Contacts of the helix formed by residues 76 - 91 (chain C) in PDB entry 1UDY
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 GLY 76 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C HIS* 4.1 8.3 - - - -
75C LEU* 1.3 74.7 - - - +
77C ILE* 1.3 60.7 + - - -
78C ILE 3.0 3.6 - - - -
79C ASP* 2.7 36.8 + - - +
80C SER* 3.1 11.1 + - - -
320C ASP* 3.8 11.0 - - - -
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Residues in contact with ILE 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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65C HIS* 3.6 25.4 - - + +
76C GLY* 1.3 71.0 - - - -
78C ILE* 1.3 61.5 + - - +
80C SER* 3.8 9.4 - - - +
81C CYS* 3.1 21.5 + - - -
102C THR* 5.8 4.3 - - + -
106C VAL* 5.7 2.9 - - + -
254C LYS* 3.7 50.5 - - + +
257C PRO* 4.0 12.8 - - + -
258C PRO* 4.1 9.2 - - + -
316C ALA* 3.9 19.3 - - + +
319C ILE* 4.0 14.6 - - + -
320C ASP* 3.0 18.9 + - - +
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Residues in contact with ILE 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 3.9 45.5 - - + +
20C GLN* 3.9 17.0 - - - +
76C GLY 2.9 0.2 + - - -
77C ILE* 1.3 77.2 - - - +
79C ASP* 1.3 61.2 + - - +
81C CYS* 3.4 3.8 + - - +
82C LEU* 3.0 32.8 + - + +
312C TYR* 5.3 0.5 - - - -
313C GLN* 5.1 4.9 - - + +
316C ALA* 3.7 9.6 - - + -
317C TRP* 3.9 35.2 - - + +
320C ASP* 2.8 29.4 + - + +
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Residues in contact with ASP 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C GLN* 3.0 37.2 - - - +
23C PHE* 4.8 7.3 - - + -
75C LEU* 3.6 30.6 - - + +
76C GLY* 2.7 32.5 + - - +
78C ILE* 1.3 75.8 - - - +
80C SER* 1.3 64.4 + - - +
82C LEU* 3.0 9.4 + - - +
83C ILE* 2.9 30.9 + - + +
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Residues in contact with SER 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C THR* 3.2 27.7 - - - +
65C HIS* 4.7 8.7 - - - +
76C GLY 3.1 9.5 + - - -
77C ILE* 3.8 16.5 - - - +
78C ILE 3.4 0.2 - - - -
79C ASP* 1.3 74.4 - - - +
81C CYS* 1.3 57.8 + - - +
83C ILE* 3.8 3.7 - - - +
84C THR* 2.8 34.4 + - - -
99C GLU* 4.4 11.4 + - - +
102C THR* 4.9 8.4 + - - +
258C PRO* 4.3 15.0 - - - -
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Residues in contact with CYS 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ILE 3.1 20.1 + - - -
78C ILE* 3.6 5.6 - - - +
79C ASP 3.2 0.2 - - - -
80C SER* 1.3 77.9 - - - +
82C LEU* 1.3 59.1 + - - +
84C THR* 3.7 2.0 - - - -
85C GLU* 2.9 33.6 + - - +
257C PRO* 3.6 15.5 - - - -
258C PRO* 3.5 32.5 - - - -
261C ALA* 3.7 11.2 - - + +
312C TYR* 3.3 31.2 - - + -
316C ALA* 4.0 7.0 - - + -
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Residues in contact with LEU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 4.9 8.1 - - + -
16C LEU* 3.5 33.7 - - + -
20C GLN* 3.9 32.8 - - + +
23C PHE* 6.4 0.4 - - + -
24C GLN* 4.4 25.2 + - + +
78C ILE* 3.0 21.1 + - + +
79C ASP* 3.2 11.2 - - - +
81C CYS* 1.3 78.1 - - - +
83C ILE* 1.3 64.0 + - + +
85C GLU* 3.7 6.2 + - - +
86C GLU* 3.6 18.7 + - - +
312C TYR* 4.3 18.2 - - + +
313C GLN* 5.4 4.9 - - + +
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Residues in contact with ILE 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 4.1 30.5 - - + +
24C GLN* 5.7 0.7 - - - +
27C ALA* 3.6 13.0 - - + -
60C GLY 5.2 1.6 - - - +
61C LEU* 3.4 42.8 - - + +
64C THR* 3.6 25.4 - - - +
75C LEU* 4.2 14.6 - - + -
79C ASP 2.9 21.3 + - - +
80C SER* 4.0 2.7 - - - +
82C LEU* 1.3 75.3 - - + +
84C THR* 1.3 66.5 + - - +
86C GLU* 2.9 15.1 + - - +
87C LEU* 2.9 24.3 - - + +
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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
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80C SER 2.8 22.2 + - - -
81C CYS* 3.8 0.4 - - - -
