Contacts of the helix formed by residues 23 - 45 (chain A) in PDB entry 5XJY
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 CYS 23 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLN 3.0 11.1 + - - +
22A THR* 1.3 88.7 - - - +
24A GLN* 1.3 75.9 + - - +
25A LEU 3.3 1.5 - - - +
26A LEU* 3.2 6.0 + - - +
27A LEU* 2.9 29.8 + - - +
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Residues in contact with GLN 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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18A ARG* 5.9 2.9 - - + -
21A GLN* 2.7 47.2 + - + +
22A THR 4.8 0.2 - - - +
23A CYS* 1.3 85.9 - - - +
25A LEU* 1.3 60.0 + - - +
28A GLU* 2.8 29.5 + - - +
650A TYR* 3.3 24.0 + - - +
654A VAL* 4.5 23.2 - - + +
657A LYS* 4.5 18.2 - - - +
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Residues in contact with LEU 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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18A ARG* 3.3 54.0 - - + +
19A ARG* 4.4 5.2 - - - +
21A GLN* 5.7 0.8 - - - +
22A THR* 5.1 7.3 - - + +
23A CYS 3.3 1.4 - - - +
24A GLN* 1.3 80.2 - - - +
26A LEU* 1.3 67.1 + - + +
28A GLU* 3.3 6.7 - - + +
29A VAL* 2.8 39.0 + - + +
692A PRO* 5.0 17.7 - - + -
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Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR* 3.3 33.9 - - - +
23A CYS* 3.2 8.7 + - - +
25A LEU* 1.3 84.4 - - + +
27A LEU* 1.3 57.7 + - - +
28A GLU 3.2 0.2 - - - -
29A VAL* 4.3 15.5 - - + -
30A ALA* 2.7 42.8 + - + +
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Residues in contact with LEU 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 CYS 2.9 13.6 + - - +
26A LEU* 1.3 75.7 - - - +
28A GLU* 1.3 56.3 + - - +
30A ALA* 4.8 0.9 - - - -
31A TRP* 2.9 60.7 + - + +
650A TYR* 3.4 48.4 - - + +
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Residues in contact with GLU 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 GLN 2.8 22.3 + - - +
25A LEU* 3.3 12.6 - - + +
27A LEU* 1.3 77.4 - - - +
29A VAL* 1.3 67.2 + - + +
31A TRP* 4.2 0.7 - - - +
32A PRO* 3.2 24.8 - - - +
647A ALA 5.5 1.0 - - - +
650A TYR* 3.3 15.3 - - - +
651A SER* 2.4 47.2 + - - -
654A VAL* 4.4 7.9 - - + +
692A PRO* 4.5 25.5 - - + +
693A LEU* 4.5 6.6 - - - +
696A SER* 5.4 5.4 - - - -
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Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 2.8 30.8 + - + +
26A LEU* 4.2 18.2 - - + +
28A GLU* 1.3 82.2 - - + +
30A ALA* 1.3 60.2 + - + +
31A TRP 3.6 0.2 - - - -
32A PRO* 4.2 9.8 - - - +
33A LEU* 3.4 21.0 - - + +
692A PRO* 5.1 7.6 - - + +
695A VAL* 4.7 19.7 - - + -
696A SER* 5.8 4.5 - - - -
699A LEU* 5.0 6.1 - - + +
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Residues in contact with ALA 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 LEU* 2.7 26.1 + - + +
27A LEU* 3.9 1.8 - - - +
29A VAL* 1.3 81.9 - - + +
31A TRP* 1.3 62.3 + - - +
32A PRO 3.6 0.7 - - - -
33A LEU* 3.6 16.7 - - + +
34A PHE* 3.3 21.5 + - - +
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Residues in contact with TRP 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 LEU* 2.9 42.1 + - + +
28A GLU 4.2 0.9 - - - +
30A ALA* 1.3 75.0 - - - +
32A PRO* 1.3 63.9 - - + +
34A PHE* 3.3 21.8 + + + +
35A ILE* 3.0 44.9 + - + +
646A LEU* 3.5 46.9 + - + +
647A ALA* 3.4 28.7 - - + +
650A TYR* 4.5 11.1 - - + +
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Residues in contact with PRO 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 GLU 3.2 17.9 - - - +
29A VAL* 4.2 8.5 - - - +
30A ALA 3.9 0.7 - - - -
31A TRP* 1.3 87.8 - - + +
33A LEU* 1.3 60.8 + - - +
35A ILE* 4.4 3.8 - - + +
36A PHE* 2.9 59.5 + - + +
647A ALA* 3.8 23.3 - - + -
648A TRP* 5.9 0.2 - - - +
696A SER* 4.4 24.0 - - - +
699A LEU* 4.8 10.3 - - + -
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Residues in contact with LEU 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 VAL* 3.4 22.2 - - + +
30A ALA* 3.6 17.5 - - + +
31A TRP 3.3 0.4 - - - -
32A PRO* 1.3 79.9 - - - +
34A PHE* 1.3 57.3 + - - +
36A PHE* 4.6 0.6 - - - +
37A LEU* 3.0 52.6 + - + +
699A LEU* 3.7 35.6 - - + +
703A ILE* 6.3 2.0 - - + -
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Residues in contact with PHE 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 ALA 3.3 9.6 + - - +
31A TRP* 3.3 24.1 + + + +
32A PRO 3.3 0.6 - - - -
33A LEU* 1.3 80.6 - - - +
