Contacts of the strand formed by residues 79 - 85 (chain A) in PDB entry 2FIN
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 THR 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A GLU* 5.5 0.7 - - + +
51A ILE 3.3 13.0 - - - +
52A THR* 3.7 12.4 - - + +
55A GLU* 3.5 21.1 + - - -
78A THR* 1.3 73.0 - - - +
80A TYR* 1.3 62.0 + - - +
81A TYR* 3.2 39.0 - - + +
93A GLY* 3.7 1.4 + - - -
94A PHE* 2.9 57.1 + - + -
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Residues in contact with TYR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A THR 3.7 1.0 - - - +
50A GLU* 3.7 0.3 - - - -
51A ILE* 3.0 61.5 + - + +
78A THR* 4.3 0.8 + - - +
79A THR* 1.3 73.1 - - - +
81A TYR* 1.3 102.8 + - - +
82A SER* 3.2 22.6 - - - -
89A ARG* 5.3 3.3 + - - -
91A ASN* 3.4 26.2 + - + -
92A PHE 3.3 24.0 - - - +
93A GLY* 3.8 8.3 - - - +
46B ALA* 3.1 32.5 + - - +
47B SER* 3.9 15.9 + - - -
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Residues in contact with TYR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL* 4.3 17.3 - - + -
49A THR 3.6 2.7 - - - -
50A GLU* 3.5 34.5 - - + -
79A THR* 3.2 30.5 - - + +
80A TYR* 1.3 92.0 - - - +
82A SER* 1.3 61.5 + - - +
83A ILE* 3.4 9.1 - - + +
90A MET 3.4 8.0 - - - +
92A PHE* 3.2 33.6 + + + +
94A PHE* 3.6 24.3 - + - -
100A ILE* 3.8 33.7 + - + +
116A LEU* 4.5 11.2 - - + -
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Residues in contact with SER 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A SER* 3.5 5.6 + - - +
48A VAL* 3.7 4.5 - - - -
49A THR* 3.3 35.3 + - - +
51A ILE* 6.2 0.2 - - - -
80A TYR* 3.2 26.2 - - - -
81A TYR* 1.3 71.2 - - - +
83A ILE* 1.3 60.6 + - - +
84A ILE* 3.0 21.9 + - - +
89A ARG* 4.7 9.4 - - - -
90A MET 4.5 0.4 - - - -
91A ASN* 3.9 11.2 - - - +
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Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 5.4 2.9 - - + -
47A SER 3.4 5.8 - - - -
48A VAL* 3.6 24.7 - - + +
81A TYR* 3.5 10.1 + - + +
82A SER* 1.3 71.2 - - - +
84A ILE* 1.3 61.8 + - - +
89A ARG* 4.8 0.2 - - - -
90A MET* 3.0 59.3 + - + +
92A PHE* 6.2 1.6 - - + -
103A ILE* 3.4 26.2 - - + -
105A GLU* 3.7 13.5 - - - +
114A ALA* 4.2 16.6 - - + -
116A LEU* 4.2 26.9 - - + -
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Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A CYS 3.9 1.0 - - - -
46A GLN* 3.0 33.6 + - + -
47A SER* 2.8 22.9 + - - +
82A SER* 3.3 17.3 - - - +
83A ILE* 1.3 75.2 - - - +
85A GLY* 1.3 61.7 + - - +
88A LEU 3.8 9.4 - - - +
89A ARG* 4.0 24.5 - - + +
105A GLU* 4.0 6.2 - - - +
151A SER* 4.0 16.4 - - - +
153A GLU* 3.3 43.5 - - + +
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Residues in contact with GLY 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LYS 4.1 0.9 - - - -
44A ILE* 3.9 15.3 - - - -
45A CYS 4.2 0.9 - - - -
46A GLN* 4.0 8.7 - - - -
83A ILE 3.9 0.6 + - - -
84A ILE* 1.3 80.5 - - - +
86A GLY* 1.3 62.0 + - - -
87A GLY 3.0 3.6 - - - -
88A LEU* 2.6 34.7 + - - +
90A MET* 4.1 7.9 - - - +
105A GLU* 4.4 7.2 - - - -
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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