Contacts of the helix formed by residues 34 - 49 (chain D) in PDB entry 1XHU
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 34 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D GLY 4.8 0.8 + - - -
31D HIS 4.7 0.2 + - - -
33D ALA* 1.3 79.7 - - - +
35D GLU* 1.3 55.4 + - - +
36D PRO* 3.1 4.0 - - - -
37D PHE* 2.7 44.5 + - - +
38D GLU 3.2 4.2 + - - -
130D THR* 3.4 33.3 + - - +
173D TRP* 4.3 4.2 - - - -
9J A 5.1 1.1 - - - -
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Residues in contact with GLU 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C GLY* 5.5 5.2 - - - -
27C THR* 3.8 29.7 - - + +
32C ALA* 6.0 3.6 - - + -
31D HIS* 3.1 30.1 + - + +
32D ALA* 5.0 1.1 - - - -
33D ALA 4.8 0.4 - - - +
34D GLY* 1.3 75.9 - - - +
36D PRO* 1.3 73.5 - - + +
38D GLU* 3.0 15.7 + - - +
39D LYS* 2.8 23.2 + - + +
107D GLU* 5.0 6.2 - - - +
8J G 2.6 41.2 + - - +
9J A 5.2 2.7 + - - -
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Residues in contact with PRO 36 (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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24C LYS* 6.1 2.7 - - + +
20D VAL* 3.9 35.8 - - + +
23D PRO* 5.8 9.2 - - + -
33D ALA 4.0 11.9 - - - +
34D GLY* 3.3 4.9 - - - -
35D GLU* 1.3 95.2 - - + +
37D PHE* 1.3 61.8 + - - +
39D LYS* 3.0 12.0 + - + +
40D LEU* 2.9 21.4 + - - +
180D LEU* 6.1 0.9 - - + -
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Residues in contact with PHE 37 (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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15D LEU* 5.1 6.7 - - + +
18D GLN* 4.9 8.7 - - + -
19D LYS* 5.0 0.9 - - - -
20D VAL* 3.5 22.4 - - + -
33D ALA 5.2 0.2 - - - -
34D GLY* 2.7 31.7 + - - +
36D PRO* 1.3 75.3 - - + +
38D GLU* 1.3 55.2 + - - +
40D LEU* 2.8 45.2 + - + +
41D VAL* 3.1 13.4 + - - +
128D VAL* 5.3 0.9 - - - -
130D THR* 4.1 10.3 - - + -
171D VAL* 3.8 21.8 - - + -
173D TRP* 3.6 27.8 - + + -
180D LEU* 3.1 31.2 - - + -
182D CYS* 3.8 28.5 - - + -
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Residues in contact with GLU 38 (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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34D GLY 3.2 4.2 + - - +
35D GLU* 3.0 18.4 + - - +
37D PHE* 1.3 74.0 - - - +
39D LYS* 1.3 67.1 + - - +
40D LEU 2.8 9.6 + - - -
41D VAL* 3.7 10.1 + - - +
42D TYR* 3.8 10.6 + - - +
107D GLU* 5.4 5.1 - - - +
114D ASP* 3.0 54.2 - - - +
115D ILE* 3.0 10.4 - - - +
128D VAL* 3.8 26.7 - - + +
130D THR* 4.8 3.2 - - + +
8J G 4.2 14.6 - - - +
9J A 5.6 1.3 - - - +
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Residues in contact with LYS 39 (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 GLU* 2.8 16.0 + - + +
36D PRO* 3.0 15.5 + - + +
38D GLU* 1.3 83.7 + - - +
40D LEU* 1.3 58.3 + - - +
42D TYR* 4.6 12.2 - - - +
43D LYS* 4.9 2.8 + - - +
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Residues in contact with LEU 40 (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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14D ILE* 6.6 0.2 - - + -
15D LEU* 5.3 11.2 - - + -
18D GLN* 4.5 27.1 - - + -
19D LYS 5.7 0.2 - - - +
20D VAL* 4.8 13.7 - - + -
36D PRO 2.9 6.9 + - - +
37D PHE* 2.8 39.9 + - + +
38D GLU 2.8 0.6 - - - -
39D LYS* 1.3 78.3 - - - +
41D VAL* 1.3 54.0 + - + +
42D TYR 2.9 1.6 - - - -
43D LYS* 2.5 49.7 + - + +
44D PHE* 3.9 4.3 + - + +
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Residues in contact with VAL 41 (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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11D ILE* 3.8 8.5 - - + +
15D LEU* 3.8 21.0 - - + +
37D PHE 3.7 11.2 - - - +
38D GLU 4.2 5.4 - - - +
40D LEU* 1.3 77.0 - - - +
42D TYR* 1.3 62.5 + - - +
43D LYS* 4.2 0.2 - - - -
