Contacts of the helix formed by residues 23 - 42 (chain A) in PDB entry 4UY3
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 MET 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ARG* 1.3 70.0 + - - +
25A SER* 3.3 7.6 + - - +
26A ASN* 3.0 47.0 + - - +
27A LYS* 3.1 43.6 + - + +
100A PHE* 4.0 26.9 - - + -
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Residues in contact with ARG 24 (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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23A MET* 1.3 80.8 - - - +
25A SER* 1.3 63.0 + - - +
26A ASN 3.1 0.2 + - - -
27A LYS* 3.1 2.3 + - - +
28A ARG* 2.8 45.8 + - - +
95A LEU* 3.8 35.6 - - + +
96A ASP* 3.3 40.4 + - - +
98A PHE* 3.3 39.1 - - + -
100A PHE* 4.3 4.5 - - + -
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Residues in contact with SER 25 (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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23A MET 3.3 6.7 + - - +
24A ARG* 1.3 78.6 - - - +
26A ASN* 1.3 62.2 + - - +
28A ARG* 3.4 35.3 + - - +
29A GLN* 3.9 9.7 + - - +
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Residues in contact with ASN 26 (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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23A MET* 3.0 42.1 + - - +
24A ARG 3.1 0.2 - - - -
25A SER* 1.3 82.1 + - - +
27A LYS* 1.3 62.8 + - - +
28A ARG 3.3 0.7 - - - -
29A GLN* 3.2 37.6 + - - +
30A ILE* 4.0 8.8 - - - +
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Residues in contact with LYS 27 (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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23A MET* 3.1 34.1 + - + +
24A ARG 3.1 7.7 + - - +
26A ASN* 1.3 77.9 + - - +
28A ARG* 1.3 64.7 + - - +
29A GLN 3.0 2.7 - - - -
30A ILE* 3.1 31.5 + - + +
31A ILE* 3.5 10.9 + - - +
95A LEU* 3.7 24.0 - - + -
100A PHE* 4.2 33.7 - - + +
103A SER* 6.0 2.0 - - - +
104A GLN* 5.0 13.0 + - + +
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Residues in contact with ARG 28 (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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24A ARG* 2.8 39.4 + - - +
25A SER* 3.4 32.0 - - - +
26A ASN 3.3 0.4 - - - -
27A LYS* 1.3 76.6 - - - +
29A GLN* 1.3 56.5 + - - +
31A ILE* 3.3 11.0 + - + +
32A GLU* 2.9 45.0 + - + +
92A GLU* 5.1 17.2 + - + +
95A LEU* 4.0 18.3 - - - +
96A ASP* 5.2 8.9 + - - +
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Residues in contact with GLN 29 (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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25A SER 3.9 6.1 + - - +
26A ASN* 3.2 38.3 + - - +
27A LYS 3.0 0.8 - - - -
28A ARG* 1.3 75.5 - - - +
30A ILE* 1.3 70.6 + - + +
32A GLU* 3.3 11.8 + - - +
33A LYS* 2.9 24.9 + - - +
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Residues in contact with ILE 30 (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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26A ASN 4.0 11.9 - - - +
27A LYS* 3.1 26.4 + - + +
29A GLN* 1.3 81.2 - - + +
31A ILE* 1.3 65.7 + - + +
33A LYS* 3.3 7.9 + - + +
34A ALA* 3.2 19.4 + - - +
104A GLN* 4.3 24.5 - - - +
107A ILE* 4.3 21.0 - - + +
111A ASN* 6.0 0.4 - - - +
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Residues in contact with ILE 31 (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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27A LYS 3.9 7.4 - - - +
28A ARG* 3.3 13.6 + - + +
29A GLN 3.2 0.4 - - - -
30A ILE* 1.3 77.6 - - + +
32A GLU* 1.3 62.4 + - + +
34A ALA* 3.1 6.6 + - - +
35A ILE* 3.1 23.7 + - + +
88A ILE* 4.0 23.8 - - + +
91A ALA* 3.8 31.9 - - + +
92A GLU* 4.1 25.6 - - + +
95A LEU* 4.0 23.1 - - + -
103A SER* 4.2 4.7 - - - +
107A ILE* 4.1 24.7 - - + -
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Residues in contact with GLU 32 (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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28A ARG* 2.9 38.0 + - + +
29A GLN* 3.3 11.1 + - - +
31A ILE* 1.3 74.6 - - + +
33A LYS* 1.3 66.0 + - - +
35A ILE* 3.1 16.8 + - + +
