Contacts of the helix formed by residues 29 - 41 (chain D) in PDB entry 4XYN
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 LYS 29 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D GLU* 4.3 15.2 + - + +
23D GLY* 3.7 31.2 - - - +
28D LEU* 1.3 72.8 - - - +
30D LYS* 1.3 54.9 + - + +
31D SER* 3.1 24.5 - - - +
32D GLU* 2.8 27.1 + - - +
33D LEU* 2.8 31.2 + - - +
58D MET* 3.2 6.7 - - - -
67D GLY 5.0 0.9 - - - +
68D GLU* 3.5 28.5 + - + +
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Residues in contact with LYS 30 (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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29D LYS* 1.3 73.6 - - + +
31D SER* 1.3 52.6 + - - +
33D LEU* 3.7 4.2 - - - +
34D LYS* 2.7 34.1 + - - +
51D GLN* 4.3 8.5 - - - +
54D VAL* 3.5 21.6 - - + +
55D ASP* 2.5 42.6 + - - +
58D MET* 2.9 42.3 - - + +
67D GLY* 4.8 7.2 + - - +
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Residues in contact with SER 31 (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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22D GLU* 3.2 27.5 + - - -
29D LYS* 3.3 16.7 - - - +
30D LYS* 1.3 79.9 - - - +
32D GLU* 1.3 61.4 + - - +
34D LYS* 3.2 14.2 - - - +
35D GLU* 2.9 34.6 + - - +
51D GLN* 5.8 4.5 - - - +
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Residues in contact with GLU 32 (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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18D TYR* 3.2 29.4 - - + +
19D SER 3.4 0.9 - - - +
21D ARG* 4.5 2.0 - - + -
22D GLU* 2.7 41.1 + - + +
27D LYS 3.0 4.2 - - - +
28D LEU* 3.3 9.6 - - + -
29D LYS* 2.8 35.0 + - + +
31D SER* 1.3 82.4 + - - +
33D LEU* 1.3 64.6 + - - +
34D LYS 3.0 0.9 - - - -
35D GLU* 3.1 11.4 + - - +
36D LEU* 2.9 24.1 + - - +
501D CA 2.3 31.3 - - - -
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Residues in contact with LEU 33 (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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28D LEU* 4.3 24.5 - - + +
29D LYS 2.8 17.8 + - - +
30D LYS* 3.9 6.1 - - - +
32D GLU* 1.3 70.7 - - - +
34D LYS* 1.3 58.8 + - - +
36D LEU* 4.3 9.6 - - + -
37D ILE* 2.8 57.0 + - + +
54D VAL* 5.7 3.1 - - + +
57D VAL* 4.0 20.0 - - + -
58D MET* 4.5 22.0 - - + +
61D LEU* 4.0 23.1 - - + -
69D CYS* 5.3 2.0 - - + -
74D PHE* 5.4 0.7 - - + -
77D PHE* 4.2 19.3 - - + -
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Residues in contact with LYS 34 (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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30D LYS 2.7 19.3 + - - +
31D SER* 3.2 13.9 - - - +
32D GLU 3.0 0.2 - - - -
33D LEU* 1.3 77.5 - - - +
35D GLU* 1.3 66.1 + - + +
37D ILE* 3.8 3.9 - - - -
38D ASN* 2.9 43.1 + - - +
48D ILE* 4.5 18.2 - - + +
49D LYS* 5.2 8.7 + - - +
51D GLN* 4.5 15.9 - - - +
54D VAL* 4.4 26.0 - - + +
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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
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18D TYR* 3.5 10.7 - - + -
21D ARG* 2.7 41.6 + - - +
22D GLU* 3.7 18.1 - - - +
31D SER* 2.9 21.6 + - - +
32D GLU* 3.1 6.2 + - - +
34D LYS* 1.3 77.9 - - + +
36D LEU* 1.3 57.3 + - - +
38D ASN* 4.7 2.2 - - - +
39D ASN* 2.9 45.7 + - - +
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Residues in contact with LEU 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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4C LEU* 3.8 27.8 - - + -
14D VAL* 4.1 11.0 - - + +
15D PHE* 4.7 0.9 - - - -
18D TYR* 3.3 44.8 - - + -
28D LEU* 4.2 15.9 - - + -
32D GLU 2.9 16.2 + - - +
33D LEU* 3.6 8.1 - - + +
35D GLU* 1.3 73.9 - - - +
37D ILE* 1.3 66.1 + - + +
40D GLU* 2.6 40.7 + - + +
41D LEU* 4.6 6.7 - - + -
74D PHE* 4.1 27.1 - - + -
77D PHE* 5.1 0.2 - - + -
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Residues in contact with ILE 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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33D LEU* 2.8 54.7 + - + +
34D LYS* 3.9 2.5 - - - +
36D LEU* 1.3 73.0 - - + +
38D ASN* 1.3 66.5 + - - +
41D LEU* 2.9 39.5 + - + +
42D SER* 3.5 0.7 + - - -
45D LEU* 3.9 28.0 - - + +
46D GLU 4.6 2.9 - - - +
47D GLU* 5.7 0.2 - - - -
48D ILE* 3.7 35.4 - - + -
57D VAL* 4.3 7.0 - - + -
77D PHE* 4.1 23.3 - - + -
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Residues in contact with ASN 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 LYS* 2.9 33.3 + - - +
35D GLU* 4.0 3.3 - - - +
37D ILE* 1.3 82.0 - - - +
39D ASN* 1.3 69.5 + - - +
42D SER* 3.8 18.4 - - - +
47D GLU* 3.9 16.2 - - + +
48D ILE* 3.0 50.2 + - - +
49D LYS* 5.6 1.0 - - - +
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Residues in contact with ASN 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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2C SER* 4.5 2.6 - - - -
18D TYR* 3.6 15.2 + - - +
21D ARG* 6.0 1.0 - - - +
35D GLU* 2.9 34.6 + - - +
38D ASN* 1.3 84.7 - - - +
40D GLU* 1.3 69.4 + - - +
41D LEU 3.8 0.7 - - - -
42D SER* 4.9 5.6 + - - -
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Residues in contact with GLU 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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2C SER* 2.9 42.3 + - - -
3C GLU* 4.9 1.5 + - + -
4C LEU* 4.0 7.1 - - + +
5C GLU* 3.6 4.4 - - - +
14D VAL* 3.6 26.5 - - + -
17D GLN* 5.3 1.5 - - - +
18D TYR* 2.3 35.5 + - + +
36D LEU* 2.6 35.0 + - + +
39D ASN* 1.3 90.6 - - - +
41D LEU* 1.3 70.6 + - - +
42D SER 3.7 1.3 - - - -
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Residues in contact with LEU 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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4C LEU* 3.5 29.2 - - + -
5C GLU* 3.6 7.2 - - + -
8C MET* 4.0 22.9 - - + -
36D LEU* 4.6 2.0 - - + -
37D ILE* 2.9 24.6 + - + +
40D GLU* 1.3 86.0 - - - +
42D SER* 1.3 66.6 + - - +
43D HIS 2.8 5.7 + - - -
44D PHE* 2.9 22.6 + - + -
45D LEU* 3.2 27.8 + - + +
77D PHE* 3.7 37.2 - - + -
81D VAL* 4.9 5.6 - - + -
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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