Contacts of the helix formed by residues 76 - 91 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A HIS* 4.1 7.9 - - - -
75A LEU* 1.3 75.2 - - - +
77A ILE* 1.3 56.7 + - - -
78A ILE 3.3 3.1 - - - -
79A ASP* 2.9 20.4 + - - +
80A SER* 2.7 33.3 + - - -
320A ASP* 3.9 11.9 - - - -
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Residues in contact with ILE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A HIS* 3.8 25.8 - - + +
76A GLY* 1.3 67.2 - - - -
78A ILE* 1.3 67.4 + - - +
80A SER* 3.1 10.1 + - - -
81A CYS* 3.0 32.9 + - - -
102A THR* 6.1 4.0 - - + -
106A VAL* 5.8 2.5 - - + -
254A LYS* 3.7 44.6 - - + +
257A PRO* 4.1 7.2 - - + -
258A PRO* 4.5 4.7 - - + -
316A ALA* 3.8 20.2 - - + -
319A ILE* 3.5 24.9 - - + -
320A ASP* 3.2 13.1 + - - +
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Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLN* 3.7 17.9 - - - +
77A ILE* 1.3 78.0 - - - +
79A ASP* 1.3 62.9 + - - +
81A CYS* 3.4 2.2 + - - +
82A LEU* 2.8 38.3 + - + +
313A GLN* 4.7 5.2 - - + +
316A ALA* 3.3 24.4 - - + +
317A TRP* 3.5 39.9 - - + +
320A ASP* 3.1 22.1 + - + +
12D PHE* 3.9 30.5 - - + +
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Residues in contact with ASP 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLN* 5.0 2.0 - - - +
20A GLN* 3.2 32.3 - - - +
23A PHE* 4.0 13.5 - - + -
75A LEU* 3.8 24.7 - - + -
76A GLY* 2.9 31.2 + - - +
78A ILE* 1.3 76.3 + - - +
80A SER* 1.3 65.2 + - - +
81A CYS 3.1 1.2 + - - -
82A LEU* 3.3 15.9 + - - +
83A ILE* 3.4 20.4 + - - +
320A ASP* 4.8 1.4 - - - +
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Residues in contact with SER 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A THR* 3.8 30.5 + - - +
65A HIS* 5.8 3.6 - - - -
76A GLY 2.7 16.4 + - - -
77A ILE* 3.1 18.4 + - - -
79A ASP* 1.3 73.5 - - - +
81A CYS* 1.3 54.9 + - - +
83A ILE* 3.8 4.7 + - - +
84A THR* 3.3 27.4 + - - -
99A GLU* 3.5 21.7 + - - +
102A THR* 4.5 5.1 + - - +
258A PRO* 4.3 8.6 - - - +
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Residues in contact with CYS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 3.0 31.0 + - - +
78A ILE* 3.7 5.2 - - - +
79A ASP 3.1 0.2 - - - -
80A SER* 1.3 73.6 - - - +
82A LEU* 1.3 64.9 - - - +
83A ILE 3.2 2.0 - - - -
84A THR* 3.3 2.6 + - - -
85A GLU* 3.1 23.6 + - - +
257A PRO* 3.8 11.0 - - - -
258A PRO* 3.7 33.4 - - - -
261A ALA* 3.7 12.0 - - + +
312A TYR* 3.3 30.9 + - + -
316A ALA* 4.2 4.9 - - + -
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 3.5 29.8 - - + -
20A GLN* 3.4 39.3 - - + +
23A PHE* 6.1 1.8 - - + -
24A GLN* 4.5 18.7 + - + +
78A ILE* 2.8 34.2 + - + +
79A ASP* 3.3 8.9 + - - +
81A CYS* 1.3 78.7 - - + +
83A ILE* 1.3 63.3 + - + +
85A GLU* 4.0 3.4 + - - +
86A GLU* 3.5 24.4 + - - +
312A TYR* 4.4 17.7 - - + +
313A GLN* 5.4 4.3 - - + +
12D PHE* 4.7 8.3 - - + -
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Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 4.1 36.3 - - + +
24A GLN* 5.6 1.1 - - - +
27A ALA* 3.8 11.7 - - + -
60A GLY 5.2 2.0 - - - +
61A LEU* 3.7 39.9 - - + +
64A THR* 4.7 13.0 - - + +
75A LEU* 4.5 14.1 - - + -
79A ASP 3.4 20.0 - - - +
80A SER* 4.0 4.7 - - - +
81A CYS 3.2 0.2 - - - -
82A LEU* 1.3 78.0 - - + +
84A THR* 1.3 65.1 + - - +
86A GLU* 3.2 6.4 + - - +
87A LEU* 3.1 35.7 + - + +
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Residues in contact with THR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A SER 3.3 13.9 + - - -
