Contacts of the helix formed by residues 27 - 38 (chain A) in PDB entry 5HNK
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 GLY 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A VAL* 3.1 13.9 + - - -
26A ASP* 1.3 68.3 + - - +
28A THR* 1.3 58.8 + - - +
30A LEU* 3.5 1.0 + - - -
31A GLY* 3.0 18.7 + - - -
47A TYR* 2.6 31.1 + - - -
65A VAL* 4.3 2.2 - - - -
66A LEU 2.7 23.3 + - - -
108A LEU* 4.3 0.2 - - - +
112A PHE* 3.8 9.8 - - - -
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Residues in contact with THR 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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26A ASP* 3.4 1.0 + - - -
27A GLY* 1.3 74.9 - - - +
29A ASN* 1.3 64.6 + - - +
31A GLY* 3.2 3.5 + - - -
32A PHE* 3.2 49.4 + - + -
66A LEU 3.9 1.6 + - - -
67A GLY* 3.6 4.2 - - - -
68A ASP* 2.8 53.9 + - + +
104A PHE* 5.3 0.2 - - - -
105A PHE* 5.7 2.7 - - + -
108A LEU* 4.5 19.4 - - + +
112A PHE* 4.0 7.2 - - - -
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Residues in contact with ASN 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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26A ASP* 3.3 31.5 + - - +
28A THR* 1.3 78.2 - - - +
30A LEU* 1.3 63.4 + - - +
32A PHE* 3.3 22.8 + - - +
33A ARG* 3.6 8.0 + - - +
68A ASP* 4.9 0.4 + - - -
150A ILE 4.7 0.2 - - - +
151A SER* 3.5 6.3 - - - -
152A THR* 2.7 54.9 + - - +
153A LYS* 3.6 26.4 - - - +
1X A 5.5 4.0 + - - +
2X A 4.0 6.3 + - - -
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Residues in contact with LEU 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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25A VAL* 4.1 12.1 - - + -
26A ASP 2.9 16.6 + - - +
27A GLY* 3.8 6.5 - - - +
28A THR 3.3 0.2 - - - -
29A ASN* 1.3 77.8 + - - +
31A GLY* 1.3 61.8 + - - +
33A ARG* 3.1 28.4 + - - +
34A PHE* 3.4 20.7 - - + -
47A TYR* 4.0 15.3 - - + +
50A THR* 4.6 7.6 - - + -
51A ILE* 3.7 35.4 - - + -
54A LEU* 5.1 3.1 - - + -
150A ILE* 5.3 5.6 - - + +
152A THR* 6.5 0.2 - - - -
169A PHE* 3.6 36.8 - - + -
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Residues in contact with GLY 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 GLY 3.0 15.8 + - - -
28A THR 3.2 5.7 + - - -
30A LEU* 1.3 76.8 - - - +
32A PHE* 1.3 55.4 + - - +
34A PHE* 3.1 20.3 + - - +
35A LYS 3.2 9.2 + - - -
43A PHE* 4.9 0.9 - - - -
47A TYR* 3.7 9.8 - - - -
104A PHE* 3.3 15.9 - - - -
108A LEU* 3.9 19.1 - - - -
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Residues in contact with PHE 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 THR* 3.2 44.5 + - + -
29A ASN* 3.6 13.9 - - - +
30A LEU 3.3 0.8 - - - -
31A GLY* 1.3 73.1 - - - +
33A ARG* 1.3 60.7 + - - +
35A LYS* 3.6 17.9 + - + -
36A HIS* 2.7 31.6 + + - -
104A PHE* 3.7 27.6 - + - -
105A PHE* 4.8 14.6 - + - -
153A LYS* 5.8 3.4 - - - -
1X A 3.5 60.8 - - - +
2X A 5.9 0.2 - - - -
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Residues in contact with ARG 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 ASN 3.6 5.6 + - - +
30A LEU* 3.1 19.3 + - + +
32A PHE* 1.3 77.6 - - - +
34A PHE* 1.3 83.2 + - + +
36A HIS* 3.3 4.5 + - - +
37A ASN* 3.1 39.4 + - + +
50A THR* 4.6 8.1 + - - +
169A PHE* 3.3 63.7 + - + +
172A ARG* 3.8 12.9 - - - +
1X A 4.3 16.5 - - + +
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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 LEU* 3.4 32.5 - - + -
31A GLY 3.1 8.7 + - - +
33A ARG* 1.3 90.2 - - + +
35A LYS* 1.3 58.4 + - - +
36A HIS 3.3 0.4 - - - -
37A ASN* 2.9 38.6 - - - +
38A ASN* 3.1 16.2 - - - +
43A PHE* 3.8 45.6 - + + +
46A SER* 3.6 29.8 - - - -
47A TYR* 3.8 27.4 - + - -
50A THR* 3.4 24.2 - - - -
104A PHE* 4.9 0.2 - - - -
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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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31A GLY 3.2 5.4 + - - +
32A PHE* 3.7 26.7 - - + +
33A ARG 3.2 0.6 - - - -
34A PHE* 1.3 77.8 - - - +
36A HIS* 1.3 74.4 + - + +
38A ASN 4.1 8.2 - - - +
39A SER* 5.1 4.5 + - - -
43A PHE* 5.6 0.2 - - - -
100A LEU* 4.9 12.6 - - - -
101A ASP* 2.7 32.9 + - - +
104A PHE* 3.7 54.3 - - + -
105A PHE* 5.8 1.0 - - - -
1X A 5.1 4.3 - - - -
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Residues in contact with HIS 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 PHE* 2.7 27.2 + - + -
33A ARG 3.3 4.1 + - - +
35A LYS* 1.3 100.8 - - + +
37A ASN* 1.3 62.9 + - - +
38A ASN* 3.4 2.4 - - - -
1X A 3.3 73.3 + + + +
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Residues in contact with ASN 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 ARG* 3.1 30.5 + - + +
34A PHE* 2.9 42.8 - - - +
36A HIS* 1.3 77.2 - - - +
38A ASN* 1.3 91.3 + - - +
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Residues in contact with ASN 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* 3.1 19.2 - - - +
35A LYS 4.1 6.3 - - - +
36A HIS 3.4 1.9 - - - -
37A ASN* 1.3 113.8 + - - +
39A SER* 1.3 58.7 + - - +
40A LYS* 3.7 34.6 - - + +
41A LYS* 4.1 29.4 + - - +
43A PHE* 5.8 4.2 - - - +
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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