Contacts of the strand formed by residues 16 - 24 (chain B) in PDB entry 1CKS
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 HIS 16 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B ASP* 3.0 8.2 + - - +
15B GLU* 1.3 100.3 + - + +
17B TYR* 1.3 89.5 + + + +
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Residues in contact with TYR 17 (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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13B PHE* 3.0 8.6 - - - +
14B ASP* 2.9 32.6 + - - +
16B HIS* 1.3 101.2 - + + +
18B GLU* 1.3 69.5 - - - +
19B TYR* 3.5 33.8 - + + -
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Residues in contact with GLU 18 (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* 3.6 24.5 + - + +
12B TYR 3.4 8.7 - - - +
13B PHE* 4.2 5.4 - - + -
17B TYR* 1.3 84.2 - - - +
19B TYR* 1.3 62.6 + - - +
54B TRP* 3.6 34.5 - - + -
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Residues in contact with TYR 19 (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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58A MET* 4.1 12.1 - - + +
11B LYS* 3.3 5.7 - - - +
12B TYR* 2.9 71.2 + + + +
13B PHE* 4.0 3.6 - - - -
14B ASP* 2.8 41.4 + - - -
17B TYR* 3.5 35.9 - + + -
18B GLU* 1.3 77.1 - - - +
20B ARG* 1.3 63.8 + - - +
54B TRP* 3.9 4.9 - - - -
57B TYR* 3.9 37.9 - + - -
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Residues in contact with ARG 20 (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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8B TYR* 4.2 16.9 - - - +
9B SER* 3.5 28.7 + - - +
10B ASP 4.5 0.4 - - - +
11B LYS* 4.0 22.2 - - + +
12B TYR* 4.4 1.1 - - - -
19B TYR* 1.3 76.5 - - - +
21B HIS* 1.3 82.5 + - - +
22B VAL* 3.7 12.9 + - + +
49B GLN 5.3 0.2 + - - -
50B GLN* 3.0 35.5 + - - +
54B TRP* 3.8 23.7 - - + +
57B TYR* 6.0 2.3 - - - -
301B SO4 3.0 39.8 + - - -
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Residues in contact with HIS 21 (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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61A GLU* 3.6 32.1 + - + +
9B SER* 3.0 39.2 + - - +
12B TYR* 2.9 30.3 + + - -
20B ARG* 1.3 83.5 - - - +
22B VAL* 1.3 67.6 + - - +
23B MET* 4.4 14.8 - - + +
60B HIS* 6.1 5.3 - + - -
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Residues in contact with VAL 22 (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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6B ILE* 3.4 27.4 - - + -
7B TYR 3.5 3.4 - - - +
8B TYR* 3.9 16.6 - - + -
20B ARG* 3.7 20.0 - - + +
21B HIS* 1.3 82.9 - - - +
23B MET* 1.3 69.1 + - - +
24B LEU* 4.1 9.7 + - + +
48B VAL* 4.3 22.7 - - + -
50B GLN* 4.3 7.4 - - - +
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Residues in contact with MET 23 (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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64A PRO* 5.2 11.2 - - + -
5B GLN 4.3 0.5 - - - +
6B ILE* 3.4 8.7 - - - +
7B TYR* 2.9 67.0 + - + +
9B SER* 5.1 2.9 - - - -
21B HIS* 4.4 19.3 - - + +
22B VAL* 1.3 76.3 - - - +
24B LEU* 1.3 66.1 - - - +
25B PRO* 3.9 0.7 - - - +
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Residues in contact with LEU 24 (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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6B ILE* 3.9 31.9 - - + -
22B VAL* 4.1 10.5 + - + +
23B MET* 1.3 77.8 - - - +
25B PRO* 1.3 75.7 - - + +
26B ARG* 3.8 0.7 + - - -
28B LEU* 4.3 13.7 - - + -
29B SER* 4.1 20.7 - - - +
32B VAL* 3.6 31.0 - - + -
46B LEU* 4.9 8.3 - - + +
48B VAL* 4.8 9.2 - - + -
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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