Contacts of the strand formed by residues 102 - 109 (chain A) in PDB entry 2DAZ
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 LYS 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A GLU* 4.2 32.7 + - + +
31A LEU 5.4 0.2 - - - +
32A GLU* 3.8 34.5 + - + +
80A ASN* 4.4 2.6 + - - -
100A PRO* 3.2 24.3 - - + +
101A SER* 1.3 77.7 - - - +
103A VAL* 1.3 62.5 + - - +
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Residues in contact with VAL 103 (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 GLU* 3.8 4.7 - - - -
31A LEU 3.4 27.3 + - - +
33A LYS* 4.1 13.0 - - + -
38A LEU* 4.1 18.6 - - + -
79A ILE* 3.3 33.4 - - + -
80A ASN* 4.0 14.4 - - + +
96A ILE* 4.7 1.1 - - + -
99A ALA* 3.5 18.4 - - + -
100A PRO 3.0 24.0 - - - +
101A SER 3.5 6.1 + - - +
102A LYS* 1.3 75.4 - - - +
104A LYS* 1.3 65.6 + - - +
105A LEU* 3.5 4.9 + - + +
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Residues in contact with LYS 104 (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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10A PHE* 4.0 8.1 + - - +
12A ASP* 5.6 1.0 - - - +
15A ILE* 3.5 23.8 - - - +
28A ILE* 3.8 22.2 - - + -
29A ILE 5.1 0.2 - - - +
30A GLU* 4.1 27.5 - - + +
78A GLU* 3.8 2.4 - - - +
79A ILE* 3.4 6.6 - - - -
80A ASN* 3.3 27.1 + - - +
81A ASN* 4.4 20.6 + - - +
103A VAL* 1.3 72.7 - - - +
105A LEU* 1.3 61.6 + - - +
106A VAL* 3.3 27.7 + - - +
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Residues in contact with LEU 105 (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 HIS 3.7 3.1 - - - +
28A ILE* 3.5 4.5 - - - +
29A ILE* 3.3 34.1 + - + +
31A LEU* 3.3 44.9 - - + -
38A LEU* 3.5 28.9 - - + -
40A LEU* 5.0 5.8 - - + -
70A MET* 4.4 10.3 - - - -
76A LEU* 4.5 14.1 - - + -
78A GLU 3.8 2.2 - - - -
79A ILE* 3.6 33.7 - - + -
96A ILE* 4.6 1.3 - - + -
103A VAL* 4.0 5.4 - - + +
104A LYS* 1.3 73.8 - - - +
106A VAL* 1.3 60.1 - - - +
107A PHE* 3.9 7.9 - - + -
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Residues in contact with VAL 106 (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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15A ILE* 3.3 34.1 - - + -
26A LEU* 3.9 16.2 - - + -
28A ILE* 3.8 20.6 - - + -
76A LEU* 4.7 1.1 - - - +
77A LEU* 2.7 41.9 + - + +
78A GLU* 2.9 28.2 + - + +
104A LYS* 3.3 35.7 - - - +
105A LEU* 1.3 72.9 - - - +
107A PHE* 1.3 55.1 + - - +
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Residues in contact with PHE 107 (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* 3.4 8.0 - - - +
27A HIS* 2.8 65.0 + + + -
29A ILE* 4.0 13.7 - - + -
69A ARG 5.1 2.2 - - - -
70A MET* 3.4 43.7 - - + -
74A ASP* 2.7 44.0 - - + -
75A GLU 3.4 24.5 - - - +
76A LEU* 3.6 15.7 - - + +
77A LEU* 4.1 5.4 - - - +
105A LEU* 4.5 6.1 - - + -
106A VAL* 1.3 75.4 - - - +
108A ILE* 1.3 66.6 + - - +
109A ARG* 4.5 1.6 - - + -
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Residues in contact with ILE 108 (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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19A TYR 4.5 2.9 - - - +
22A LEU* 3.0 51.6 - - + -
23A PRO* 4.9 0.4 - - + -
24A GLY* 3.3 27.8 - - - +
25A GLU 3.4 19.7 - - - +
26A LEU* 4.2 5.2 - - + +
73A GLY 4.2 0.9 - - - +
74A ASP* 3.2 8.7 - - - -
75A GLU* 3.1 49.6 + - + +
77A LEU* 4.4 3.4 - - + -
107A PHE* 1.3 81.1 - - - +
109A ARG* 1.3 64.0 - - - +
110A ASN* 3.9 6.5 + - + +
113A ALA* 6.4 0.4 - - + -
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Residues in contact with ARG 109 (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 GLY* 3.0 2.5 - - - -
25A GLU* 2.8 43.1 + - + +
27A HIS* 4.1 29.8 - - + +
69A ARG 5.4 2.4 + - - -
71A ARG* 3.7 38.2 - - - +
74A ASP* 3.8 16.3 + - - +
107A PHE* 4.2 1.1 - - - -
108A ILE* 1.3 71.5 - - - +
110A ASN* 1.3 63.9 + - - +
111A GLU 5.6 0.4 - - - +
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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