44D PHE* 3.7 3.9 + - - +
45D LEU* 3.0 47.1 + - + +
115D ILE* 5.1 2.7 - - + -
126D LEU* 4.6 6.1 - - + -
128D VAL* 4.5 14.1 - - + -
169D LEU* 3.6 33.7 - - + -
171D VAL* 4.6 7.2 - - + -
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Residues in contact with TYR 42 (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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38D GLU* 3.8 12.5 + - - +
39D LYS* 4.6 10.1 - - - +
40D LEU 2.7 6.5 + - - +
41D VAL* 1.3 75.3 - - - +
43D LYS* 1.3 66.5 - - - +
45D LEU* 4.1 3.2 - - - +
46D LYS* 3.2 27.0 + - + +
53D THR* 3.7 26.5 - - + -
54D PHE 4.5 7.6 - - - -
55D LYS* 4.6 6.5 - - + -
58D GLU* 2.6 42.6 + - - -
115D ILE* 4.5 21.4 - - + +
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Residues in contact with LYS 43 (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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39D LYS 4.9 2.6 + - - +
40D LEU* 2.5 29.8 + - + +
42D TYR* 1.3 76.0 - - - +
44D PHE* 1.3 55.3 + - - +
46D LYS* 2.7 28.3 + - - +
47D GLU* 3.0 12.2 + - - +
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Residues in contact with PHE 44 (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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7D ILE* 3.5 4.3 - - + -
10D ASP* 4.2 8.3 - - + -
11D ILE* 3.4 50.0 - - + -
14D ILE* 3.4 45.8 - - + -
15D LEU* 6.5 0.9 - - + -
40D LEU* 3.9 5.0 + - + +
41D VAL* 3.7 6.3 + - - +
43D LYS* 1.3 78.9 - - - +
45D LEU* 1.3 59.1 + - - +
47D GLU* 2.8 32.5 + - + +
48D ASN* 3.0 50.8 + - - -
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Residues in contact with LEU 45 (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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4D ILE* 4.3 13.7 - - + -
7D ILE* 5.6 3.8 - - + -
11D ILE* 4.0 12.3 - - + +
41D VAL* 3.0 32.9 + - + +
42D TYR* 4.1 4.3 - - - +
44D PHE* 1.3 79.9 - - - +
46D LYS* 1.3 55.8 + - - +
48D ASN* 4.5 4.7 - - - +
49D LEU* 3.2 47.1 + - + +
53D THR* 2.9 23.9 + - + +
115D ILE* 4.5 12.6 - - + -
117D LEU* 4.1 13.0 - - + -
126D LEU* 3.6 31.4 - - + -
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Residues in contact with LYS 46 (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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42D TYR* 3.2 19.0 + - + +
43D LYS* 2.7 12.8 + - - +
45D LEU* 1.3 78.9 - - - +
47D GLU* 1.3 59.3 + - - +
48D ASN 3.1 2.5 - - - -
49D LEU 3.6 3.4 - - - -
50D SER* 2.7 39.1 + - - -
53D THR* 3.8 16.8 - - + -
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Residues in contact with GLU 47 (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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43D LYS 3.0 6.4 + - - +
44D PHE* 2.8 30.0 + - + +
46D LYS* 1.3 79.0 - - - +
48D ASN* 1.3 65.6 + - - +
50D SER* 4.9 2.8 + - - -
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Residues in contact with ASN 48 (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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7D ILE* 3.5 19.6 - - + +
44D PHE* 3.0 62.1 + - - -
45D LEU* 4.5 2.6 - - - +
46D LYS 3.1 0.2 - - - -
47D GLU* 1.3 86.0 - - - +
49D LEU* 1.3 74.0 + - + +
50D SER 3.7 2.1 + - - -
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Residues in contact with LEU 49 (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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3D PHE* 4.1 24.7 - - + +
7D ILE* 5.1 15.0 - - + -
45D LEU* 3.2 40.1 + - + +
46D LYS 3.4 2.7 - - - -
48D ASN* 1.3 91.3 - - + +
50D SER* 1.3 54.3 + - - +
51D ASP 3.0 8.8 + - - +
52D LEU* 3.0 21.2 + - + +
53D THR* 2.9 29.3 + - - +
117D LEU* 4.1 11.4 - - + -
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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