Contacts of the helix formed by residues 35 - 46 (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 ILE 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A PHE* 3.2 35.7 + - + +
31A ALA* 3.3 32.7 + - + +
34A GLU* 1.3 76.8 - - - +
36A ILE* 1.3 66.9 + - - +
38A VAL* 3.0 5.4 + - - +
39A ALA* 2.9 23.3 + - + -
52A LEU* 4.3 12.1 - - + -
87A LEU* 4.2 17.3 - - + +
90A GLY* 3.8 2.5 - - - -
91A CYS* 3.8 34.3 - - + +
94A VAL* 4.3 23.6 - - + -
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Residues in contact with ILE 36 (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 3.0 13.9 + - - +
32A ARG* 4.0 22.2 - - + +
35A ILE* 1.3 78.6 - - - +
37A PRO* 1.3 68.1 - - + +
38A VAL 3.0 6.1 + - - -
39A ALA* 3.6 12.6 + - - +
40A ALA* 4.7 4.0 + - - +
89A TYR* 3.9 28.0 - - + -
90A GLY* 3.9 16.2 - - - -
269A ARG* 4.0 29.2 - - - +
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Residues in contact with PRO 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ARG 3.8 7.4 - - - +
33A GLU* 3.1 27.6 - - - +
34A GLU 3.5 11.4 - - - +
35A ILE 3.3 4.9 - - - +
36A ILE* 1.3 96.3 - - + +
38A VAL* 1.3 67.2 + - + +
40A ALA* 6.5 0.2 - - - -
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Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLU 3.4 20.4 - - - +
35A ILE 3.0 7.7 + - - +
37A PRO* 1.3 90.0 - - + +
39A ALA* 1.3 66.8 + - - +
40A ALA* 3.2 3.8 - - - -
41A GLU* 3.2 18.6 + - + +
42A TYR* 3.4 36.3 + - + -
52A LEU* 4.0 14.4 - - + -
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Residues in contact with ALA 39 (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* 2.9 17.9 + - + +
36A ILE* 3.6 6.1 + - - +
38A VAL* 1.3 78.7 - - - +
40A ALA* 1.3 58.7 + - - +
42A TYR* 3.3 10.6 + - - +
43A ASP* 2.9 27.4 + - - +
90A GLY 4.3 7.9 - - - +
91A CYS* 3.5 34.8 - - + -
94A VAL* 5.5 2.7 - - + -
364A LYS* 3.9 9.2 - - + -
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Residues in contact with ALA 40 (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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36A ILE 4.7 4.0 + - - +
38A VAL* 3.2 1.5 - - - -
39A ALA* 1.3 79.0 - - - +
41A GLU* 1.3 61.7 + - - +
43A ASP* 3.2 9.5 + - - +
44A ARG* 3.0 44.8 + - - +
358A THR 6.0 0.9 - - - +
364A LYS* 4.9 7.6 - - + +
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Residues in contact with GLU 41 (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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38A VAL* 3.2 14.7 + - + +
40A ALA* 1.3 77.7 - - - +
42A TYR* 1.3 61.8 + - + +
44A ARG* 2.7 38.4 + - - +
45A THR* 2.8 51.9 + - + +
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Residues in contact with TYR 42 (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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38A VAL* 3.4 41.6 + - + -
39A ALA* 3.3 10.2 + - - +
40A ALA 3.3 0.4 - - - -
41A GLU* 1.3 78.2 - - + +
43A ASP* 1.3 61.7 + - - +
45A THR* 3.7 4.0 - - - -
46A GLY* 2.9 28.2 + - - -
47A GLU* 3.1 44.0 + - + -
48A TYR 3.7 11.0 - - - -
49A PRO* 3.9 11.9 - - + -
51A PRO* 3.5 30.1 - - - +
52A LEU* 4.2 16.8 - - + -
94A VAL* 5.5 1.6 - - + -
219A CYS* 3.5 24.3 - - + +
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Residues in contact with ASP 43 (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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39A ALA 2.9 6.4 + - - +
40A ALA* 3.4 10.2 - - - +
41A GLU 3.2 0.2 - - - -
42A TYR* 1.3 76.9 - - - +
44A ARG* 1.3 64.2 + - - +
46A GLY 4.3 0.3 + - - -
218A ARG* 2.9 63.3 + - - +
219A CYS* 4.8 3.1 - - - +
363A GLU* 4.6 1.0 - - - +
364A LYS* 3.4 34.4 - - + +
367A ARG* 2.7 34.6 + - - -
368A ASP* 5.0 1.4 - - - +
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Residues in contact with ARG 44 (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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40A ALA* 3.0 31.5 - - - +
41A GLU* 2.7 46.9 + - - +
43A ASP* 1.3 85.7 - - + +
45A THR* 1.3 67.1 + - + +
46A GLY* 3.4 0.9 + - - -
218A ARG* 4.5 10.7 + - - +
358A THR* 4.5 18.4 + - - -
359A GLU* 4.7 10.3 + - - +
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Residues in contact with THR 45 (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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41A GLU* 2.8 48.3 + - + +
42A TYR* 3.7 7.4 - - - -
44A ARG* 1.3 74.4 - - + +
46A GLY* 1.3 60.6 + - - +
47A GLU* 2.9 33.6 + - - +
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Residues in contact with GLY 46 (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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42A TYR 2.9 16.5 + - - -
43A ASP 4.3 0.2 + - - -
44A ARG 3.3 3.0 - - - -
45A THR* 1.3 76.4 - - - +
47A GLU* 1.3 63.8 + - - +
48A TYR 3.5 1.9 + - - -
211A LYS* 3.3 30.5 + - - +
218A ARG* 3.5 22.9 - - - +
219A CYS* 4.1 2.6 - - - +
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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