Contacts of the strand formed by residues 34 - 40 (chain A) in PDB entry 3QHT
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 GLU 34 (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* 2.7 38.8 + - + +
28A VAL 3.3 9.9 - - - +
29A SER* 4.3 16.6 - - - +
32A SER 4.5 3.1 - - - +
33A SER* 1.3 74.1 + - - +
35A ILE* 1.3 67.3 + - - +
36A PHE* 4.0 21.3 - - + -
100A GOL 2.4 50.4 + - - +
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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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27A LYS* 3.5 2.8 - - - -
28A VAL 2.7 39.5 + - - -
33A SER* 4.3 9.9 - - - +
34A GLU* 1.3 79.5 - - - +
36A PHE* 1.3 65.3 + - - +
37A PHE* 3.4 31.5 - - + -
51A ALA 4.7 0.7 - - - +
52A PHE* 3.6 31.0 - - + +
55A ARG* 3.8 35.7 - - + -
56A GLN* 4.6 0.4 - - - +
100A GOL 4.7 0.9 - - - +
83C TYR* 3.8 19.7 - - + -
84C SER 3.4 12.6 - - - +
85C TYR* 4.2 11.0 - - + -
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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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26A LEU 3.6 4.0 - - - +
27A LYS* 3.6 45.5 - - + -
34A GLU* 4.0 21.5 - - + -
35A ILE* 1.3 72.5 - - - +
37A PHE* 1.3 61.8 + - - +
100A GOL 3.7 21.3 - - - -
33C ARG* 5.2 4.9 - - - +
73C TYR* 3.9 30.3 - + + -
75C TYR* 3.7 20.5 - - - +
83C TYR* 2.9 6.1 - - - +
84C SER* 2.7 50.0 + - - +
87C PRO* 4.0 16.2 - - + -
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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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24A ILE 4.1 0.2 - - - -
25A ASN* 3.3 10.6 - - - +
26A LEU* 2.8 37.8 + - + +
28A VAL* 3.6 29.8 - - + -
35A ILE* 3.4 38.4 - - + -
36A PHE* 1.3 75.7 - - - +
38A LYS* 1.3 61.3 - - - +
39A ILE* 4.0 3.8 - - + -
48A LEU* 3.5 40.8 - - + -
51A ALA* 3.7 23.8 - - + -
52A PHE* 4.1 7.9 - - + -
75C TYR* 4.6 4.1 + - - -
81C LEU* 3.8 21.8 - - + -
82C TYR 3.3 2.7 - - - -
83C TYR* 3.5 18.8 - - + -
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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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21A GLU* 4.1 8.7 - - - -
23A HIS* 3.4 30.2 - - + -
24A ILE 3.3 9.6 - - - +
25A ASN* 2.8 34.3 + - - +
37A PHE* 1.3 70.1 - - - +
39A ILE* 1.3 58.5 + - - +
99A GOL 3.2 33.1 + - - -
31C TYR* 4.0 25.0 + - - +
33C ARG* 4.1 12.1 - - - +
47C GLU* 4.0 12.3 + - - -
75C TYR* 4.5 6.3 + - + +
81C LEU* 3.3 4.9 - - - +
82C TYR* 2.8 37.3 + - + +
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Residues in contact with ILE 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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23A HIS* 3.6 8.1 - - - +
24A ILE* 2.6 47.4 + - + +
26A LEU* 3.7 28.9 - - + -
37A PHE* 4.8 5.2 - - + -
38A LYS* 1.3 76.1 - - - +
40A LYS* 1.3 69.2 + - - +
43A THR* 3.7 31.2 - - + +
44A PRO 4.6 2.5 - - - +
45A LEU* 4.1 22.4 - - + -
48A LEU* 4.2 9.2 - - + -
78A PRO* 4.2 6.3 - - + -
81C LEU* 4.1 25.8 - - + -
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Residues in contact with LYS 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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22A THR* 3.7 26.0 - - - +
23A HIS* 3.8 21.6 - - + +
24A ILE* 5.4 0.2 - - - -
39A ILE* 1.3 76.9 - - - +
41A LYS* 1.3 64.7 + - - +
42A THR* 3.0 15.3 + - - +
43A THR* 3.0 33.5 + - - +
78A PRO* 3.6 11.2 - - - +
79B GLU* 3.3 11.7 + - - +
80B ASP* 3.3 23.6 + - - +
82B ASP* 2.7 38.0 + - - +
80C ASP* 4.0 16.5 + - - +
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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
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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