Contacts of the strand formed by residues 81 - 90 (chain Z) in PDB entry 6F0X
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 VAL 81 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72Z LEU* 4.2 19.1 - - + -
75Z TRP* 4.0 16.5 + - + -
76Z LEU* 4.5 16.4 - - + +
79Z CYS* 3.9 6.1 - - - +
80Z SER* 1.3 76.7 - - - +
82Z GLN* 1.3 79.0 + - - +
83Z LYS 3.2 24.7 - - - +
84Z LEU* 5.7 0.2 - - + -
104Z ILE* 3.7 26.4 - - + +
106Z CYS* 5.3 2.8 - - - +
155Z ILE* 3.7 17.3 - - + -
156Z TYR 3.3 14.8 - - - +
157Z THR* 3.6 8.3 - - - +
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Residues in contact with GLN 82 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79Z CYS 3.1 18.4 + - - +
80Z SER 2.6 19.6 + - - +
81Z VAL* 1.3 72.9 - - - +
83Z LYS* 1.3 62.6 + - + +
103Z ASP* 3.3 3.3 - - - +
104Z ILE* 2.3 52.8 + - - +
106Z CYS 6.2 0.9 - - - +
156Z TYR* 2.8 19.3 + - + +
158Z ASP* 2.8 48.3 + - - +
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Residues in contact with LYS 83 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81Z VAL* 3.2 12.3 - - - +
82Z GLN* 1.3 84.0 - - + +
84Z LEU* 1.3 59.8 + - - +
85Z VAL* 4.8 9.2 - - + -
99Z ARG* 6.0 2.5 - - - +
101Z GLN* 3.5 22.1 - - + +
102Z PHE 3.2 5.6 - - - +
103Z ASP* 3.2 20.0 - - + +
104Z ILE* 3.6 2.9 - - - -
155Z ILE* 3.3 4.6 - - - +
156Z TYR* 3.1 55.9 + - + +
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Residues in contact with LEU 84 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Z PHE* 3.4 48.2 - - + -
28Z ILE* 5.0 8.7 - - + -
68Z VAL* 5.7 3.8 - - + -
72Z LEU* 4.2 20.2 - - + -
81Z VAL* 5.7 0.2 - - + -
83Z LYS* 1.3 75.7 - - - +
85Z VAL* 1.3 66.7 + - - +
86Z VAL* 5.3 6.7 - - + -
100Z TRP 3.6 0.2 - - - +
102Z PHE* 2.4 58.7 + - + +
104Z ILE* 3.8 11.7 - - + -
153Z LEU* 6.1 3.1 - - + -
154Z LEU 3.9 2.7 - - - +
155Z ILE* 3.4 23.8 - - + -
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Residues in contact with VAL 85 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83Z LYS* 4.8 8.7 - - + -
84Z LEU* 1.3 86.1 - - - +
86Z VAL* 1.3 71.6 + - - +
87Z VAL* 3.7 11.9 - - + -
99Z ARG* 3.5 43.7 - - + +
100Z TRP 3.0 11.7 - - - +
101Z GLN* 3.6 27.8 - - + +
153Z LEU* 3.9 2.3 - - - +
154Z LEU* 2.7 49.8 + - + +
155Z ILE* 5.6 0.4 - - - -
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Residues in contact with VAL 86 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28Z ILE* 4.5 25.8 - - + -
31Z ILE* 6.1 3.4 - - + -
32Z LEU* 4.6 12.8 - - + -
84Z LEU* 5.3 7.0 - - + -
85Z VAL* 1.3 76.3 - - - +
87Z VAL* 1.3 62.6 + - - +
88Z ILE* 3.7 9.0 + - + +
98Z GLU 3.8 0.3 - - - +
99Z ARG* 3.3 2.3 - - - -
100Z TRP* 3.0 47.1 + - + +
102Z PHE* 5.7 4.9 - - + -
151Z PHE* 3.9 21.5 - - + -
152Z ASP 3.7 2.5 - - - -
153Z LEU* 3.5 28.0 - - + -
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Residues in contact with VAL 87 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85Z VAL* 3.7 7.9 - - + -
86Z VAL* 1.3 69.9 - - - +
88Z ILE* 1.3 58.6 + - - +
89Z SER* 4.0 4.8 + - - +
96Z VAL* 3.5 40.8 - - + -
98Z GLU 3.3 3.1 - - - +
99Z ARG* 3.5 26.7 - - + +
151Z PHE* 3.2 1.7 - - - -
152Z ASP* 2.7 48.0 + - + +
154Z LEU* 3.6 31.9 - - + -
173Z GLN* 3.8 11.9 - - + -
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Residues in contact with ILE 88 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Z ILE* 4.9 1.3 - - + -
32Z LEU* 3.9 13.9 - - + -
35Z ARG* 5.7 0.2 - - + -
37Z ILE* 3.6 37.5 - - + -
86Z VAL* 4.5 6.7 - - + +
87Z VAL* 1.3 65.8 - - - +
89Z SER* 1.3 67.0 + - - +
96Z VAL* 3.4 2.1 - - - +
97Z LEU* 2.9 23.9 + - + -
98Z GLU* 2.3 72.0 + - + +
100Z TRP* 4.4 6.3 - - + +
145Z LEU* 5.2 0.9 - - + -
149Z CYS* 3.8 13.2 - - + -
150Z SER 3.4 11.9 - - - +
151Z PHE* 3.6 16.4 - - + -
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Residues in contact with SER 89 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87Z VAL* 4.0 6.9 + - - +
88Z ILE* 1.3 74.8 - - - +
90Z ASN* 1.3 65.2 + - - +
94Z GLY* 3.1 20.0 + - - -
95Z GLU 3.1 7.4 - - - -
96Z VAL* 3.1 27.7 - - - +
97Z LEU* 3.9 2.0 - - - +
149Z CYS* 3.1 13.6 - - - +
150Z SER* 2.6 36.5 + - - +
151Z PHE* 5.6 0.9 - - - -
173Z GLN* 5.6 0.2 + - - -
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Residues in contact with ASN 90 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89Z SER* 1.3 80.8 - - - +
91Z ILE* 1.3 89.1 + - - +
92Z GLU 3.9 2.9 + - - +
93Z SER* 2.3 31.0 + - - +
94Z GLY* 3.1 25.1 - - - +
95Z GLU* 2.7 21.5 + - + +
97Z LEU* 4.8 5.1 - - + +
147Z VAL* 4.2 14.5 - - - +
148Z SER 3.9 7.3 - - - +
149Z CYS* 4.6 7.2 - - - -
150Z SER* 3.3 11.0 + - - -
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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