Contacts of the helix formed by residues 28 - 39 (chain A) in PDB entry 4PCW
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 SER 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ASP* 4.4 12.3 + - - +
23A ASN* 5.5 3.1 - - - -
27A LEU* 1.3 75.7 - - - +
29A LYS* 1.3 66.6 + - - +
30A LYS* 3.7 5.6 + - - +
31A GLU* 3.0 35.9 + - - +
32A LEU* 2.9 22.2 + - - +
57A MET* 4.2 2.5 - - - -
66A LYS 4.6 7.6 - - - -
67A LYS* 4.9 6.0 - - - +
102A CA 3.8 1.6 - - - -
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Residues in contact with LYS 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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28A SER* 1.3 74.9 - - - +
30A LYS* 1.3 56.8 + - - +
32A LEU* 3.4 2.6 + - - +
33A LYS* 3.0 27.8 + - - +
53A VAL* 4.0 15.9 - - + +
54A ASP* 2.9 56.7 + - - +
57A MET* 4.0 37.6 - - + +
66A LYS* 4.8 11.3 + - - +
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Residues in contact with LYS 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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28A SER* 3.3 6.6 + - - +
29A LYS* 1.3 80.5 - - - +
31A GLU* 1.3 58.5 + - + +
33A LYS* 3.3 17.5 + - + +
34A GLU* 2.9 34.1 + - + +
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Residues in contact with GLU 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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17A TYR* 3.1 30.6 - - - +
18A SER 3.4 0.6 - - - +
20A LYS* 3.3 13.3 - - + +
21A ASP* 2.9 39.5 + - - +
26A THR 3.4 4.2 - - - +
27A LEU* 3.4 7.8 - - + -
28A SER* 3.0 28.3 + - - +
29A LYS 3.3 0.4 - - - -
30A LYS* 1.3 78.3 - - + +
32A LEU* 1.3 59.9 + - - +
34A GLU* 3.3 9.2 - - - +
35A LEU* 2.9 28.1 + - - +
102A CA 2.3 23.8 - - - -
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Residues in contact with LEU 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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27A LEU* 4.3 24.3 - - + +
28A SER 2.9 17.6 + - - +
29A LYS* 3.7 4.7 - - - +
31A GLU* 1.3 74.5 - - - +
33A LYS* 1.3 54.7 + - - +
35A LEU* 3.0 11.6 + - + +
36A LEU* 2.6 68.9 + - + +
53A VAL* 5.1 4.0 - - + +
56A PHE* 4.6 2.0 - - + -
57A MET* 3.8 42.2 - - + +
60A LEU* 4.4 20.6 - - + -
68A ILE* 4.4 7.9 - - + -
73A PHE* 5.8 1.6 - - + -
76A MET* 5.1 3.4 - - + -
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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 LYS 3.0 14.5 + - - +
30A LYS* 3.5 21.8 - - - +
31A GLU 3.3 0.2 - - - -
32A LEU* 1.3 76.7 - - - +
34A GLU* 1.3 60.8 + - - +
36A LEU* 3.3 12.4 + - - +
37A GLU* 2.3 67.0 + - + +
45A LYS* 5.2 0.9 - - - +
49A ASP* 3.2 35.3 + - - +
50A PRO* 4.2 7.9 - - - +
53A VAL* 3.7 22.6 - - + +
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Residues in contact with GLU 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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17A TYR* 3.2 18.7 - - + -
20A LYS* 3.1 29.4 - - + +
30A LYS* 2.9 21.1 + - + +
31A GLU* 3.3 12.8 - - - +
32A LEU 3.2 0.2 - - - -
33A LYS* 1.3 75.6 - - - +
35A LEU* 1.3 62.3 + - - +
37A GLU* 3.1 20.6 + - - +
38A LYS* 3.0 50.3 + - - +
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Residues in contact with LEU 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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13A LEU* 4.2 13.0 - - + +
14A PHE* 4.7 2.9 - - - -
17A TYR* 3.5 40.8 - - + -
27A LEU* 3.9 27.4 - - + -
31A GLU 2.9 13.5 + - - +
32A LEU* 3.0 12.3 + - + +
34A GLU* 1.3 74.3 - - - +
36A LEU* 1.3 63.6 + - + +
37A GLU 3.1 1.0 + - - -
39A GLU* 3.2 29.5 + - + +
40A PHE* 3.1 42.5 + - + -
73A PHE* 4.2 13.7 - - + -
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Residues in contact with LEU 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 LEU* 2.6 50.2 + - + +
33A LYS* 3.7 7.9 - - - +
35A LEU* 1.3 73.1 - - - +
37A GLU* 1.3 57.7 + - - +
38A LYS 3.5 0.2 - - - -
40A PHE* 2.7 55.0 - - + +
41A ARG* 3.7 5.9 - - - +
44A LEU* 4.8 1.6 - - + -
45A LYS* 3.5 43.7 - - + +
47A PRO* 4.5 7.3 - - - +
53A VAL* 4.9 4.7 - - + -
56A PHE* 4.1 29.2 - - + -
76A MET* 4.7 0.2 - - + -
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Residues in contact with GLU 37 (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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33A LYS* 2.3 56.7 + - + +
34A GLU* 3.5 15.0 - - - +
35A LEU 3.0 0.8 - - - -
36A LEU* 1.3 81.4 - - + +
38A LYS* 1.3 65.6 + - + +
41A ARG* 3.6 39.2 + - - +
45A LYS* 5.8 1.3 - - - +
47A PRO* 5.6 1.8 - - + -
49A ASP* 3.0 27.8 - - + +
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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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16A GLN* 5.6 1.3 - - - +
17A TYR* 3.4 26.0 - - + +
34A GLU* 3.0 40.6 - - - +
35A LEU 3.2 1.4 + - - -
36A LEU 3.5 0.4 - - - -
37A GLU* 1.3 89.6 + - + +
39A GLU* 1.3 68.2 + - + +
40A PHE* 3.3 4.4 + - - -
41A ARG* 4.7 4.2 + - - +
2B THR* 5.5 2.9 - - - +
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Residues in contact with GLU 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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13A LEU* 3.1 36.9 - - + +
16A GLN* 4.3 9.7 + - - +
17A TYR* 3.2 36.9 + - + +
35A LEU* 3.2 10.9 + - + +
38A LYS* 1.3 82.1 - - - +
40A PHE* 1.3 75.2 + - + +
1B SER 4.2 3.0 - - - +
2B THR* 3.5 42.8 - - - +
3B LEU* 4.1 3.3 + - + -
4B LEU* 4.4 5.4 + - - +
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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