Contacts of the strand formed by residues 77 - 85 (chain F) in PDB entry 6X0A
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 TRP 77 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2F PRO* 3.5 22.0 - - + +
4F ILE* 3.3 28.2 - - + +
73F LEU* 4.3 0.9 - - - +
74F ALA* 3.0 39.1 + - + +
75F GLU* 3.3 33.8 - - + -
76F GLY* 1.3 82.3 - - - +
78F ILE* 1.3 65.3 + - - +
79F GLU* 2.8 43.8 + - + +
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Residues in contact with ILE 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F PRO 3.0 10.7 + - - +
3F ILE* 3.5 10.2 - - + +
4F ILE* 2.9 30.1 + - - +
42F LEU* 3.0 49.4 - - + +
43F ALA* 3.4 12.1 - - + +
46F PRO* 4.7 2.7 - - + -
71F TYR* 3.8 27.8 - - + -
72F ARG 3.9 3.4 - - - +
73F LEU* 3.8 18.6 - - + -
77F TRP* 1.3 76.9 - - - +
79F GLU* 1.3 63.0 + - - +
80F ILE* 3.9 16.8 + - + -
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Residues in contact with GLU 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F ILE* 3.3 12.6 - - + +
71F TYR* 3.3 4.7 - - - +
72F ARG* 2.6 79.8 + - + +
74F ALA* 3.4 12.6 - - + +
77F TRP* 2.8 40.7 + - + +
78F ILE* 1.3 70.1 - - - +
80F ILE* 1.3 64.4 + - - +
81F VAL* 3.4 8.5 + - + +
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Residues in contact with ILE 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F ILE* 3.7 23.8 - - + -
4F ILE 2.8 11.7 + - - +
5F ARG* 3.3 9.9 - - + -
6F SER* 3.1 25.5 + - - -
9F ALA* 3.7 5.1 - - + +
13F LEU* 6.3 0.4 - - + -
39F ILE* 3.4 36.3 - - + -
42F LEU* 3.9 10.5 - - + -
69F ILE* 4.1 7.0 - - + -
70F LEU 4.1 5.2 - - - +
71F TYR* 3.7 20.0 - - + -
78F ILE* 4.2 4.7 - - + -
79F GLU* 1.3 70.1 - - - +
81F VAL* 1.3 61.3 + - - +
83F ILE* 3.9 28.0 - - + -
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Residues in contact with VAL 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F SER* 2.6 30.1 + - - +
8F ALA* 6.3 0.2 - - + -
9F ALA* 3.3 4.1 - - - +
70F LEU* 3.0 17.7 + - + +
71F TYR* 4.5 5.4 - - - -
72F ARG* 4.5 13.7 - - + +
79F GLU* 3.8 20.0 - - + +
80F ILE* 1.3 73.4 - - - +
82F ARG* 1.3 78.3 + - + +
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Residues in contact with ARG 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F ALA* 4.0 23.7 - - + +
9F ALA* 4.0 4.3 - - - -
12F ASP* 2.6 43.9 + - - +
69F ILE* 3.8 1.6 - - - +
70F LEU* 2.9 39.6 + - + +
80F ILE* 3.7 1.4 - - - +
81F VAL* 1.3 96.6 - - + +
83F ILE* 1.3 71.6 + - - +
84F VAL* 3.8 27.6 - - + +
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Residues in contact with ILE 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ALA* 3.9 14.8 - - + +
12F ASP* 2.7 28.9 + - + +
13F LEU* 3.9 34.1 - - + -
16F ILE* 3.5 28.3 - - + +
35F ILE* 5.0 8.5 - - + -
64F ILE* 5.8 0.9 - - + -
67F TYR* 4.5 13.6 - - + -
68F LEU 3.2 13.2 - - - +
69F ILE* 4.3 22.0 - - + -
80F ILE* 3.9 20.2 - - + -
82F ARG* 1.3 81.0 - - - +
84F VAL* 1.3 59.0 + - - +
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Residues in contact with VAL 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F TYR* 3.6 5.4 - - - -
68F LEU* 2.8 33.8 + - + +
70F LEU* 4.7 14.2 - - + +
82F ARG* 3.8 43.0 - - + +
83F ILE* 1.3 77.0 - - - +
85F HIS* 1.3 85.3 + - + +
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Residues in contact with HIS 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ASN 3.0 22.1 + - - -
23C ASP 3.0 22.4 + - - -
25C PRO* 5.8 0.9 - - + +
66F ASN* 3.7 23.8 + - + +
67F TYR* 3.4 32.4 - + + -
68F LEU* 5.0 1.6 - - - +
84F VAL* 1.3 92.1 - - + +
86F GLY* 1.3 90.7 + - - +
87F ALA 5.2 0.4 - - - -
88F ARG* 3.1 44.1 + - + +
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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