Contacts of the helix formed by residues 33 - 45 (chain A) in PDB entry 1P4X
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 THR 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A LYS* 6.5 1.3 - - - -
31A ASP 4.7 4.7 - - - +
32A MET* 1.3 76.4 - - - +
34A ILE* 1.3 64.1 + - - +
35A LYS* 3.6 8.9 + - - +
36A GLU* 3.0 46.5 + - - +
37A PHE* 3.0 21.0 + - - -
70A HIS* 4.5 9.2 + - + -
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Residues in contact with ILE 34 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A PHE* 3.6 35.0 - - + +
23A LYS* 3.5 52.5 - - + +
26A VAL* 5.2 9.2 - - + -
27A LYS* 5.3 7.0 - - + +
32A MET 3.8 1.1 + - - +
33A THR* 1.3 71.2 - - - +
35A LYS* 1.3 66.1 + - - +
37A PHE* 3.1 14.4 + - + +
38A ILE* 3.0 27.7 + - + +
111A PHE* 5.1 2.2 - - + -
136A PHE* 3.9 27.6 - - + -
140A MET* 4.5 3.6 - - + -
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Residues in contact with LYS 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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33A THR* 3.3 8.2 + - - +
34A ILE* 1.3 78.8 - - - +
36A GLU* 1.3 58.5 + - - +
38A ILE* 3.2 3.0 + - - +
39A LEU* 3.0 33.7 + - + +
62A TYR* 4.0 46.7 - - + +
66A ASP* 3.0 38.9 + - - +
67A LEU* 4.7 4.7 - - + -
70A HIS* 3.0 37.9 + - + +
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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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31A ASP 4.6 1.4 - - - +
32A MET* 3.4 24.9 - - + +
33A THR* 3.0 44.5 + - - +
35A LYS* 1.3 77.8 - - - +
37A PHE* 1.3 60.3 + - - +
39A LEU* 3.4 7.9 + - - +
40A LEU* 3.2 28.4 + - - +
70A HIS* 3.2 31.4 + - + +
73A VAL* 3.8 26.2 - - + +
74A LEU* 4.1 18.7 - - + +
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Residues in contact with PHE 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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26A VAL* 5.9 3.8 - - + -
30A VAL* 3.9 17.0 - - + -
32A MET* 3.4 40.1 - - + -
33A THR 3.0 25.4 + - - -
34A ILE* 3.1 10.9 + - + +
36A GLU* 1.3 76.1 - - - +
38A ILE* 1.3 58.0 + - - +
40A LEU* 3.6 4.9 + - + +
41A THR* 2.8 31.5 + - - -
107A ARG* 3.8 40.6 - - + -
108A VAL* 5.3 0.7 - - - +
110A LEU* 4.6 4.5 - - + -
111A PHE* 3.5 53.6 - + + +
114A ILE* 4.2 12.6 - - + -
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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 ILE* 3.0 20.5 + - + +
35A LYS 3.6 6.7 - - - +
37A PHE* 1.3 76.3 - - - +
39A LEU* 1.3 60.8 + - - +
41A THR* 3.3 5.4 + - - -
42A TYR* 3.0 24.3 + - - +
60A LEU* 4.8 2.7 - - + -
62A TYR* 3.6 35.0 - - + +
111A PHE* 4.7 3.6 - - + -
136A PHE* 3.8 29.8 - - + -
137A LEU* 3.2 31.6 - - + +
140A MET* 3.7 28.5 - - + -
141A MET* 4.3 3.1 - - + -
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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 LYS* 3.0 22.2 + - + +
36A GLU* 3.7 8.1 - - - +
38A ILE* 1.3 76.2 - - - +
40A LEU* 1.3 57.7 + - - +
42A TYR* 3.2 5.9 + - + +
43A LEU* 2.9 36.3 + - + +
56A ILE* 4.2 13.5 - - + -
