Contacts of the strand formed by residues 114 - 121 (chain D) in PDB entry 5DG4
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 114 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A THR* 4.7 6.5 - - - +
8D TRP* 3.7 4.5 - - - -
11D GLU* 2.8 37.4 + - - +
110D ILE* 3.3 6.2 - - - +
111D GLU 2.9 36.7 + - - +
112D GLY 3.2 0.8 + - - -
113D ASP* 1.3 94.1 - - - +
115D LEU* 1.3 61.6 + - - +
116D TYR* 3.6 28.3 + - + +
129D VAL* 4.0 6.5 - - + +
130D PHE 3.2 11.0 - - - +
131D LYS* 4.0 20.6 - - + +
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Residues in contact with LEU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D GLN* 4.8 0.9 - - + +
8D TRP* 3.5 39.1 - - + +
40D LYS* 4.5 5.2 - - + -
42D ILE* 3.7 30.1 - - + -
108D GLN* 3.8 31.4 - - + +
109D TRP 3.6 3.4 - - - +
110D ILE* 3.8 15.9 - - + -
114D LYS* 1.3 73.0 - - - +
116D TYR* 1.3 70.7 + - - +
117D LEU* 4.2 3.4 - - + -
129D VAL* 3.4 4.5 - - - +
130D PHE* 2.8 57.9 + - + -
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Residues in contact with TYR 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D LYS 3.8 0.6 - - - +
108D GLN* 3.2 7.8 - - - +
109D TRP* 2.8 70.8 + + + +
111D GLU* 3.5 46.9 + - + +
114D LYS* 3.6 37.7 + - + +
115D LEU* 1.3 74.8 - - - +
117D LEU* 1.3 61.3 + - - +
118D GLU 4.3 0.2 - - - -
128D GLN 3.5 2.5 - - - +
129D VAL* 3.6 33.2 - - + +
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Residues in contact with LEU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D LYS* 4.0 24.5 - - - +
106D TRP* 3.8 29.2 - - + -
107D LYS 3.3 13.9 - - - +
108D GLN* 3.7 23.3 - - + +
115D LEU* 4.2 6.5 - - + -
116D TYR* 1.3 76.2 - - - +
118D GLU* 1.3 62.8 + - - +
119D LEU* 4.1 17.5 - - + -
126D CYS 3.6 1.4 - - - +
127D ARG* 3.6 2.3 - - - -
128D GLN* 2.8 63.8 + - + +
130D PHE* 4.6 0.9 - - + -
201D ACT 4.2 8.3 - - + +
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Residues in contact with GLU 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D TRP* 3.0 6.7 - - - +
107D LYS* 2.8 49.8 + - + +
109D TRP* 3.9 27.9 - - + -
117D LEU* 1.3 73.3 - - - +
119D LEU* 1.3 61.3 + - - +
120D THR* 4.0 6.5 + - + +
125D VAL* 4.3 11.5 - - + +
126D CYS 3.3 4.0 - - - +
127D ARG* 3.2 44.4 + - + +
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Residues in contact with LEU 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D PHE* 4.7 10.3 - - + -
19D TYR* 3.7 33.9 - - + +
105D GLY 3.7 3.8 - - - +
106D TRP* 4.1 23.3 - - + -
117D LEU* 4.1 18.6 - - + -
118D GLU* 1.3 74.6 - - - +
120D THR* 1.3 61.8 + - - +
125D VAL* 3.3 4.0 - - - -
126D CYS* 2.8 62.5 + - + +
128D GLN* 4.0 20.9 - - - +
201D ACT 5.2 4.3 - - + -
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Residues in contact with THR 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D TYR* 3.7 7.8 + - - -
103D ASN* 2.9 18.5 + - - -
104D ARG* 3.3 3.5 - - - +
105D GLY* 2.9 37.2 + - - +
106D TRP* 4.9 0.6 - - - -
107D LYS* 6.5 1.1 - - + -
118D GLU* 4.0 9.6 + - + +
119D LEU* 1.3 79.8 - - - +
121D CYS* 1.3 66.4 + - - +
122D GLY 5.5 1.3 - - - -
124D GLN 3.4 4.5 - - - -
125D VAL* 3.9 25.8 - - + -
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Residues in contact with CYS 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D TYR* 4.0 16.3 - - + -
22D ALA* 3.7 28.0 - - + +
23D LEU* 3.5 28.3 - - + -
101D LYS* 3.8 27.8 - - - -
102D GLU 4.2 0.7 - - - -
103D ASN 3.5 5.4 - - - -
104D ARG* 4.3 3.6 - - + +
120D THR* 1.3 76.4 - - - +
122D GLY* 1.3 69.1 + - - +
123D ASP 3.1 0.2 + - - -
124D GLN* 2.9 26.0 + - - +
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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