Contacts of the strand formed by residues 104 - 109 (chain N) in PDB entry 7K63
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 THR 104 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55N TYR 3.7 0.5 - - - +
56N GLN* 3.7 1.2 - - - -
57N GLN* 2.9 42.1 + - - +
59N PRO* 6.2 0.2 - - - +
103N ALA* 1.3 76.2 - - - +
105N TYR* 1.3 64.4 + - - +
106N TYR* 3.4 37.7 + - + +
120N GLY* 4.1 2.5 - - - -
121N THR 3.3 23.3 - - - +
122N LYS* 4.0 24.0 + - + +
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Residues in contact with TYR 105 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25N GLN* 3.0 12.7 + - - +
40N ILE* 4.6 13.0 - - + -
54N TRP* 4.7 5.2 - - + -
55N TYR 3.2 16.4 - - - +
56N GLN* 3.2 26.1 + - + -
66N LEU* 3.6 26.5 - - + -
81N PHE* 4.1 11.1 - + - -
92N LEU* 4.1 22.9 - - + -
94N ILE* 4.7 4.2 - - + +
101N ASP* 2.8 26.6 + - - +
103N ALA 3.7 15.3 - - - -
104N THR* 1.3 73.6 - - - +
106N TYR* 1.3 61.8 + - - +
120N GLY* 3.3 1.0 - - - -
121N THR* 3.0 40.4 + - + +
123N LEU* 3.7 29.4 - - + +
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Residues in contact with TYR 106 (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* 3.6 2.5 - - - -
54N TRP* 3.5 4.5 - - - -
55N TYR* 2.9 42.6 + - + -
57N GLN* 3.3 37.7 + - + -
63N PRO* 5.7 0.7 - - + -
104N THR* 3.4 32.9 + - + +
105N TYR* 1.3 73.9 - - - +
107N CYS* 1.3 68.2 + - - +
117N PHE* 4.3 6.1 - - + -
118N GLY 3.4 20.6 - - - +
119N SER 4.2 4.3 - - - -
120N GLY* 3.5 19.7 - - - -
188N GLN* 3.8 4.7 + - - -
193N GLY* 5.2 5.5 - - - -
194N LEU* 3.6 41.1 - - + -
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Residues in contact with CYS 107 (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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23N MET* 3.9 8.5 - - - -
25N GLN* 3.6 11.9 + - - -
42N CYS* 3.3 28.9 - - - -
52N LEU* 3.8 20.9 - - + -
53N SER 3.2 6.5 - - - -
54N TRP* 3.9 19.6 - - + -
106N TYR* 1.3 74.5 - - - +
108N LEU* 1.3 62.8 + - - +
117N PHE* 3.2 7.3 - - - +
118N GLY* 2.9 44.4 + - - -
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Residues in contact with LEU 108 (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* 3.3 5.2 - - - +
53N SER 2.9 33.7 + - - +
55N TYR* 3.3 42.0 - - + +
107N CYS* 1.3 78.1 - - - +
109N GLN* 1.3 79.9 + - - +
110N HIS* 3.8 10.1 + - + +
115N TYR* 3.9 12.1 - - + -
116N THR 3.4 15.3 - - - +
117N PHE* 3.7 35.9 - - + -
255N THR* 4.3 4.9 - - - +
256N LEU* 3.9 21.1 - - + -
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Residues in contact with GLN 109 (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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21N ILE* 4.3 20.1 - - + +
23N MET* 3.5 32.3 - - + +
48N ILE* 3.7 20.6 - - + +
51N TYR 3.4 5.4 - - - +
52N LEU* 4.4 2.2 - - + +
108N LEU* 1.3 77.2 - - - +
110N HIS* 1.3 59.1 + - - +
111N GLY 3.1 16.1 + - - -
112N GLU* 3.3 18.5 + - - +
114N PRO 2.6 31.1 + - - -
115N TYR* 3.4 6.3 - - - +
116N THR* 3.0 39.4 + - - +
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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