Contacts of the strand formed by residues 5 - 15 (chain B) in PDB entry 1DKS
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 5 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A SER* 2.9 33.4 - - - -
10A ASP* 3.5 17.7 + - + +
12A TYR* 5.0 9.2 - - - -
21A HIS* 4.3 14.0 - - - -
2B LYS* 1.3 80.5 - - - +
6B ILE* 1.3 74.5 + - + +
7B TYR* 3.5 26.1 + - + +
23B MET* 3.9 5.9 - - - +
25B PRO* 3.9 12.6 - - - +
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Residues in contact with ILE 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A TYR 4.0 0.2 - - - +
9A SER* 3.7 16.5 - - - -
10A ASP* 4.1 10.3 + - - +
5B GLN* 1.3 84.5 - - - +
7B TYR* 1.3 64.7 + - - +
8B TYR* 3.6 21.3 - - + +
22B VAL* 3.2 32.8 - - + -
23B MET 3.4 4.5 - - - +
24B LEU* 3.8 21.1 - - + -
25B PRO* 4.0 11.9 - - + -
28B ILE* 4.0 11.9 - - + -
47B GLY* 3.7 33.9 - - - +
48B VAL* 3.8 4.0 - - + +
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Residues in contact with TYR 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 3.4 38.7 - + + -
8A TYR 3.2 13.2 - - - -
9A SER* 3.8 12.1 - - - -
21A HIS* 2.7 38.5 + + - -
23A MET* 3.6 36.9 - - + +
2B LYS* 6.3 0.2 - - + -
5B GLN* 3.5 34.6 - - + +
6B ILE* 1.3 75.4 - - - +
8B TYR* 1.3 62.0 + - - +
22B VAL* 3.6 0.7 - - - -
23B MET* 2.7 51.6 + - + +
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Residues in contact with TYR 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 3.5 2.4 - - - -
8A TYR* 2.7 50.9 + - + +
9A SER 4.2 4.7 - - - -
10A ASP* 2.7 48.4 + - - -
6B ILE* 3.6 20.7 - - + +
7B TYR* 1.3 75.9 - - - +
9B SER* 1.3 61.0 + - - +
20B ARG* 3.9 29.8 - - - +
21B HIS 4.0 4.7 - - - -
22B VAL* 3.9 16.2 - - + +
47B GLY 3.8 0.2 + - - -
48B VAL* 3.7 14.4 - - + -
49B GLN 3.1 35.4 + - - -
50B GLN* 4.0 7.6 - - + -
300B PO4 5.7 2.0 - - - -
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Residues in contact with SER 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS* 4.1 9.3 - - - +
6A ILE 3.8 9.6 - - - -
7A TYR* 3.7 10.0 - - - -
8A TYR* 4.0 7.5 - - - -
8B TYR* 1.3 77.3 - - - +
10B ASP* 1.3 74.2 + - - +
11B LYS* 4.6 1.9 - - - +
20B ARG* 3.4 17.3 + - - +
21B HIS* 3.2 58.4 + - - -
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Residues in contact with ASP 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LYS* 5.3 4.1 - - + +
6A ILE* 3.4 23.3 + - - +
8A TYR* 2.7 37.8 + - - -
47A GLY 3.9 6.1 - - - +
49A GLN* 3.7 27.2 + - + +
9B SER* 1.3 89.6 + - - +
11B LYS* 1.3 70.8 + - - +
12B TYR* 3.9 2.8 + - - +
19B TYR 4.0 3.3 - - - +
20B ARG* 4.1 2.6 - - - -
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Residues in contact with LYS 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLN* 5.5 2.6 + - - -
9B SER 4.9 2.2 - - - -
10B ASP* 1.3 80.9 - - - +
12B TYR* 1.3 61.8 + - - +
13B ASP* 5.9 0.9 - - - +
18B GLU* 3.2 35.9 + - + +
19B TYR 2.9 11.7 - - - +
20B ARG* 3.0 38.8 - - + +
54B TRP* 3.8 12.3 - - + -
71B ARG* 4.1 1.8 - - - +
300B PO4 3.3 19.9 + - - -
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Residues in contact with TYR 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A HIS* 4.3 38.8 - + + +
10B ASP 3.9 2.4 + - - +
11B LYS* 1.3 75.2 - - - +
13B ASP* 1.3 67.2 + - - +
14B ASP* 5.1 3.4 - - + -
18B GLU* 4.7 0.2 - - - -
19B TYR* 2.6 89.0 + + + +
20B ARG* 5.2 0.7 - - - -
57B TYR* 5.6 3.0 + - - -
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Residues in contact with ASP 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LYS* 5.9 0.5 - - - +
12B TYR* 1.3 86.1 - - - +
14B ASP* 1.3 70.7 + - - +
17B PHE 3.0 14.1 - - - +
18B GLU* 3.5 17.3 - - + +
19B TYR* 4.6 0.2 - - - -
73B LEU* 3.7 22.0 - - + +
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Residues in contact with ASP 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B TYR* 5.1 4.9 - - + -
13B ASP* 1.3 85.0 - - - +
15B GLU* 1.3 68.4 + - + +
16B GLU* 2.9 15.3 + - - +
17B PHE* 2.8 33.4 + - - +
19B TYR* 3.1 31.2 + - + -
73B LEU* 3.9 9.7 - - - +
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Residues in contact with GLU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ASP* 1.3 83.3 - - + +
16B GLU* 1.3 88.2 + - + +
73B LEU* 4.3 7.8 - - - +
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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