Contacts of the strand formed by residues 54 - 62 (chain A) in PDB entry 2HUE
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 ASP 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A THR* 4.0 19.5 - - + +
44A TYR 3.4 4.9 - - - -
45A VAL* 3.9 11.5 - - - +
50A SER 4.3 1.2 - - - +
51A LEU* 3.0 26.2 + - - +
52A ASP 3.3 3.8 - - - +
53A HIS* 1.3 81.3 - - - +
55A GLN* 1.3 62.2 + - - +
56A GLU 4.2 0.6 + - - +
129B ARG* 2.7 44.7 + - - -
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Residues in contact with GLN 55 (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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43A THR* 4.4 2.2 - - - -
44A TYR* 2.9 42.7 + - + +
53A HIS 4.1 6.8 + - - +
54A ASP* 1.3 79.2 - - - +
56A GLU* 1.3 64.6 + - - +
57A LEU* 3.4 12.9 + - + +
79A PRO* 3.4 10.3 - - - +
80A SER* 2.7 51.6 + - - +
83A LEU* 3.6 27.4 + - + +
84A ILE* 3.5 20.4 - - - +
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Residues in contact with GLU 56 (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 LYS* 3.0 40.2 + - + +
42A LEU 3.4 16.8 - - - +
43A THR* 4.2 12.3 + - + +
54A ASP* 4.2 1.2 + - - +
55A GLN* 1.3 73.3 - - - +
57A LEU* 1.3 61.6 + - - +
58A ASP 3.4 7.7 - - - +
59A SER* 3.4 25.5 - - - -
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Residues in contact with LEU 57 (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 TYR* 3.9 29.4 - - + -
42A LEU* 2.8 33.8 + - + +
43A THR 5.0 0.2 - - - -
44A TYR* 4.0 21.5 - - + +
55A GLN* 3.7 18.8 - - + +
56A GLU* 1.3 78.3 - - - +
58A ASP* 1.3 65.2 + - - +
76A ALA* 4.1 4.5 - - + +
77A ASP* 3.6 29.7 + - - +
78A PRO 3.9 1.6 - - - +
79A PRO* 3.7 31.2 - - + -
95A ILE* 5.5 1.3 - - + -
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Residues in contact with ASP 58 (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 LYS* 3.5 0.3 - - - -
42A LEU* 3.0 27.5 + - + -
56A GLU* 3.4 11.2 - - - +
57A LEU* 1.3 81.9 - - - +
59A SER* 1.3 79.3 + - - +
74A PHE* 3.4 31.2 - - + -
75A SER 3.7 7.3 + - - +
76A ALA* 3.5 29.7 - - + -
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Residues in contact with SER 59 (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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39A GLU* 2.4 34.3 + - - +
40A TRP 3.2 7.9 - - - -
41A LYS* 4.5 0.7 - - - -
56A GLU* 3.4 16.4 - - - -
58A ASP* 1.3 88.9 + - - +
60A ILE* 1.3 66.1 + - - +
61A LEU* 4.2 1.6 + - - +
74A PHE* 4.0 3.0 - - - -
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Residues in contact with ILE 60 (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 LEU 3.8 0.7 - - - +
39A GLU* 3.3 2.5 - - - -
40A TRP* 2.9 46.7 + - + -
59A SER* 1.3 77.0 + - - +
61A LEU* 1.3 66.6 + - - +
62A VAL* 4.0 17.4 + - + -
72A PHE* 3.6 55.4 - - + -
73A VAL 5.5 2.2 - - - +
74A PHE* 4.0 7.4 - - + -
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Residues in contact with LEU 61 (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 ASP* 3.7 30.7 - - + +
38A LEU 3.4 13.5 - - - +
39A GLU* 4.0 25.8 - - + +
59A SER* 4.2 1.9 + - - +
60A ILE* 1.3 78.6 - - - +
62A VAL* 1.3 63.0 + - - +
63A GLY 4.5 0.2 + - - -
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Residues in contact with VAL 62 (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 PHE* 5.5 7.2 - - + -
37A ASP* 3.3 5.4 - - - -
38A LEU* 2.8 45.8 + - + +
40A TRP* 5.2 7.0 - - + +
60A ILE* 4.2 27.1 - - + +
61A LEU* 1.3 81.0 - - - +
63A GLY* 1.3 61.5 + - - +
64A PRO 3.8 13.2 - - - +
65A VAL* 4.2 9.4 - - + +
66A PRO* 4.3 15.9 - - + -
72A PHE* 5.9 3.1 - - + -
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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