Contacts of the strand formed by residues 89 - 94 (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 ASP 89 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42N CYS 3.6 3.1 - - - +
43N LYS* 3.4 31.4 - - + +
85N GLY* 3.6 4.3 - - - -
86N SER 3.1 27.9 + - - +
88N GLN* 1.3 84.1 - - - +
90N PHE* 1.3 59.6 + - - +
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Residues in contact with PHE 90 (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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41N THR* 3.3 6.6 - - - -
42N CYS* 2.8 39.7 + - + +
43N LYS* 5.3 0.2 + - - -
44N ALA* 5.0 2.7 - - + -
48N ILE* 3.5 29.6 - - + -
50N SER* 3.7 10.5 - - - -
52N LEU* 3.4 28.7 - - + -
54N TRP* 4.5 7.2 - - + +
70N ALA* 3.6 32.3 - - + -
84N SER 3.6 5.8 - - - +
85N GLY* 3.9 9.9 - - - -
86N SER* 3.6 14.4 - - - -
87N GLY 3.2 37.7 - - - -
88N GLN* 4.0 8.5 - - - -
89N ASP* 1.3 73.5 - - - +
91N SER* 1.3 60.9 + - - +
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Residues in contact with SER 91 (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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39N THR* 3.1 27.4 - - - +
40N ILE 3.2 8.1 + - - -
41N THR* 3.9 8.3 - - - +
54N TRP* 4.0 10.9 + - - -
82N SER 4.8 0.2 - - - -
83N GLY* 3.4 3.3 - - - -
84N SER* 3.0 47.0 + - - +
90N PHE* 1.3 77.2 - - - +
92N LEU* 1.3 63.9 + - - +
93N THR* 4.3 2.1 + - - -
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Residues in contact with LEU 92 (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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38N VAL 3.9 0.3 - - - +
39N THR* 3.1 5.5 - - - +
40N ILE* 2.4 54.0 + - + +
54N TRP* 3.7 44.2 - - + -
66N LEU* 4.9 4.0 - - + -
67N ILE* 3.8 29.6 - - + -
81N PHE* 4.8 8.5 - - + -
82N SER 3.8 6.5 - - - +
83N GLY 4.7 0.4 - - - +
91N SER* 1.3 73.4 + - - +
93N THR* 1.3 69.7 + - - +
94N ILE* 4.2 17.9 - - + -
105N TYR* 4.1 26.0 - - + -
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Residues in contact with THR 93 (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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37N ARG* 3.7 36.8 - - + +
38N VAL 3.4 2.7 - - - -
39N THR* 3.8 15.6 + - - +
80N ARG 3.3 0.5 - - - +
81N PHE* 3.2 6.6 - - - +
82N SER* 2.8 52.2 + - - -
84N SER* 5.7 1.6 + - - -
91N SER* 4.3 2.8 + - - -
92N LEU* 1.3 77.6 + - - +
94N ILE* 1.3 69.8 + - - +
95N ASN* 4.1 9.4 - - - +
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Residues in contact with ILE 94 (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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36N GLU 4.1 1.0 - - - +
37N ARG* 3.3 2.4 - - - +
38N VAL* 2.8 43.1 + - + +
40N ILE* 3.6 31.0 - - + -
80N ARG* 3.6 31.0 - - + +
81N PHE* 3.5 33.2 - - + -
92N LEU* 4.2 12.8 - - + -
93N THR* 1.3 76.3 - - - +
95N ASN* 1.3 63.2 + - - +
96N ASN 4.5 1.6 - - - +
97N LEU* 3.8 24.2 - - + -
101N ASP* 4.3 2.5 - - - +
105N TYR* 4.7 11.9 - - + +
123N LEU* 5.1 2.2 - - + -
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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