Contacts of the strand formed by residues 54 - 60 (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 TRP 54 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LYS* 3.7 29.8 - - + -
18B GLU* 3.6 54.5 - - + -
19B TYR* 3.9 12.6 - - - -
20B ARG* 3.8 24.9 - - + -
40B GLU* 4.1 5.4 + - - +
43B TRP* 3.3 21.5 + - + -
50B GLN* 3.6 36.8 - - + +
51B SER* 3.1 28.8 + - - +
52B LEU 3.5 2.5 - - - -
53B GLY* 1.3 79.6 - - - +
55B VAL* 1.3 61.5 + - - +
301B SO4 3.1 24.3 + - - -
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Residues in contact with VAL 55 (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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38B MET 6.0 0.2 - - - +
43B TRP* 5.0 0.7 - - - +
53B GLY 3.6 11.8 + - - +
54B TRP* 1.3 80.7 - - - +
56B HIS* 1.3 70.0 + - - +
57B TYR* 3.1 23.7 + - + +
15C GLU* 3.7 22.9 - - - +
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Residues in contact with HIS 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B VAL* 5.0 4.9 - - + -
36B HIS 5.0 0.9 - - - -
37B LEU* 3.5 28.2 - - + +
38B MET* 3.1 66.8 + - + +
43B TRP* 4.0 20.2 - - + +
55B VAL* 1.3 76.4 - - - +
57B TYR* 1.3 57.1 + - - +
58B MET 3.4 22.4 + - - -
59B ILE* 3.8 25.8 - - + +
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Residues in contact with TYR 57 (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* 5.4 1.7 + - - -
19B TYR* 3.9 35.4 - + - -
20B ARG 6.0 2.2 - - - -
37B LEU* 3.9 8.3 - - - -
55B VAL* 3.1 22.1 + - + +
56B HIS* 1.3 75.0 - - - +
58B MET* 1.3 90.2 + - + +
14C ASP* 3.3 26.8 - - + +
15C GLU* 3.4 26.0 + - - +
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Residues in contact with MET 58 (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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37B LEU* 3.8 4.8 - - - +
56B HIS* 3.4 18.3 + - - -
57B TYR* 1.3 112.9 - - + +
59B ILE* 1.3 80.4 - - - +
60B HIS* 3.9 10.0 + - + -
61B GLU* 5.4 2.7 - - + +
12C TYR* 4.8 15.5 - - + -
13C PHE 3.5 14.4 - - - +
14C ASP* 4.1 14.1 - - + +
19C TYR* 5.3 4.9 - - - -
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Residues in contact with ILE 59 (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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32B VAL* 5.5 3.1 - - + -
33B PRO 4.5 15.3 - - - +
34B LYS* 5.5 2.0 - - - +
36B HIS 4.6 2.2 - - - +
37B LEU* 4.0 4.9 - - + -
56B HIS* 3.8 29.4 - - + +
58B MET* 1.3 87.9 - - - +
60B HIS* 1.3 75.0 + - - +
61B GLU 3.4 2.4 + - - -
62B PRO* 5.8 1.6 - - + -
11C LYS 5.4 1.1 - - - +
12C TYR* 3.5 22.8 - - + -
13C PHE* 3.0 52.7 + - + +
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Residues in contact with HIS 60 (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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21B HIS* 6.1 4.9 - + - -
58B MET* 3.9 10.9 + - + -
59B ILE* 1.3 86.9 - - - +
61B GLU* 1.3 100.1 + - + +
62B PRO* 3.5 5.4 - - - +
63B GLU* 3.7 22.3 + - + +
12C TYR* 4.1 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