83C ILE* 1.3 74.4 - - - +
85C GLU* 1.3 57.6 + - - +
87C LEU* 3.2 12.4 + - - +
88C ALA* 2.9 28.4 + - - +
95C GLN* 3.1 17.6 + - - +
99C GLU* 2.9 37.6 + - - +
258C PRO* 3.3 25.1 - - - +
261C ALA* 3.9 5.2 - - + -
262C GLY* 3.7 11.7 - - - +
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Residues in contact with GLU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C CYS 2.9 18.4 + - - +
82C LEU 4.0 5.2 - - - +
83C ILE 3.2 0.2 - - - -
84C THR* 1.3 76.5 - - - +
86C GLU* 1.3 73.0 + - - +
89C TYR* 3.4 20.3 + - - +
261C ALA* 3.7 13.2 - - + +
264C VAL* 3.3 26.3 - - + +
265C GLY* 3.6 12.4 - - - -
268C GLN* 4.2 5.4 - - - +
309C ARG* 2.8 37.0 + - - -
312C TYR* 2.4 32.4 + - - +
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Residues in contact with GLU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLN* 4.0 31.0 + - + +
27C ALA* 3.6 22.4 - - + -
28C ARG* 2.9 49.6 + - - +
31C ALA* 3.1 20.3 - - - +
32C ARG* 4.3 8.8 + - - -
82C LEU 3.6 14.0 - - - +
83C ILE 2.9 8.5 + - - +
85C GLU* 1.3 90.8 - - - +
87C LEU* 1.3 64.3 + - - +
89C TYR* 3.3 14.6 - - - +
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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
----------------------------------------------------------
27C ALA* 3.7 27.6 - - + +
30C PHE* 4.9 4.5 - - + -
31C ALA* 4.5 4.5 - - - -
35C ILE* 4.4 16.8 - - + +
61C LEU* 4.6 13.7 - - + +
83C ILE* 2.9 28.7 + - + +
84C THR* 3.5 14.4 - - - +
86C GLU* 1.3 73.1 - - - +
88C ALA* 1.3 53.6 + - - +
89C TYR 3.0 4.3 - - - -
90C GLY* 2.7 26.0 + - - -
91C CYS 3.3 9.0 + - - +
95C GLN* 3.7 16.8 - - + -
98C ILE* 3.8 40.6 - - + -
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Residues in contact with ALA 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 THR 2.9 19.1 + - - +
87C LEU* 1.3 72.9 - - - +
89C TYR* 1.3 60.6 - - - +
90C GLY 3.2 0.9 + - - -
91C CYS* 3.4 8.9 + - - -
92C THR* 3.5 27.2 + - + +
95C GLN* 3.5 13.9 - - + +
262C GLY* 3.2 37.0 - - - +
265C GLY* 4.1 7.2 - - - -
266C LEU* 4.3 8.1 + - - +
269C ARG* 5.6 0.2 - - - +
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Residues in contact with TYR 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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31C ALA* 5.1 0.2 - - + -
32C ARG* 3.4 46.9 + - + +
36C ILE* 3.9 19.5 - - + -
85C GLU 3.4 12.2 + - - +
86C GLU* 3.3 15.3 - - - +
87C LEU 2.9 0.4 + - - -
88C ALA* 1.3 78.6 - - - +
90C GLY* 1.3 59.4 + - - +
265C GLY* 3.6 10.3 + - - +
268C GLN* 4.0 12.8 - - + -
269C ARG* 3.0 76.7 + - - +
272C ASP* 2.8 37.9 + - - +
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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
----------------------------------------------------------
31C ALA* 4.5 4.9 - - - -
35C ILE* 4.0 13.2 - - - -
36C ILE* 3.8 22.2 - - - +
39C ALA* 4.1 9.5 - - - +
86C GLU 3.8 1.6 + - - -
87C LEU 2.7 10.3 + - - -
88C ALA 3.9 0.2 - - - -
89C TYR* 1.3 82.1 - - - +
91C CYS* 1.3 62.2 + - - +
269C ARG* 3.0 17.8 + - - -
364C LYS* 4.8 1.9 + - - -
365C LEU* 5.9 0.9 - - - +
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Residues in contact with CYS 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ILE* 3.9 11.0 - - + +
39C ALA* 3.9 17.7 - - + -
42C TYR* 6.4 0.7 - - - -
87C LEU 3.3 4.9 + - - +
88C ALA 3.4 5.1 + - - -
90C GLY* 1.3 80.5 - - - +
92C THR* 1.3 59.7 + - - +
93C GLY* 3.0 30.1 + - - -
94C VAL* 3.4 14.9 + - + +
95C GLN* 3.2 19.4 + - - +
217C GLN* 5.9 0.7 - - - -
219C CYS* 4.7 5.8 - - - -
364C LYS* 3.2 31.0 - - - +
368C ASP* 5.8 0.2 - - - -
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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
------------------------------------------------------------
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