36A GLU* 3.0 40.0 + - - +
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Residues in contact with LYS 33 (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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29A GLN 2.9 13.5 + - - +
30A ILE* 3.5 10.5 - - - +
32A GLU* 1.3 75.4 - - - +
34A ALA* 1.3 57.7 + - - +
36A GLU* 3.4 14.8 + - + +
37A ARG* 3.0 28.2 + - - +
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Residues in contact with ALA 34 (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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30A ILE 3.2 10.4 + - - +
31A ILE 3.1 11.3 + - - +
33A LYS* 1.3 76.2 - - - +
35A ILE* 1.3 59.0 + - - +
37A ARG* 3.2 7.9 + - - +
38A LYS* 2.9 29.1 + - - +
88A ILE* 4.4 13.2 - - + +
107A ILE* 4.4 26.5 - - + -
110A ALA* 5.3 1.1 - - + -
111A ASN* 4.8 7.0 - - - +
114A MET* 3.9 15.2 - - + +
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Residues in contact with ILE 35 (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 ILE* 3.1 19.0 + - + +
32A GLU* 3.1 17.5 + - + +
34A ALA* 1.3 74.2 - - - +
36A GLU* 1.3 61.2 + - + +
38A LYS* 3.3 9.1 + - + +
39A ASN* 3.1 40.9 + - - +
88A ILE* 3.9 30.3 - - + -
92A GLU* 4.2 15.7 - - - +
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Residues in contact with GLU 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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32A GLU* 3.0 31.7 + - - +
33A LYS* 3.7 18.5 - - + +
35A ILE* 1.3 76.5 - - + +
37A ARG* 1.3 63.1 - - - +
39A ASN* 3.5 7.2 + - - +
40A GLU* 3.1 28.4 + - - +
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Residues in contact with ARG 37 (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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33A LYS 3.0 17.7 + - - +
34A ALA* 3.2 6.9 + - - +
36A GLU* 1.3 75.8 - - - +
38A LYS* 1.3 65.3 + - - +
40A GLU* 3.4 13.4 + - + +
41A ILE* 3.1 35.8 + - + +
111A ASN* 2.9 51.9 + - - +
114A MET* 3.6 21.5 - - - +
115A ASP* 2.7 37.1 + - - +
118A GLU* 3.5 29.4 + - - +
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Residues in contact with LYS 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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34A ALA 2.9 15.4 + - - +
35A ILE* 3.3 9.8 + - + +
37A ARG* 1.3 75.6 - - - +
39A ASN* 1.3 74.6 + - - +
40A GLU 3.1 0.5 + - - -
41A ILE* 3.2 6.1 + - - +
42A GLU* 2.8 47.7 + - - +
81A LEU* 4.2 18.6 - - + -
84A VAL* 4.4 20.6 - - + -
85A GLU* 3.7 36.5 + - - +
88A ILE* 4.7 7.9 - - + -
114A MET* 3.7 15.4 - - - -
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Residues in contact with ASN 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* 3.1 35.7 + - - +
36A GLU* 4.0 6.5 - - - +
37A ARG 3.3 0.2 - - - -
38A LYS* 1.3 84.1 + - - +
40A GLU* 1.3 60.1 + - - +
42A GLU* 3.8 27.1 - - - +
43A THR* 3.5 17.3 - - - +
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Residues in contact with GLU 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 GLU* 3.1 18.7 + - - +
37A ARG* 3.7 17.4 - - + +
38A LYS 3.1 0.6 - - - -
39A ASN* 1.3 77.6 - - - +
41A ILE* 1.3 69.3 + - + +
42A GLU 3.2 0.4 - - - -
43A THR* 2.5 35.0 + - - +
44A LEU* 3.9 2.3 + - - +
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Residues in contact with ILE 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 ARG* 3.1 19.8 + - + +
38A LYS* 3.2 13.7 - - - +
40A GLU* 1.3 77.9 - - + +
42A GLU* 1.3 62.0 + - - +
43A THR 3.0 6.4 + - - -
44A LEU* 3.3 34.8 + - + +
46A PHE* 5.1 0.3 - - - -
81A LEU* 4.4 11.4 - - + -
114A MET* 3.5 40.4 - - + +
117A TYR* 3.6 33.6 + - + -
118A GLU* 3.8 28.3 - - + +
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Residues in contact with GLU 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 LYS* 2.8 52.3 + - - +
39A ASN* 3.8 20.1 - - - +
40A GLU 3.2 0.2 - - - -
41A ILE* 1.3 77.8 - - - +
43A THR* 1.3 59.2 + - + +
44A LEU 3.5 2.8 + - - +
81A LEU* 4.1 27.0 - - + +
117A TYR* 5.1 2.0 - - - -
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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