Contacts of the helix formed by residues 80 - 92 (chain C) in PDB entry 1UHG
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 HIS 80 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39C ALA* 3.7 23.1 - - + -
42C TYR* 4.5 6.7 - + - -
43C LEU* 3.7 27.4 - - + +
63C PRO 4.3 0.4 - - - -
64C GLY 2.9 27.4 + - - -
65C PHE* 3.3 49.0 - + + -
70C GLU* 4.5 5.2 + - + -
79C VAL* 1.3 81.7 - - + +
81C SER* 1.3 65.1 + - - +
82C SER 3.4 2.0 - - - -
83C LEU* 3.0 5.4 + - + +
84C ARG* 2.8 26.0 + - + +
124C LEU* 4.3 1.0 - - + +
125C TYR* 2.7 34.4 + + - +
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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
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63C PRO* 3.8 15.1 + - - +
64C GLY* 4.1 3.5 - - - -
78C ASN* 2.8 41.6 + - - -
79C VAL 3.1 3.2 - - - -
80C HIS* 1.3 74.6 - - - +
82C SER* 1.3 65.8 + - - +
83C LEU 2.9 0.2 + - - -
84C ARG* 4.5 1.1 - - - +
85C ASP* 2.7 44.8 + - - +
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Residues in contact with SER 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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3C ILE* 3.7 20.9 - - - +
62C LEU* 3.6 18.9 - - - +
63C PRO* 3.1 37.4 + - - -
65C PHE* 3.9 6.1 - - - -
80C HIS 3.4 0.2 - - - -
81C SER* 1.3 81.0 + - - +
83C LEU* 1.3 59.8 + - - +
85C ASP* 4.6 3.7 - - - +
86C ILE* 3.6 24.3 + - - +
373C THR* 5.9 0.2 - - - +
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Residues in contact with LEU 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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3C ILE* 3.9 15.3 - - + -
32C ILE* 3.4 42.6 - - + +
35C MET* 3.9 16.6 - - + +
36C SER* 3.6 35.7 - - - +
39C ALA* 4.0 5.8 - - + -
59C PHE* 4.9 2.0 - - + -
62C LEU* 5.3 0.2 - - + -
65C PHE* 4.1 17.7 - - + -
80C HIS 3.0 6.6 + - - +
81C SER 3.0 0.6 - - - -
82C SER* 1.3 77.8 + - - +
84C ARG* 1.3 66.7 + - + +
85C ASP 3.2 1.8 - - - -
86C ILE* 3.3 15.5 + - - +
87C LEU* 3.4 12.8 + - + +
125C TYR* 3.9 14.4 - - + +
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Residues in contact with ARG 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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77C VAL 5.2 0.2 + - - -
78C ASN* 3.5 23.0 + - - +
79C VAL 2.9 28.7 + - - +
80C HIS* 2.8 21.4 + - - +
81C SER* 4.3 0.4 - - - +
83C LEU* 1.3 70.1 - - + +
85C ASP* 1.3 62.1 + - - +
87C LEU* 3.9 9.0 - - + -
88C ASN* 2.9 54.1 + - - +
123C GLU 3.8 16.6 + - - -
124C LEU* 2.9 47.8 + - - +
125C TYR* 3.8 24.9 - - + +
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Residues in contact with ASP 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ASN* 3.4 23.4 + - - +
81C SER* 2.7 37.3 + - - +
82C SER* 4.6 4.7 - - - +
84C ARG* 1.3 73.2 + - - +
86C ILE* 1.3 64.5 + - + +
88C ASN* 4.1 5.5 - - - +
89C GLN* 3.2 25.0 + - - +
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Residues in contact with ILE 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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3C ILE* 3.7 26.9 - - + -
32C ILE* 4.1 13.2 - - + -
82C SER 3.6 20.4 - - - +
83C LEU 3.3 5.6 + - - +
84C ARG 3.2 0.2 - - - -
85C ASP* 1.3 80.0 - - + +
87C LEU* 1.3 58.6 + - - +
89C GLN* 3.1 11.0 + - - +
90C ILE* 3.0 34.0 + - + +
370C HIS* 4.3 21.5 - - + -
373C THR* 3.9 11.4 - - + +
375C ALA* 3.8 19.1 - - + -
377C LEU* 3.9 26.5 - - + -
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Residues in contact with LEU 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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32C ILE* 4.0 37.5 - - + +
33C ALA* 4.9 1.3 - - - +
36C SER* 3.3 33.0 - - - +
83C LEU* 3.4 12.3 + - + +
84C ARG* 3.9 10.8 - - + +
86C ILE* 1.3 77.2 - - - +
88C ASN* 1.3 71.0 + - - +
90C ILE* 3.5 13.3 + - + +
91C THR* 3.0 31.1 + - + +
99C PHE* 4.7 2.7 - - + -
101C LEU* 4.0 27.6 - - + -
125C TYR* 4.8 11.0 - - + -
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Residues in contact with ASN 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 ARG* 2.9 48.6 + - - +
85C ASP* 4.1 5.4 - - - +
87C LEU* 1.3 80.2 - - - +
89C GLN* 1.3 63.3 + - - +
91C THR* 3.3 12.0 + - - -
92C LYS* 3.2 31.9 - - - +
124C LEU 5.3 5.1 + - - -
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Residues in contact with GLN 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 ASP 3.2 13.1 + - - +
86C ILE* 3.1 14.1 + - - +
88C ASN* 1.3 79.8 - - - +
90C ILE* 1.3 64.3 + - + +
91C THR 3.4 0.5 + - - -
92C LYS* 3.5 22.0 + - - +
97C TYR* 3.8 10.5 + - - +
238C THR* 3.8 24.2 - - - +
370C HIS* 2.6 40.6 + - - -
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Residues in contact with ILE 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 ILE* 3.0 30.0 + - + +
87C LEU* 3.7 13.7 - - + +
89C GLN* 1.3 81.1 - - + +
91C THR* 1.3 61.0 + - - +
92C LYS 3.4 1.7 - - - +
94C ASN* 4.8 0.3 + - - -
97C TYR* 3.4 32.9 - - + +
99C PHE* 3.1 67.0 + - + +
238C THR* 5.8 0.9 - - - +
239C MET* 5.0 10.8 - - + -
370C HIS* 4.6 14.8 - - + -
377C LEU* 4.2 20.2 - - + -
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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 LEU* 3.0 21.8 + - + +
88C ASN* 3.3 12.1 + - - -
89C GLN 3.3 0.2 - - - -
90C ILE* 1.3 75.3 - - - +
92C LYS* 1.3 60.3 + - - +
93C PRO 3.6 0.3 - - - -
99C PHE* 3.9 37.4 - - + +
101C LEU* 4.6 19.7 - - + +
93D PRO* 2.6 42.4 - - - +
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Residues in contact with LYS 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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88C ASN* 3.2 26.9 - - - +
89C GLN* 3.5 15.9 + - - +
90C ILE 3.4 2.0 - - - +
91C THR* 1.3 79.8 + - - +
93C PRO* 1.3 78.4 - - + +
94C ASN* 3.3 17.7 + - - +
92D LYS* 6.1 3.6 - - - +
93D PRO* 4.2 4.0 - - + -
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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