Contacts of the strand formed by residues 52 - 57 (chain N) in PDB entry 7K60
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 LEU 52 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23N MET* 4.2 11.4 - - + -
42N CYS* 3.8 20.2 - - - -
48N ILE* 3.7 22.9 - - + -
50N SER 2.8 6.0 + - - +
51N TYR* 1.3 74.4 - - - +
53N SER* 1.3 69.5 + - - +
54N TRP* 3.2 36.3 - - + +
68N TYR 3.8 0.2 - - - -
69N TYR* 3.4 5.1 + - - +
70N ALA* 2.8 30.5 + - + +
90N PHE* 3.8 39.7 - - + -
107N CYS* 4.2 3.8 - - + -
108N LEU 3.2 12.1 - - - +
109N GLN* 4.7 0.2 - - + -
110N HIS* 4.1 2.0 - - - -
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Residues in contact with SER 53 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52N LEU* 1.3 77.6 + - - +
54N TRP* 1.3 66.2 + - - +
55N TYR* 3.7 17.1 - - - -
67N ILE 3.2 13.7 - - - -
68N TYR* 3.8 4.3 - - - -
107N CYS* 3.2 6.8 - - - +
108N LEU* 2.8 34.0 + - - -
110N HIS* 3.5 8.3 - - - -
255N THR* 2.6 39.2 + - - +
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Residues in contact with TRP 54 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25N GLN* 4.0 13.9 - - - -
40N ILE* 3.7 33.7 - - + -
41N THR 4.1 2.2 - - - -
42N CYS* 4.0 28.0 - - + -
52N LEU* 3.2 21.2 - - + +
53N SER* 1.3 79.4 - - - +
55N TYR* 1.3 57.1 + - - +
65N THR* 3.6 5.5 + - - -
66N LEU* 2.8 33.8 + - + -
67N ILE* 2.9 35.2 + - + +
70N ALA* 5.4 3.1 + - - -
83N GLY* 5.4 1.3 - - - -
84N SER 5.6 0.4 + - - -
90N PHE* 4.9 0.6 - - - +
91N SER* 4.0 17.4 + - - +
92N LEU* 3.6 53.4 - - + -
105N TYR* 4.7 7.4 - - + -
106N TYR 3.5 14.8 - - - -
107N CYS* 4.1 9.6 - - + -
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Residues in contact with TYR 55 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53N SER* 3.7 16.2 - - - -
54N TRP* 1.3 76.4 - - - +
56N GLN* 1.3 60.2 + - - +
57N GLN 4.0 0.2 + - - -
63N PRO* 4.4 13.2 - - + -
64N LYS 3.4 4.5 - - - +
65N THR* 3.6 23.3 - - - -
66N LEU* 4.5 3.6 - - - -
104N THR 3.8 0.5 - - - +
105N TYR* 3.2 8.2 - - - +
106N TYR* 2.8 49.5 + - + +
108N LEU* 3.4 35.5 - - + +
117N PHE* 4.5 8.1 - + + -
194N LEU* 6.0 0.9 - - + -
255N THR* 2.6 27.0 + - - -
256N LEU* 3.0 36.5 + - + +
259N TRP* 3.6 25.4 - + - -
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Residues in contact with GLN 56 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55N TYR* 1.3 71.0 - - - +
57N GLN* 1.3 61.4 + - - +
58N LYS* 3.3 40.9 + - - +
62N SER 4.3 1.0 - - - +
63N PRO* 3.5 0.8 - - - +
64N LYS* 2.8 64.8 + - + +
66N LEU* 3.5 30.0 - - + +
81N PHE* 4.6 6.4 - - - -
100N ASP 4.3 4.8 + - - -
101N ASP* 5.2 2.3 + - - +
103N ALA* 3.7 17.2 - - + +
104N THR 3.8 2.7 - - - -
105N TYR* 3.8 18.7 + - + -
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Residues in contact with GLN 57 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55N TYR 4.0 0.4 + - - -
56N GLN* 1.3 73.1 - - - +
58N LYS* 1.3 69.2 + - - +
59N PRO* 3.9 1.1 - - + +
60N TRP 5.4 2.3 + - - -
61N LYS 3.3 22.8 + - - +
62N SER 4.7 0.4 - - - -
63N PRO* 3.7 27.9 - - + +
103N ALA* 3.7 3.5 - - - -
104N THR* 2.9 47.2 + - + +
106N TYR* 3.2 25.6 - - + -
188N GLN* 2.6 44.2 + - - +
194N LEU* 4.0 1.8 - - - +
244N TYR* 3.8 3.5 + - - -
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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