Contacts of the helix formed by residues 76 - 91 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D HIS* 3.7 11.0 - - - -
75D LEU* 1.3 75.7 - - - +
77D ILE* 1.3 65.8 + - - -
78D ILE 3.3 3.4 - - - -
79D ASP* 2.9 28.0 + - - +
80D SER* 3.0 13.5 + - - -
320D ASP* 4.0 11.7 - - - -
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Residues in contact with ILE 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D HIS* 3.6 25.6 - - + +
76D GLY* 1.3 70.4 - - - -
78D ILE* 1.3 64.4 + - - +
80D SER* 3.1 10.3 + - - +
81D CYS* 2.8 21.7 + - - -
102D THR* 6.0 3.4 - - + -
106D VAL* 5.8 2.5 - - + -
254D LYS* 3.6 46.2 - - + +
257D PRO* 4.1 3.4 - - + -
258D PRO* 4.1 17.0 - - + -
316D ALA* 3.9 18.2 - - + -
319D ILE* 3.6 20.2 - - + -
320D ASP* 3.0 17.9 + - - +
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Residues in contact with ILE 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.3 43.3 - - + -
20D GLN* 3.9 18.8 - - - +
77D ILE* 1.3 76.8 - - - +
79D ASP* 1.3 80.4 + - - +
81D CYS* 3.1 4.8 + - - +
82D LEU* 2.9 34.5 + - + +
312D TYR* 5.2 3.1 - - + -
313D GLN* 4.3 17.7 - - + +
316D ALA* 3.6 23.2 - - + +
317D TRP* 4.9 4.5 - - + +
320D ASP* 3.0 20.8 + - - +
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Residues in contact with ASP 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D GLN* 3.0 36.0 + - - +
23D PHE* 4.0 12.4 - - + -
64D THR* 4.9 0.2 - - - -
75D LEU* 3.8 31.1 - - + +
76D GLY* 2.9 28.0 + - - +
78D ILE* 1.3 89.1 - - - +
80D SER* 1.3 62.1 + - - +
82D LEU* 3.2 8.5 + - - +
83D ILE* 3.1 30.9 + - - +
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Residues in contact with SER 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D THR* 3.3 26.5 - - - +
65D HIS* 4.6 8.5 - - - +
76D GLY 3.0 10.7 + - - -
77D ILE* 3.4 15.5 - - - +
79D ASP* 1.3 75.3 - - - +
81D CYS* 1.3 57.7 + - - +
83D ILE* 3.5 4.8 + - - +
84D THR* 2.9 33.7 + - - -
99D GLU* 4.1 10.1 - - - +
102D THR* 5.2 9.4 + - - +
258D PRO* 4.6 14.6 - - - -
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Residues in contact with CYS 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D ILE* 2.8 19.0 + - - -
78D ILE* 3.4 9.9 - - - +
80D SER* 1.3 76.3 - - - +
82D LEU* 1.3 64.0 + - - +
84D THR* 4.5 1.6 - - - -
85D GLU* 3.1 26.5 + - - +
257D PRO* 3.6 21.1 - - - -
258D PRO* 3.5 33.0 - - - -
261D ALA* 3.6 9.6 - - + +
312D TYR* 3.5 29.3 + - + -
316D ALA* 4.2 3.8 - - - -
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Residues in contact with LEU 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 4.1 17.5 - - + -
16D LEU* 3.2 43.3 - - + -
20D GLN* 3.4 33.7 - - + +
23D PHE* 5.8 2.7 - - + -
24D GLN* 4.5 17.0 + - + +
78D ILE* 2.9 22.2 + - + +
79D ASP* 3.2 11.2 + - - +
81D CYS* 1.3 77.2 - - - +
83D ILE* 1.3 63.6 + - + +
85D GLU* 3.8 7.8 + - - +
86D GLU* 3.8 18.5 + - - +
312D TYR* 4.6 11.2 - - + +
313D GLN* 5.1 3.6 - - - +
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Residues in contact with ILE 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D PHE* 4.1 37.2 - - + -
24D GLN* 5.2 1.3 - - - +
27D ALA* 4.1 7.0 - - + -
60D GLY 4.8 3.6 - - - +
61D LEU* 3.8 37.2 - - + +
64D THR* 3.8 23.3 - - - +
75D LEU* 4.7 5.6 - - + -
79D ASP 3.1 18.7 + - - +
80D SER* 3.9 4.7 - - - +
82D LEU* 1.3 77.2 - - + +
84D THR* 1.3 66.3 + - - +
86D GLU* 3.4 6.6 + - - +
87D LEU* 3.2 34.9 + - + +
99D GLU* 6.0 0.9 - - - +
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Residues in contact with THR 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D SER 2.9 16.7 + - - -
