Contacts of the helix formed by residues 30 - 41 (chain A) in PDB entry 2HH3
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 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ILE* 3.1 30.9 + - - +
28A ARG 2.9 2.6 + - - -
29A SER* 1.3 78.8 - - - +
31A GLU* 1.3 58.9 + - - +
32A MET 3.2 2.7 - - - -
33A ILE* 3.1 13.3 - - - +
34A LYS* 2.9 38.5 + - - +
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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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28A ARG* 2.8 26.2 + - + +
29A SER* 3.2 6.6 - - - -
30A GLY* 1.3 78.3 - - - +
32A MET* 1.3 56.5 + - - +
34A LYS* 3.3 13.8 + - + +
35A LYS* 3.0 27.3 + - + +
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Residues in contact with MET 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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24A VAL* 3.8 11.7 - - + +
25A VAL* 3.5 12.8 - - - +
26A ILE 3.3 15.8 + - - +
27A GLY* 4.0 7.4 - - - +
28A ARG 4.9 0.2 - - - +
30A GLY 3.2 0.4 - - - -
31A GLU* 1.3 80.5 + - - +
33A ILE* 1.3 56.6 + - - +
35A LYS* 3.0 18.3 + - + +
36A ILE* 3.0 40.8 + - + +
77A LEU* 4.7 16.8 - - + -
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Residues in contact with ILE 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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25A VAL* 3.2 23.4 + - + +
26A ILE* 3.8 21.5 - - + -
30A GLY* 3.1 20.3 + - - +
32A MET* 1.3 76.2 - - - +
34A LYS* 1.3 63.3 + - + +
36A ILE* 3.3 6.8 + - + +
37A GLN* 2.9 43.1 + - - +
44A ILE* 3.5 48.0 - - + +
46A PHE* 3.7 27.4 - - + -
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Residues in contact with LYS 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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29A SER* 3.1 27.7 + - - -
30A GLY* 2.9 23.5 + - - +
31A GLU* 3.5 10.4 - - + +
32A MET 3.2 0.2 - - - -
33A ILE* 1.3 79.6 - - + +
35A LYS* 1.3 53.9 + - - +
37A GLN* 3.3 13.0 + - - +
38A ASN* 2.7 34.7 + - - +
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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 GLU 3.0 13.9 + - - +
32A MET* 3.0 21.5 + - + +
34A LYS* 1.3 74.3 - - - +
36A ILE* 1.3 58.4 + - + +
38A ASN* 3.9 11.2 - - + +
39A ASP* 2.6 70.7 + - - +
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Residues in contact with ILE 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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25A VAL* 4.1 24.0 - - + +
32A MET* 3.0 25.5 + - + +
33A ILE* 3.4 22.7 - - + +
35A LYS* 1.3 74.5 - - + +
37A GLN* 1.3 60.3 + - - +
38A ASN 3.1 0.2 + - - -
39A ASP* 3.2 2.6 + - - +
40A ALA* 2.8 36.8 + - + +
44A ILE* 3.6 19.3 - - + -
70A ALA 4.9 1.1 - - - +
73A ILE* 3.6 40.0 - - + +
74A ILE* 4.3 9.9 - - + -
77A LEU* 4.9 8.5 - - + -
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Residues in contact with GLN 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 ILE* 2.9 34.2 + - - +
34A LYS* 3.6 11.4 - - - +
36A ILE* 1.3 75.4 - - - +
38A ASN* 1.3 58.0 + - - +
41A GLY* 2.8 23.3 + - - -
42A VAL* 3.0 30.8 + - - +
43A ARG* 3.3 31.2 + - - +
44A ILE* 3.0 54.7 + - + +
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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 LYS 2.7 18.4 + - - +
35A LYS* 3.4 16.9 - - - +
36A ILE 3.1 0.2 - - - -
37A GLN* 1.3 79.9 - - - +
39A ASP* 1.3 84.6 + - - +
41A GLY* 3.4 7.8 + - - -
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Residues in contact with ASP 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* 2.6 46.4 + - - +
36A ILE* 4.2 2.2 - - - +
38A ASN* 1.3 101.4 + - - +
40A ALA* 1.3 61.7 + - - +
66A ARG* 4.6 4.5 + - - -
69A HIS* 5.9 2.1 - - - -
73A ILE* 5.2 6.3 - - + -
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Residues in contact with ALA 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 ILE* 2.8 17.8 + - + +
39A ASP* 1.3 78.0 - - - +
41A GLY* 1.3 59.5 + - - +
42A VAL* 3.8 7.6 - - + -
66A ARG* 2.8 40.5 + - - +
69A HIS* 5.6 4.9 - - + -
70A ALA* 3.7 25.1 - - + +
73A ILE* 3.6 23.7 - - + +
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Residues in contact with GLY 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 GLN 2.8 12.0 + - - -
38A ASN 3.4 6.4 + - - -
39A ASP 3.4 2.4 - - - -
40A ALA* 1.3 79.8 - - - +
42A VAL* 1.3 62.7 + - - +
62A GLY* 5.5 0.3 - - - -
63A PRO* 4.3 9.2 - - - +
66A ARG* 4.1 8.0 - - - +
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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