Contacts of the helix formed by residues 37 - 48 (chain A) in PDB entry 1UXI
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 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A VAL 3.7 0.2 + - - -
36A GLU* 1.3 72.9 - - - +
38A VAL* 1.3 54.6 + - - +
40A GLN* 2.5 26.8 + - - -
41A GLY* 2.8 32.1 + - - -
219B LEU* 3.5 37.2 - - - +
221B LYS* 5.3 1.6 - - - -
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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
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10A ALA 3.6 24.0 - - - +
33A ASP* 4.4 9.2 - - - +
35A VAL* 3.6 31.4 - - + +
36A GLU 3.2 2.6 + - - +
37A GLY* 1.3 77.2 - - - +
39A PRO* 1.3 71.2 - - + +
42A LYS* 3.2 38.2 + - - +
1310A NAD 4.7 4.3 - - - +
219B LEU 3.8 2.1 + - - +
220B LEU* 3.9 21.5 - - + +
221B LYS* 6.3 0.7 - - + -
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Residues in contact with PRO 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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10A ALA* 3.9 21.5 - - + -
31A LEU* 3.4 26.3 - - + +
33A ASP* 3.6 9.6 - - + -
35A VAL 3.1 20.2 - - - +
38A VAL* 1.3 91.3 - - + +
40A GLN* 1.3 73.1 + - - +
42A LYS* 4.3 2.1 - - + +
43A ALA* 3.1 17.2 + - - +
61A GLY* 3.1 13.5 - - - -
62A THR 3.3 23.3 - - - +
63A ASN* 3.6 5.8 - - - +
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Residues in contact with GLN 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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37A GLY* 2.5 39.9 + - - +
39A PRO* 1.3 83.1 - - - +
41A GLY* 1.3 63.5 + - - +
43A ALA* 3.8 1.6 - - - +
44A LEU* 3.0 25.1 + - - +
61A GLY* 3.7 17.0 + - - +
62A THR* 3.4 24.9 - - - +
63A ASN* 3.2 20.4 + - - +
219B LEU* 3.9 17.3 - - + -
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Residues in contact with GLY 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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37A GLY 2.8 19.4 + - - -
40A GLN* 1.3 73.7 - - - +
42A LYS* 1.3 56.2 + - - +
44A LEU* 3.2 3.0 + - - +
45A ASP* 2.8 33.0 + - - +
216B ILE* 4.2 7.2 - - - +
219B LEU* 3.5 23.7 - - - +
220B LEU* 4.0 12.6 - - - -
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Residues in contact with LYS 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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10A ALA* 2.8 31.7 + - + +
11A GLY* 4.0 12.7 - - - -
15A SER* 3.9 14.3 + - - -
31A LEU* 4.4 12.1 - - + -
38A VAL* 3.2 32.1 + - - +
39A PRO* 4.3 2.5 - - + +
41A GLY* 1.3 74.4 - - - +
43A ALA* 1.3 57.4 + - - +
45A ASP* 3.7 6.4 - - - +
46A LEU* 3.0 31.6 + - - +
1310A NAD 5.3 0.2 + - - -
12B PHE* 6.2 0.7 - - - -
220B LEU* 3.8 16.7 - - + +
226B TYR* 3.4 28.0 + - + +
227B TYR* 3.8 12.8 - - + -
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Residues in contact with ALA 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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31A LEU* 4.2 6.5 - - + +
39A PRO 3.1 21.3 + - - +
40A GLN 3.8 2.0 - - - +
42A LYS* 1.3 78.3 - - - +
44A LEU* 1.3 56.8 + - - +
47A TYR* 2.9 29.3 + - - +
59A VAL* 3.5 29.9 - - + +
60A THR 3.5 9.0 - - - -
61A GLY* 3.3 23.3 - - - +
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Residues in contact with LEU 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 GLN 3.0 17.5 + - - +
41A GLY* 3.7 4.0 - - - +
43A ALA* 1.3 74.5 - - - +
45A ASP* 1.3 57.5 + - - +
47A TYR* 3.0 17.0 + - + +
48A GLU* 2.8 65.8 + - + +
59A VAL 5.2 0.4 - - - -
155B PHE* 4.6 4.9 - - + -
158B MET* 5.0 3.6 - - + -
208B ARG* 3.8 13.9 - - - +
215B GLU* 3.3 40.2 - - + +
216B ILE* 4.2 10.1 - - + -
219B LEU* 4.6 8.1 - - + -
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Residues in contact with ASP 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 GLY 2.8 18.5 + - - +
42A LYS* 3.7 6.0 - - - +
44A LEU* 1.3 76.6 - - - +
46A LEU* 1.3 60.9 + - - +
48A GLU* 3.3 9.3 + - - +
49A ALA 3.5 0.7 + - - -
216B ILE* 3.8 18.4 - - + +
220B LEU* 5.4 1.1 - - + +
225B ALA* 3.3 11.8 - - - +
226B TYR* 2.6 31.3 + - - -
227B TYR* 2.9 20.0 + - + -
228B ALA* 2.8 37.4 + - - +
229B PRO* 3.5 3.3 - - - +
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Residues in contact with LEU 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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15A SER 4.9 1.3 - - - +
18A ALA* 3.8 20.6 - - + +
19A HIS* 3.8 34.3 - - + +
22A ALA* 4.3 16.2 - - + -
31A LEU* 5.6 1.3 - - + -
42A LYS 3.0 18.8 + - - +
43A ALA 4.0 3.4 - - - +
45A ASP* 1.3 73.6 - - - +
47A TYR* 1.3 67.0 + - - +
49A ALA* 3.1 17.5 + - - +
50A SER 3.7 2.8 + - - -
55A PHE* 4.3 6.5 - - + -
59A VAL* 4.3 15.7 - - + -
20B TRP* 4.4 19.5 - - + -
227B TYR* 3.7 32.1 - - + +
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Residues in contact with TYR 47 (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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43A ALA 2.9 20.5 + - - +
44A LEU* 3.0 14.6 + - + +
46A LEU* 1.3 78.2 - - - +
48A GLU* 1.3 56.5 + - - +
49A ALA 3.1 0.2 - - - -
50A SER* 2.4 40.7 + - - -
55A PHE* 5.7 0.9 - - - -
57A VAL* 3.0 32.1 - - + -
58A ARG* 4.5 10.3 - - + +
59A VAL* 4.3 17.5 - - + +
154B THR* 3.5 21.4 + - + +
157B ALA* 5.7 0.5 - - - +
158B MET* 3.3 48.0 + - + +
164B VAL* 5.2 8.6 - - + +
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Residues in contact with GLU 48 (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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44A LEU* 2.8 45.7 + - + +
45A ASP* 3.6 6.4 - - - +
46A LEU 3.2 0.6 - - - -
47A TYR* 1.3 76.4 - - - +
49A ALA* 1.3 58.7 + - - +
50A SER 3.3 0.4 - - - -
51A PRO* 3.3 13.9 - - - +
150B ALA* 3.4 19.1 - - - +
151B ARG* 3.0 47.7 + - + +
154B THR* 3.4 16.5 + - + +
155B PHE* 3.3 24.0 - - + -
212B GLY 4.8 1.9 - - - +
215B GLU* 4.6 1.4 - - - +
216B ILE* 3.3 15.7 - - - +
228B ALA* 3.9 8.5 - - + +
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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