Contacts of the strand formed by residues 124 - 132 (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 GLN 124 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D ASN* 2.8 29.3 + - - +
18D GLY* 3.4 36.2 - - - +
19D TYR* 4.2 5.5 - - - -
22D ALA* 3.8 12.1 - - + -
119D LEU 3.9 0.2 - - - +
120D THR* 3.4 5.2 - - - -
121D CYS 2.9 33.6 + - - +
122D GLY 4.8 0.3 - - - +
123D ASP* 1.3 105.9 + - - +
125D VAL* 1.3 62.2 + - - +
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Residues in contact with VAL 125 (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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14D GLU* 4.1 1.0 - - - +
15D ASN* 3.0 25.9 + - - +
19D TYR* 5.0 0.4 - - - -
118D GLU* 4.3 13.5 - - + +
119D LEU 3.3 8.7 - - - +
120D THR* 3.9 19.7 - - + -
123D ASP 4.0 6.4 + - - +
124D GLN* 1.3 81.3 - - - +
126D CYS* 1.3 70.6 + - - +
127D ARG* 3.9 47.6 + - + +
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Residues in contact with CYS 126 (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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13D ASN* 3.5 22.4 - - - -
14D GLU 3.2 16.2 - - - +
15D ASN 3.6 10.5 - - - +
16D PHE* 3.6 21.5 - - - -
19D TYR* 3.7 16.7 - - + +
117D LEU 3.6 1.4 - - - +
118D GLU* 3.3 4.5 - - - -
119D LEU* 2.8 53.7 + - + +
125D VAL* 1.3 74.6 - - - +
127D ARG* 1.3 60.4 + - - +
128D GLN* 3.8 5.6 - - - -
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Residues in contact with ARG 127 (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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12D SER* 4.1 3.1 + - - +
13D ASN* 3.7 1.6 + - - -
14D GLU* 2.8 64.2 + - + +
117D LEU 3.6 3.4 - - - -
118D GLU* 3.2 33.4 + - + +
125D VAL* 3.9 35.2 + - + +
126D CYS* 1.3 76.8 - - - +
128D GLN* 1.3 61.4 + - - +
129D VAL* 5.3 4.2 - - + +
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Residues in contact with GLN 128 (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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10D MET* 3.5 13.0 - - + +
12D SER 3.3 7.0 - - - +
13D ASN* 3.3 34.2 + - - +
16D PHE* 3.9 13.3 - - - -
38D GLN* 4.3 8.4 + - - +
40D LYS* 5.2 0.3 + - - -
116D TYR* 3.5 2.9 - - - +
117D LEU* 2.8 50.3 + - + +
119D LEU* 4.0 13.2 - - + +
126D CYS* 3.8 13.9 - - - -
127D ARG* 1.3 74.1 - - - +
129D VAL* 1.3 67.4 + - - +
130D PHE* 3.5 30.9 - - + -
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Residues in contact with VAL 129 (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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35A ARG* 5.1 5.6 - - - +
10D MET* 3.6 3.5 - - - -
11D GLU* 2.8 54.5 + - + +
12D SER* 3.0 29.7 + - - +
114D LYS* 4.0 11.9 - - + -
115D LEU 3.4 5.4 - - - +
116D TYR* 3.6 36.8 - - + -
127D ARG* 5.3 3.6 - - + -
128D GLN* 1.3 81.4 - - - +
130D PHE* 1.3 59.9 + - - +
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Residues in contact with PHE 130 (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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8D TRP* 3.6 32.5 - - + -
9D GLU 3.2 5.6 - - - +
10D MET* 3.4 40.2 - - + -
11D GLU* 4.7 1.1 - - - -
38D GLN* 4.1 17.9 - - + -
39D THR 4.8 0.2 - - - -
40D LYS* 3.7 33.7 - - + -
53D THR* 5.1 0.4 - - + -
114D LYS* 3.2 8.1 - - - +
115D LEU* 2.8 55.1 + - + +
117D LEU* 4.6 2.7 - - + -
128D GLN* 3.5 38.1 - - + -
129D VAL* 1.3 79.0 - - - +
131D LYS* 1.3 60.5 + - - +
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Residues in contact with LYS 131 (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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8D TRP* 3.8 2.0 - - - -
9D GLU* 2.7 40.4 + - + +
11D GLU* 3.8 20.1 + - + +
113D ASP* 2.3 44.5 + - - +
114D LYS* 4.0 20.3 - - + +
130D PHE* 1.3 74.4 - - - +
132D LYS* 1.3 75.5 + - - +
133D LYS* 3.3 0.7 + - - -
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Residues in contact with LYS 132 (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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5D ASN 3.5 25.3 + - - -
6D GLY* 3.8 10.7 - - - -
7D THR 3.6 8.4 - - - +
8D TRP* 3.4 34.1 - - + -
113D ASP* 2.8 29.0 + - + +
131D LYS* 1.3 81.0 - - - +
133D LYS* 1.3 71.1 + - - +
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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