60A LEU* 3.9 20.9 - - + -
62A TYR* 5.0 2.9 - - + -
67A LEU* 3.9 26.7 - - + -
70A HIS* 3.5 35.4 - - + -
71A ILE* 4.7 10.1 - - + -
74A LEU* 3.9 20.4 - - + -
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Residues in contact with LEU 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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32A MET* 3.5 40.4 - - + -
36A GLU 3.2 12.9 + - - +
37A PHE* 3.8 6.1 - - + +
39A LEU* 1.3 74.3 - - - +
41A THR* 1.3 64.7 + - - +
43A LEU* 3.4 5.1 + - + -
44A PHE* 2.9 25.3 + - - +
74A LEU* 3.9 23.8 - - + -
79A TYR* 3.9 31.6 - - + -
104A ILE* 3.6 20.8 - - + +
107A ARG* 3.8 17.0 - - + -
108A VAL* 3.9 13.0 - - + -
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Residues in contact with THR 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 PHE 2.8 22.6 + - - -
38A ILE* 3.5 8.5 - - - -
39A LEU 3.2 0.2 - - - -
40A LEU* 1.3 76.2 - - - +
42A TYR* 1.3 65.8 + - - +
44A PHE* 3.3 1.8 + - - +
45A HIS* 3.2 41.0 + - + -
108A VAL* 4.0 13.3 - - + +
111A PHE* 3.7 8.1 - - - -
133A SER* 3.5 50.6 - - - +
134A LYS* 3.9 3.6 - - - +
137A LEU* 4.4 9.2 - - + -
249A PHE* 5.1 1.1 - - + -
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Residues in contact with TYR 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 14.0 + - - +
39A LEU* 3.4 9.4 - - + +
41A THR* 1.3 79.6 - - - +
43A LEU* 1.3 74.5 + - + +
45A HIS 3.2 8.3 + - - -
46A GLN* 3.2 38.4 + - - +
51A LEU* 4.0 0.8 - - + +
55A LYS* 3.1 35.2 + - - +
56A ILE* 3.9 31.0 - - + -
59A ASP* 3.3 34.1 + - + -
60A LEU* 3.8 23.1 - - + -
137A LEU* 4.3 7.4 - - + +
248A VAL* 4.3 7.6 - - + -
249A PHE* 3.7 27.2 - + - -
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Residues in contact with LEU 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* 2.9 23.3 + - + +
40A LEU* 3.8 7.6 - - + +
42A TYR* 1.3 90.8 - - + +
44A PHE* 1.3 61.2 + - - +
46A GLN* 3.5 24.0 - - - +
51A LEU* 4.2 8.5 - - + -
56A ILE* 4.1 20.6 - - + -
71A ILE* 5.8 1.6 - - + -
74A LEU* 4.3 18.6 - - + -
80A ILE* 3.8 32.8 - - + -
94A ILE* 5.1 2.0 - - + -
96A ILE* 4.1 18.6 - - + +
101A ARG* 3.3 16.3 + - - -
104A ILE* 4.6 9.2 - - + -
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Residues in contact with PHE 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 LEU 2.9 17.5 + - - +
41A THR 3.6 3.8 - - - +
42A TYR 3.2 0.2 - - - -
43A LEU* 1.3 76.7 - - - +
45A HIS* 1.3 90.8 + + - +
46A GLN 3.0 7.6 + - - -
101A ARG* 3.1 30.4 + - + +
104A ILE* 3.9 10.5 - - + +
105A ALA* 3.5 43.3 - - + -
108A VAL* 4.0 16.8 - - + -
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Residues in contact with HIS 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 THR* 3.2 32.2 + - + -
42A TYR 3.2 3.2 + - - -
44A PHE* 1.3 101.1 - + - +
46A GLN* 1.3 63.7 + - - +
47A GLN* 4.7 0.2 - - - +
108A VAL* 5.0 1.2 - - - +
133A SER* 4.2 14.1 + - - -
134A LYS* 2.9 45.4 + - + +
249A PHE* 3.1 41.3 - + + -
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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