35A ILE* 1.3 76.2 + - + +
37A LEU* 3.9 2.3 - - - +
38A ILE* 3.0 59.1 + - + +
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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 TRP* 3.0 39.1 + - + +
32A PRO* 4.5 3.8 - - + +
34A PHE* 1.3 93.5 - - + +
36A PHE* 1.3 70.5 + - + +
38A ILE* 3.3 7.9 + - + +
39A LEU* 2.9 29.3 + - + +
643A PHE* 4.5 17.7 - - + +
646A LEU* 3.8 34.3 - - + -
647A ALA* 6.2 1.3 - - + +
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Residues in contact with PHE 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 PRO* 2.9 43.8 + - + +
33A LEU* 4.6 0.4 - - - +
35A ILE* 1.3 82.9 - - + +
37A LEU* 1.3 59.3 + - + +
39A LEU* 4.1 6.0 - - + +
40A ILE* 2.9 29.6 + - - +
643A PHE* 3.2 53.6 - + + -
644A MET* 3.5 22.9 - - + -
647A ALA* 5.1 6.3 - - + -
696A SER 5.6 0.4 - - - -
699A LEU* 5.5 2.5 - - + -
700A LEU* 3.5 36.1 - - + -
703A ILE* 4.0 22.4 - - + +
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Residues in contact with LEU 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 LEU* 3.0 39.8 + - + +
34A PHE* 4.1 3.4 - - - +
36A PHE* 1.3 77.1 - - - +
38A ILE* 1.3 60.4 + - + +
40A ILE* 3.2 17.2 - - + +
41A SER* 3.0 26.0 + - - -
703A ILE* 3.7 30.1 - - + -
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Residues in contact with ILE 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 PHE* 3.0 49.0 + - + +
35A ILE* 3.8 7.9 - - + +
37A LEU* 1.3 77.6 - - + +
39A LEU* 1.3 57.9 + - + +
41A SER* 3.1 12.9 + - - -
42A VAL* 3.0 32.9 + - + +
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Residues in contact with LEU 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* 2.9 19.0 + - + +
36A PHE* 4.1 7.6 - - + +
38A ILE* 1.3 78.7 - - + +
40A ILE* 1.3 57.8 + - - +
42A VAL* 3.0 14.3 + - + +
43A ARG 3.0 22.7 + - - -
632A PHE* 3.6 26.2 - - + -
636A MET* 4.5 9.0 - - + -
643A PHE* 3.6 55.2 - - + -
709A LEU* 5.7 4.0 - - + -
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Residues in contact with ILE 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 PHE 2.9 18.8 + - - +
37A LEU* 3.2 35.9 - - + +
38A ILE 3.3 0.2 - - - -
39A LEU* 1.3 73.4 - - - +
41A SER* 1.3 59.0 + - - +
43A ARG* 3.4 5.3 + - + +
44A LEU* 3.0 26.9 + - + +
703A ILE* 4.4 11.4 - - + +
707A GLY* 3.3 33.7 - - - +
708A ASN 4.5 0.7 - - - +
709A LEU* 3.7 42.8 - - + -
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Residues in contact with SER 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 LEU 3.0 14.6 + - - -
38A ILE* 3.1 18.4 + - - -
40A ILE* 1.3 78.1 - - - +
42A VAL* 1.3 58.4 + - - +
44A LEU* 3.0 6.1 + - - +
45A SER* 3.0 30.5 + - - -
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Residues in contact with VAL 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 ILE* 3.0 21.3 + - + +
39A LEU* 3.0 18.9 + - + +
41A SER* 1.3 73.0 - - - +
43A ARG* 1.3 66.8 + - - +
45A SER* 3.9 10.4 + - - +
46A TYR* 4.1 23.7 + - + -
632A PHE* 3.6 27.0 - - + -
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Residues in contact with ARG 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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39A LEU 3.0 9.3 + - - +
40A ILE* 3.4 12.8 - - + +
41A SER 3.2 0.2 - - - -
42A VAL* 1.3 75.1 - - - +
44A LEU* 1.3 66.5 + - + +
45A SER 3.0 1.1 - - - -
46A TYR* 2.8 45.0 + - - +
47A PRO* 5.8 1.1 - - - -
48A PRO* 5.8 4.5 - - - +
630A ASP* 5.7 5.1 + - - -
632A PHE* 3.3 32.0 - - + +
633A LEU* 3.3 49.1 - - - +
707A GLY 5.3 0.9 - - - +
708A ASN* 3.0 42.7 + - + +
709A LEU* 3.6 27.7 + - + +
711A PRO* 6.0 0.4 - - - +
1472A LYS* 5.4 7.5 - - - +
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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 ILE* 3.0 16.4 + - + +
41A SER* 3.0 7.9 + - - +
43A ARG* 1.3 81.3 - - + +
45A SER* 1.3 58.7 + - - +
46A TYR 3.5 1.3 - - - -
47A PRO* 5.0 8.9 - - + +
708A ASN* 5.0 15.0 - - + +
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Residues in contact with SER 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 SER* 3.0 14.3 + - - -
42A VAL* 4.2 7.9 - - - -
43A ARG 2.9 0.4 + - - -
44A LEU* 1.3 78.9 - - - +
46A TYR* 1.3 81.0 + - - +
47A PRO* 3.3 10.5 - - - +
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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
------------------------------------------------------------
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