81D CYS* 4.0 2.5 - - - -
83D ILE* 1.3 74.0 - - - +
85D GLU* 1.3 62.2 + - - +
87D LEU* 3.2 10.2 + - - +
88D ALA* 2.8 29.6 + - - +
95D GLN* 3.3 19.8 + - - +
99D GLU* 2.4 40.2 + - + +
258D PRO* 3.5 23.3 - - - +
261D ALA* 3.9 2.5 - - + -
262D GLY* 3.5 13.5 - - - +
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Residues in contact with GLU 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D CYS 3.1 17.8 + - - +
82D LEU* 4.0 5.8 - - - +
83D ILE 3.3 0.2 - - - -
84D THR* 1.3 77.7 - - - +
86D GLU* 1.3 72.8 + - - +
89D TYR* 3.2 18.5 + - - +
261D ALA 3.6 16.6 - - - +
264D VAL* 3.3 28.0 - - + +
265D GLY* 3.4 13.3 - - - -
268D GLN* 4.8 3.8 - - - +
309D ARG* 2.5 39.3 + - - -
312D TYR* 2.5 27.6 + - - +
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Residues in contact with GLU 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D GLN* 3.9 31.3 + - + +
27D ALA* 3.8 15.3 - - + -
28D ARG* 2.9 55.7 + - - +
31D ALA* 3.4 13.3 - - - +
32D ARG* 4.2 10.4 + - - -
82D LEU 3.8 13.4 + - - +
83D ILE 3.4 6.6 + - - +
84D THR 3.3 0.2 - - - -
85D GLU* 1.3 87.5 - - - +
87D LEU* 1.3 65.2 + - - +
89D TYR* 3.1 21.9 - - - +
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Residues in contact with LEU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ALA* 3.7 34.3 - - + +
30D PHE* 4.1 18.6 - - + -
31D ALA* 4.2 4.9 - - + +
35D ILE* 4.4 14.8 - - + +
61D LEU* 4.2 12.6 - - + +
83D ILE* 3.2 26.0 + - + +
84D THR* 3.2 12.7 + - - +
86D GLU* 1.3 76.2 - - - +
88D ALA* 1.3 66.9 + - - +
90D GLY* 2.7 16.6 + - - -
91D CYS 3.3 8.3 + - - +
95D GLN* 3.9 16.4 - - + -
98D ILE* 4.1 31.4 - - + -
99D GLU* 5.8 0.7 - - - +
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Residues in contact with ALA 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D THR 2.8 20.7 + - - +
85D GLU 3.9 4.7 - - - +
87D LEU* 1.3 72.1 - - - +
89D TYR* 1.3 62.5 + - - +
91D CYS* 3.1 15.7 + - - -
92D THR* 3.5 19.7 + - + +
95D GLN* 3.7 16.3 - - - +
262D GLY* 3.1 36.6 - - - +
265D GLY* 4.2 3.6 - - - -
266D LEU* 4.4 5.4 + - - +
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Residues in contact with TYR 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D ARG* 3.5 43.4 + - + +
36D ILE* 3.7 19.5 - - + -
85D GLU 3.2 11.3 + - - +
86D GLU* 3.1 19.1 - - - +
87D LEU 2.9 0.6 + - - -
88D ALA* 1.3 81.1 - - - +
90D GLY* 1.3 50.8 + - - +
265D GLY* 3.5 15.0 - - - +
268D GLN* 4.0 13.7 - - + -
269D ARG* 2.7 80.2 + - - +
272D ASP* 2.8 35.9 + - - +
276D LYS* 4.9 5.0 + - - -
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Residues in contact with GLY 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ALA* 4.4 5.4 - - - +
35D ILE* 3.7 13.2 - - - +
36D ILE* 3.6 23.7 - - - +
39D ALA* 3.7 13.2 - - - +
86D GLU 3.7 2.0 + - - -
87D LEU 2.7 15.1 + - - -
88D ALA 3.8 0.2 - - - -
89D TYR* 1.3 75.8 - - - +
91D CYS* 1.3 63.5 + - - +
269D ARG* 3.2 13.5 + - - -
364D LYS* 4.7 1.9 + - - -
365D LEU* 6.1 0.3 - - - +
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Residues in contact with CYS 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D ILE* 3.8 15.9 - - + +
39D ALA* 3.9 11.2 - - + -
42D TYR* 6.3 0.9 - - - -
87D LEU 3.3 4.3 + - - +
88D ALA 3.1 7.2 + - - -
90D GLY* 1.3 82.6 - - - +
92D THR* 1.3 56.3 + - - +
93D GLY* 3.0 22.4 - - - -
94D VAL* 3.3 21.9 - - + +
95D GLN* 3.0 27.2 + - - +
217D GLN* 6.0 0.2 - - - -
219D CYS* 4.6 4.3 - - - -
364D LYS* 3.3 28.9 - - - +
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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