Contacts of the strand formed by residues 85 - 91 (chain C) in PDB entry 6K7O
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 ALA 85 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C GLN* 3.7 23.3 - - + -
39C GLN 3.4 24.5 - - - +
40C LYS* 3.9 6.3 - - + +
41C PRO* 4.8 3.4 - - - -
83C ASP 3.1 6.0 + - - +
84C PHE* 1.3 81.2 - - - +
86C THR* 1.3 67.0 + - - +
87C TYR* 3.9 8.9 - - + -
106C THR 3.8 0.3 - - - +
107C LYS* 4.5 0.6 - - - +
108C VAL* 2.9 31.8 + - - +
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Residues in contact with THR 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C GLN* 3.3 34.1 + - - +
41C PRO* 6.5 0.9 - - + -
85C ALA* 1.3 80.3 - - - +
87C TYR* 1.3 61.7 + - - +
88C TYR* 3.3 34.2 + - - -
105C GLY 5.5 0.7 - - - -
106C THR 3.3 11.4 - - - -
107C LYS* 3.8 33.9 - - + -
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Residues in contact with TYR 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C GLN* 2.9 21.3 + - - -
21C ILE* 3.8 20.6 - - + -
36C TRP* 4.9 2.0 - - + -
37C TYR 3.2 9.9 - - - +
38C GLN* 3.5 23.6 + - + -
48C LEU* 3.5 33.2 - - + -
63C PHE* 3.7 10.1 - + - -
74C LEU* 3.7 15.3 - - + -
76C ILE* 3.8 12.6 - - + +
83C ASP* 2.5 42.7 + - - +
85C ALA* 3.9 17.5 - - + -
86C THR* 1.3 75.3 - - - +
88C TYR* 1.3 60.7 - - - +
105C GLY* 3.3 2.4 - - - -
106C THR 2.9 16.9 + - - +
108C VAL* 3.9 22.4 - - + -
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Residues in contact with TYR 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLN* 3.9 4.3 + - - -
44B LYS 4.3 0.7 + - - -
45B GLY* 3.6 16.4 - - - -
46B LEU* 3.8 42.4 + - + -
6C GLN* 3.2 3.8 - - - +
36C TRP* 3.2 9.3 - - - -
37C TYR* 2.7 49.0 + - + +
39C GLN* 3.7 22.5 + - + -
86C THR* 3.3 37.7 + - - -
87C TYR* 1.3 71.9 - - - +
89C CYS* 1.3 60.5 + - - +
102C PHE* 4.0 18.6 - + + -
103C GLY 3.5 19.7 - - - -
104C GLY 4.1 4.6 + - - -
105C GLY* 3.5 23.1 - - - -
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Residues in contact with CYS 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C MET* 4.4 4.0 - - - +
6C GLN* 2.9 26.3 + - - -
23C CYS* 2.0 54.1 - - + -
34C LEU* 4.6 4.5 - - + -
35C ALA 3.3 8.3 - - - +
36C TRP* 3.8 16.1 - - + -
88C TYR* 1.3 74.3 - - - +
90C GLN* 1.3 59.9 + - - +
102C PHE* 3.4 3.5 - - - -
103C GLY* 2.8 34.5 + - - -
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Residues in contact with GLN 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B TYR* 5.2 10.3 - - - -
38B VAL* 5.3 1.6 - - - +
48B TRP* 4.4 7.9 - - - -
107B TRP 5.4 2.4 - - - +
108B ALA* 5.6 0.5 - - - -
109B SER* 4.3 8.5 + - - -
4C MET* 5.3 1.3 - - - -
33C TYR 3.7 0.5 - - - +
34C LEU* 3.2 9.6 - - - +
35C ALA* 2.8 32.1 + - + +
37C TYR* 2.9 36.6 + - + -
88C TYR 4.2 0.2 + - - -
89C CYS* 1.3 75.6 - - - +
91C GLN* 1.3 67.4 + - - +
92C SER* 5.4 5.1 + - - -
101C THR* 3.3 35.8 + - - +
102C PHE* 3.3 36.7 - - + -
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Residues in contact with GLN 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ILE* 4.3 12.9 + - - +
4C MET* 3.7 29.2 - - + -
29C ILE* 3.6 30.9 - - + +
33C TYR 3.3 4.0 - - - -
90C GLN* 1.3 78.4 - - - +
92C SER* 1.3 60.1 + - - +
93C TYR* 3.4 9.2 + - - +
94C ASP 3.0 42.8 + - - -
95C TRP* 3.6 0.7 + - - -
98C VAL* 3.9 15.0 - - - +
100C ASN 4.8 0.4 + - - -
101C THR* 3.2 45.4 + - - +
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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