Contacts of the strand formed by residues 72 - 79 (chain P) in PDB entry 1DFU
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 72 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30P ILE* 4.2 12.3 - - + -
60P VAL* 3.3 6.2 - - - +
61P LEU* 2.6 50.2 + - + +
63P ILE* 3.7 21.8 - - + -
70P ILE* 3.6 22.0 - - + -
71P LYS* 1.3 82.8 - - - +
73P LYS* 1.3 64.6 + - - +
91P PHE* 3.5 33.0 - - + -
92P VAL 3.2 14.6 - - - +
93P ARG* 4.2 5.2 - - - -
94P ALA* 3.9 2.9 - - - +
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Residues in contact with LYS 73 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57P TYR 5.6 2.9 - - - +
58P SER* 3.6 26.0 + - - +
59P GLU 4.0 10.3 - - - +
60P VAL* 3.9 24.6 - - + +
61P LEU* 4.8 0.9 - - - -
72P VAL* 1.3 80.5 - - - +
74P ALA* 1.3 66.9 + - - +
75P GLN 3.2 0.5 + - - -
91P PHE* 3.5 7.0 - - - -
92P VAL* 2.9 40.9 + - + +
94P ALA* 4.0 11.9 - - + -
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Residues in contact with ALA 74 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56P PHE* 4.0 25.6 + - + +
57P TYR* 3.6 46.7 + - + +
59P GLU 4.9 1.0 + - - -
61P LEU* 4.3 7.5 - - + +
73P LYS* 1.3 75.1 - - - +
75P GLN* 1.3 61.6 + - - +
76P ASP 5.0 1.1 - - - +
77P VAL* 5.2 0.2 - - + -
89P ILE* 5.1 3.4 - - + -
90P ASP 3.9 5.6 - - - +
91P PHE* 4.3 7.9 - - + -
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Residues in contact with GLN 75 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103M U 3.1 47.3 + - - +
104M A 3.7 14.4 + - - -
31P TYR* 3.4 17.9 - - + +
73P LYS 3.2 0.6 + - - -
74P ALA* 1.3 75.2 - - - +
76P ASP* 1.3 65.5 + - + +
90P ASP* 2.9 14.5 + - + +
92P VAL* 4.1 27.8 - - + +
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Residues in contact with ASP 76 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102M G 4.9 8.5 + - - -
103M U 5.2 9.1 - - - +
75N G 5.2 3.5 + - - -
57P TYR* 6.2 0.6 - - - -
74P ALA* 3.7 1.4 - - - +
75P GLN* 1.3 84.7 - - + +
77P VAL* 1.3 96.7 + - - +
78P GLN* 4.1 10.6 + - - +
88P HIS* 5.9 0.4 - - - -
89P ILE* 3.4 3.3 - - - +
90P ASP* 2.9 47.3 + - + +
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Residues in contact with VAL 77 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57P TYR* 3.3 38.1 - - + +
74P ALA* 5.2 0.9 - - + -
76P ASP* 1.3 96.0 + - - +
78P GLN* 1.3 64.9 + - - +
79P ARG* 3.9 31.1 + - + +
86P LEU* 3.9 17.0 - - + -
88P HIS 3.5 9.4 - - - +
89P ILE* 3.9 18.8 - - + -
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Residues in contact with GLN 78 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101M A 5.6 1.0 + - - -
75N G 3.8 16.0 - - - +
76N G 2.6 62.5 + - - +
77N U 4.1 1.4 - - - +
76P ASP* 4.2 9.8 + - - +
77P VAL* 1.3 78.6 - - - +
79P ARG* 1.3 56.6 + - - +
86P LEU 3.8 0.5 - - - -
87P GLN* 2.8 49.6 + - - +
88P HIS* 2.9 28.9 + - + +
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Residues in contact with ARG 79 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51P GLN* 3.2 25.4 + - - -
57P TYR* 3.6 18.8 + - - -
77P VAL* 3.9 21.3 + - + +
78P GLN* 1.3 78.4 - - - +
80P HIS* 1.3 71.0 + - - +
81P PRO* 3.4 5.4 - - - +
83P LYS 5.5 0.9 - - - +
85P LYS 3.6 7.6 - - - +
86P LEU* 4.2 11.8 - - + +
87P GLN* 4.3 7.9 - - - +
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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