Contacts of the strand formed by residues 74 - 80 (chain F) in PDB entry 3SDI
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 ILE 74 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69F VAL* 3.3 8.5 - - - +
70F VAL* 2.8 44.0 + - + +
72F ARG 3.6 1.2 + - - -
73F HIS* 1.3 107.3 - - + +
75F GLY* 1.3 71.3 + - - +
76F CYS* 4.3 5.2 - - - -
107F ILE* 4.0 9.9 - - + -
109F ILE* 3.7 20.4 - - + -
112F PHE* 3.8 50.0 - - + -
139F GLY* 3.5 15.7 - - - +
221F HIS* 4.2 4.3 - - - -
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Residues in contact with GLY 75 (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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48F PHE* 3.4 11.9 - - - -
67F ILE* 5.0 0.4 - - - -
68F GLN 3.5 4.7 - - - -
73F HIS 4.3 0.4 - - - -
74F ILE* 1.3 74.5 - - - +
76F CYS* 1.3 61.7 + - - -
138F PHE* 3.1 24.6 - - - +
139F GLY 3.0 14.2 + - - -
215F CYS* 5.7 0.2 - - - +
221F HIS* 3.4 28.8 - - - -
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Residues in contact with CYS 76 (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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48F PHE* 5.5 0.4 - - - -
66F LYS 4.4 1.0 - - - +
67F ILE* 3.6 6.4 - - - +
68F GLN* 2.7 39.9 + - - +
70F VAL* 3.9 26.9 - - - -
74F ILE* 4.3 1.6 - - - -
75F GLY* 1.3 76.3 - - - -
77F VAL* 1.3 60.8 + - - +
78F TYR* 4.9 2.3 - - + -
89F VAL* 4.0 22.9 - - + -
112F PHE* 4.2 14.8 - - - -
116F LEU* 5.2 3.4 - - - -
136F THR* 4.2 10.1 - - + -
137F ILE 3.5 4.3 - - - -
138F PHE* 3.6 18.4 - - + -
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Residues in contact with VAL 77 (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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37F SER* 3.9 16.6 - - - -
38F ILE 4.1 13.0 - - - +
48F PHE* 4.4 13.2 - - + -
49F ALA 4.6 1.6 - - - +
50F VAL* 3.7 32.1 - - + -
66F LYS* 5.1 3.4 - - + -
67F ILE* 3.9 22.2 - - + +
76F CYS* 1.3 74.2 - - - +
78F TYR* 1.3 63.8 + - - +
136F THR* 3.2 3.6 - - - +
137F ILE* 2.6 63.7 + - + +
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Residues in contact with TYR 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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35F THR* 5.9 0.7 - - - +
37F SER* 3.6 8.7 + - - -
50F VAL* 4.7 8.0 - - - +
66F LYS* 4.1 24.8 + - + +
68F GLN* 2.7 31.6 + - - -
76F CYS 4.9 3.8 - - - -
77F VAL* 1.3 82.9 - - - +
79F SER* 1.3 63.0 + - - +
82F ILE* 3.7 46.6 + - + +
85F GLY* 3.6 29.6 - - - -
86F ARG* 3.4 17.3 - - - +
89F VAL* 3.9 8.1 - - + -
134F VAL* 4.4 11.4 - - + -
135F SER 3.0 20.4 - - - +
136F THR* 3.9 17.9 - - + +
137F ILE 4.7 0.2 - - - +
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Residues in contact with SER 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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31F VAL* 3.4 7.8 - - - +
35F THR* 2.7 31.1 + - - +
37F SER* 2.6 27.9 + - - -
78F TYR* 1.3 73.2 + - - +
80F GLY* 1.3 59.0 + - - +
82F ILE* 5.3 1.6 - - - -
134F VAL* 3.4 6.3 - - - -
135F SER 3.0 28.9 + - - -
165F THR* 3.2 18.6 + - - +
166F GLY* 4.0 11.2 - - - -
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Residues in contact with GLY 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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30F ALA 3.7 21.1 - - - -
31F VAL* 3.8 4.0 - - - -
34F GLY* 4.1 12.9 - - - -
35F THR 4.9 0.6 - - - +
79F SER* 1.3 75.9 - - - +
81F LEU* 1.3 61.8 + - - -
82F ILE* 3.2 18.3 + - - +
133F GLY 3.4 8.7 - - - -
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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