81A CYS* 3.3 4.6 + - - -
83A ILE* 1.3 77.8 - - - +
85A GLU* 1.3 58.3 + - - +
87A LEU* 3.1 11.8 + - - +
88A ALA* 2.7 34.0 + - - +
95A GLN* 3.1 26.1 + - - +
99A GLU* 3.0 27.8 + - - -
258A PRO* 3.4 22.9 - - - +
261A ALA* 3.9 3.6 - - + -
262A GLY* 3.6 13.0 - - - +
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Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A CYS 3.1 15.6 + - - +
82A LEU 4.2 4.9 - - - +
83A ILE 3.4 0.2 - - - -
84A THR* 1.3 76.9 - - - +
86A GLU* 1.3 77.2 + - - +
88A ALA* 4.5 0.4 - - - -
89A TYR* 3.1 20.6 + - - +
261A ALA 3.3 24.2 - - - +
264A VAL* 3.3 11.5 - - + +
265A GLY* 3.3 24.2 - - - +
268A GLN* 4.5 9.9 - - - +
309A ARG* 2.7 44.4 + - - -
312A TYR* 3.4 16.7 + - - +
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Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLN* 3.9 25.4 + - + +
27A ALA* 3.7 15.7 - - + -
28A ARG* 2.6 58.4 + - - +
31A ALA* 3.3 15.6 - - - +
32A ARG* 4.7 5.9 + - - -
82A LEU 3.5 17.1 + - - +
83A ILE 3.2 7.8 + - - +
84A THR 3.2 0.4 - - - -
85A GLU* 1.3 89.8 - - - +
87A LEU* 1.3 64.9 + - - +
89A TYR* 3.1 22.5 - - - +
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA* 3.6 35.7 - - + +
30A PHE* 4.3 9.2 - - + -
31A ALA* 4.2 4.9 - - + -
35A ILE* 4.2 12.3 - - + +
61A LEU* 4.0 18.4 - - + +
83A ILE* 3.1 28.1 + - + +
84A THR* 3.4 12.3 - - - +
86A GLU* 1.3 74.3 - - - +
88A ALA* 1.3 64.7 + - - +
90A GLY* 2.9 13.2 + - - -
91A CYS 3.3 11.8 + - - +
94A VAL* 6.2 0.4 - - + -
95A GLN* 3.8 16.2 - - + -
98A ILE* 4.4 34.1 - - + -
99A GLU* 6.0 0.2 - - - +
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A THR 2.7 20.8 + - - +
85A GLU 3.8 4.0 - - - +
87A LEU* 1.3 73.0 - - - +
89A TYR* 1.3 64.3 + - - +
90A GLY 3.1 1.4 + - - -
91A CYS* 3.3 9.0 + - - -
92A THR* 3.6 24.1 + - + +
95A GLN* 3.7 19.2 - - + +
262A GLY* 3.2 31.6 - - - +
265A GLY* 4.0 4.9 - - - -
266A LEU* 4.3 3.8 + - - -
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Residues in contact with TYR 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA* 5.5 0.2 - - + -
32A ARG* 3.4 47.0 + - + -
36A ILE* 3.9 18.6 - - + -
85A GLU* 3.1 14.5 + - - +
86A GLU* 3.1 20.9 - - - +
88A ALA* 1.3 77.1 - - - +
90A GLY* 1.3 57.8 + - - +
265A GLY 3.7 11.2 - - - +
268A GLN* 4.0 12.8 - - + -
269A ARG* 2.9 67.7 + - - +
272A ASP* 2.7 37.6 + - - +
273A GLU* 5.3 0.9 + - - -
276A LYS* 5.0 6.2 + - - -
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Residues in contact with GLY 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA* 4.2 6.7 - - - +
35A ILE* 3.8 13.2 - - - -
36A ILE* 3.9 22.8 - - - +
39A ALA* 4.3 6.6 - - - +
86A GLU 3.7 2.6 + - - -
87A LEU 2.9 8.1 + - - -
88A ALA 3.6 0.2 - - - -
89A TYR* 1.3 80.2 - - - +
91A CYS* 1.3 64.8 + - - +
269A ARG* 3.1 18.5 + - - -
364A LYS* 5.2 1.6 + - - -
365A LEU* 6.0 0.2 - - - +
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Residues in contact with CYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ILE* 3.8 10.5 - - + +
39A ALA* 3.5 25.1 - - + -
42A TYR* 6.2 0.2 - - - -
87A LEU 3.3 5.4 + - - +
88A ALA 3.3 4.8 + - - -
90A GLY* 1.3 80.3 - - - +
92A THR* 1.3 57.6 + - - +
93A GLY* 2.9 23.2 + - - -
94A VAL* 3.1 19.1 + - + +
95A GLN* 2.9 26.3 + - - +
219A CYS* 4.6 5.8 - - - -
364A LYS* 3.4 26.2 - - - +
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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