C GLU* 1.3 74.8 - - + +
85C TYR* 1.3 61.2 + - - +
87C LYS* 3.1 11.1 + - - +
88C THR* 2.8 37.4 + - + -
108C VAL* 4.0 14.1 - - + -
109C ASP* 6.1 1.8 - - - -
112C VAL* 4.1 22.0 - - + -
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Residues in contact with TYR 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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81C PRO 2.8 18.5 + - - +
82C ALA* 3.5 7.9 - - - +
83C GLU 3.3 0.2 - - - -
84C ILE* 1.3 75.8 - - - +
86C ASP* 1.3 64.0 + - - +
88C THR* 3.0 20.3 + - - -
89C ARG* 3.1 48.6 + - + +
102C MET* 3.5 26.2 - - - +
105C ALA* 5.0 7.0 - - + -
106C SER* 5.4 0.2 - - - -
109C ASP* 3.8 24.2 - - + +
259C PRO* 4.5 4.4 - - + +
281C ILE 3.8 4.0 + - - -
282C GLY* 3.4 29.7 - - - -
285C SER* 4.1 10.8 - - - +
286C GLY* 4.1 7.7 - - - -
289C ARG* 3.6 33.7 - - - -
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Residues in contact with ASP 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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82C ALA 3.2 9.7 + - - +
83C GLU* 3.4 9.7 - - - +
84C ILE 3.3 0.2 - - - -
85C TYR* 1.3 82.8 - - - +
87C LYS* 1.3 69.3 + - - +
89C ARG* 4.1 4.4 - - - +
90C LYS* 3.2 50.5 + - - +
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Residues in contact with LYS 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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73C MET* 3.9 17.7 - - + +
74C LEU* 4.5 12.8 - - + -
77C GLN* 3.1 40.3 + - - +
78C PRO* 4.8 5.1 + - - +
83C GLU* 3.1 35.9 + - - +
84C ILE* 3.1 8.4 + - - +
86C ASP* 1.3 84.7 - - - +
88C THR* 1.3 65.5 + - - +
90C LYS* 4.2 5.8 - - + +
91C SER* 3.3 23.6 + - - -
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Residues in contact with THR 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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70C MET* 4.0 32.3 - - + +
73C MET* 4.5 6.5 - - + -
74C LEU* 4.3 12.3 - - + -
84C ILE* 2.8 36.5 + - + +
85C TYR* 3.0 14.0 + - - -
87C LYS* 1.3 70.1 - - - +
89C ARG* 1.3 71.2 + - - +
91C SER* 3.0 22.2 + - - -
92C LEU* 3.7 4.5 + - - +
105C ALA* 3.3 28.6 + - + +
108C VAL* 4.6 7.2 - - + -
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Residues in contact with ARG 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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85C TYR* 3.1 55.2 + - + +
86C ASP* 4.1 4.7 - - - +
88C THR* 1.3 79.2 + - - +
90C LYS* 1.3 63.8 + - - +
92C LEU* 3.1 14.7 + - - +
93C HIS* 3.1 13.5 + - - +
96C GLY 5.5 0.2 - - - +
97C TYR* 3.8 54.4 + - + +
101C SER* 6.1 2.7 - - - -
102C MET* 3.4 34.0 - - - +
105C ALA* 4.6 8.0 - - + +
257C TYR 4.9 6.5 + - - -
258C GLY* 4.9 1.8 - - - -
259C PRO* 5.3 6.3 - - - +
289C ARG* 5.9 0.4 - - - +
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Residues in contact with LYS 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 ASP* 3.2 39.9 + - - +
87C LYS* 4.2 5.8 - - + +
88C THR 3.3 0.2 - - - -
89C ARG* 1.3 80.5 - - - +
91C SER* 1.3 60.7 + - - +
92C LEU 3.3 0.2 + - - -
93C HIS* 3.0 39.0 + - + +
97C TYR* 4.8 6.7 - - - +
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Residues in contact with SER 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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70C MET* 4.7 6.9 - - - +
73C MET* 3.8 22.8 - - - +
87C LYS 3.3 15.6 + - - -
88C THR* 3.0 14.8 + - - -
89C ARG 3.1 1.0 - - - -
90C LYS* 1.3 78.1 - - - +
92C LEU* 1.3 72.5 + - - +
94C PHE* 6.0 0.5 - - - +
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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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66C ALA* 5.3 11.0 - - + +
70C MET* 3.6 26.9 - - + -
88C THR 3.7 2.4 + - - +
89C ARG* 3.1 7.5 + - - +
91C SER* 1.3 94.6 + - - +
93C HIS* 1.3 53.6 + - - +
94C PHE* 3.0 4.3 - - - -
95C VAL* 2.6 46.4 + - + +
96C GLY 3.3 8.8 + - - +
101C SER* 3.5 33.2 - - - -
104C ALA* 5.3 0.2 - - + -
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Residues in contact with HIS 93 (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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89C ARG 3.1 8.4 + - - +
90C LYS* 3.0 30.0 + - + +
91C SER 3.7 0.4 - - - -
92C LEU* 1.3 77.0 - - - +
94C PHE* 1.3 106.8 + + - +
96C GLY* 3.1 20.0 + - - -
97C TYR* 3.4 47.1 + + + +
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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