Contacts of the helix formed by residues 26 - 37 (chain E) in PDB entry 2XQL
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 PRO 26 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18E SER* 3.6 7.4 - - - +
24E GLN 3.5 0.4 - - - -
25E PHE* 1.3 87.8 - - + +
27E VAL* 1.3 67.5 + - - +
28E GLY 3.2 0.9 - - - +
29E ARG* 3.6 42.2 - - + +
30E VAL* 3.1 22.5 + - + +
52E ALA* 4.7 0.2 - - - -
37F TYR* 4.7 4.5 - - + -
40F TYR* 3.4 43.3 - - + +
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Residues in contact with VAL 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E ARG* 3.6 33.4 - - + +
18E SER* 3.1 30.3 + - - +
23E LEU* 4.2 19.3 - - + -
25E PHE 3.1 7.1 + - - +
26E PRO* 1.3 69.6 - - - +
28E GLY* 1.3 53.3 + - - +
30E VAL* 3.1 5.5 + - - +
31E HIS* 2.8 32.4 + - - +
45E ALA 5.6 0.2 - - - +
48E PRO* 3.7 9.2 - - + +
49E VAL* 4.0 32.5 - - + +
52E ALA* 4.2 10.1 - - + -
121F TYR* 5.2 1.8 - - + -
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Residues in contact with GLY 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E ARG* 3.3 27.0 + - - +
18E SER* 4.7 1.6 + - - -
26E PRO* 3.2 1.0 - - - +
27E VAL* 1.3 80.2 - - - +
29E ARG* 1.3 62.8 + - - +
31E HIS* 2.9 13.9 + - - +
32E ARG* 2.9 12.5 + - - +
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Residues in contact with ARG 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E PRO* 3.4 33.0 + - + +
27E VAL 3.3 0.6 - - - -
28E GLY* 1.3 74.3 - - - +
30E VAL* 1.3 63.4 + - - +
32E ARG* 2.9 12.1 + - + +
33E LEU* 2.9 36.0 + - + +
36F SER* 2.6 46.4 + - - +
37F TYR* 3.9 22.8 - - - -
39F ILE* 6.2 0.6 - - - +
40F TYR* 3.7 21.3 + - - -
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Residues in contact with VAL 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E PHE* 5.7 1.3 - - + -
26E PRO* 3.1 18.6 + - + +
27E VAL 3.5 7.0 - - - +
29E ARG* 1.3 79.6 - - + +
31E HIS* 1.3 61.2 + - - +
33E LEU* 3.4 6.8 + - - +
34E LEU* 3.0 48.4 + - + +
48E PRO* 3.7 24.5 - - + +
51E LEU* 4.0 10.1 - - + -
52E ALA* 4.1 17.5 - - + -
55E LEU* 4.3 13.9 - - + -
37F TYR* 4.7 11.4 - - + +
70F PHE* 4.0 10.5 - - + -
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Residues in contact with HIS 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E ARG* 3.6 28.1 + - - +
27E VAL 2.8 12.5 + - - +
28E GLY 2.9 12.3 + - - +
30E VAL* 1.3 77.5 - - - +
32E ARG* 1.3 59.0 + - - +
34E LEU* 3.4 6.0 + - - +
35E ARG* 3.1 57.7 + - - +
43E VAL* 3.6 26.7 + - + +
44E GLY 3.8 8.1 + - - -
45E ALA* 4.9 3.2 - - - -
48E PRO* 3.2 35.6 - - + +
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Residues in contact with ARG 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E GLY 2.9 9.7 + - - +
29E ARG* 2.9 13.4 + - - +
31E HIS* 1.3 76.1 + - - +
33E LEU* 1.3 68.8 + - - +
35E ARG* 3.1 22.8 + - + +
36E LYS* 2.8 70.0 + - + +
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Residues in contact with LEU 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E ARG* 2.9 31.0 + - + +
30E VAL* 3.7 4.5 - - - +
32E ARG* 1.3 87.5 - - + +
34E LEU* 1.3 63.1 + - - +
36E LYS* 4.5 12.6 - - + -
37E GLY* 3.1 22.7 + - - -
39E TYR* 4.2 4.9 - - - -
37F TYR* 3.7 23.6 - - + +
67F ASN* 5.2 7.0 - - - +
70F PHE* 3.4 32.5 - - + -
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Residues in contact with LEU 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E VAL* 3.0 47.2 + - + +
31E HIS* 3.7 7.0 - - - +
32E ARG 3.2 0.2 - - - -
33E LEU* 1.3 78.0 - - - +
35E ARG* 1.3 62.8 + - - +
39E TYR* 3.8 27.4 + - + +
40E ALA 4.4 0.9 + - - -
43E VAL* 3.8 27.3 - - + +
47E ALA* 5.3 4.0 - - + -
48E PRO* 4.9 8.3 - - + -
51E LEU* 3.6 17.9 - - + -
70F PHE* 3.7 7.6 - - + -
74F ALA* 4.0 25.6 - - + -
89F ILE* 4.5 24.0 - - + -
94F ILE* 5.1 3.4 - - + -
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Residues in contact with ARG 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E HIS* 3.1 51.0 + - + +
32E ARG* 3.2 23.1 - - - +
34E LEU* 1.3 78.7 - - - +
36E LYS* 1.3 65.1 + - - +
38E ASN* 3.1 20.4 + - - -
40E ALA 4.9 5.8 - - - +
42E ARG* 6.4 0.9 - - - -
43E VAL* 4.1 13.6 - - + +
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Residues in contact with LYS 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E ARG* 2.8 62.8 + - + +
33E LEU* 4.2 10.5 - - + +
35E ARG* 1.3 73.5 - - - +
37E GLY* 1.4 55.5 + - - +
38E ASN* 2.9 28.4 + - - +
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Residues in contact with GLY 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E LEU 3.1 10.2 + - - -
35E ARG 3.2 0.2 - - - -
36E LYS* 1.4 77.0 - - - +
38E ASN* 1.3 67.8 + - - +
39E TYR* 3.1 31.8 + - - -
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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