Contacts of the strand formed by residues 77 - 82 (chain D) in PDB entry 2FPO
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 GLY 77 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54D ALA 3.5 4.8 + - - +
55D GLN* 3.7 20.9 + - - -
56D CYS* 2.9 26.9 + - - +
71D LEU* 4.2 2.7 - - - -
75D ALA* 3.2 3.4 - - - +
76D ALA* 1.3 82.1 - - - +
78D ALA* 1.3 61.2 - - - +
102D ASN* 3.2 14.6 - - - -
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Residues in contact with ALA 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D GLN* 4.4 1.3 - - - +
56D CYS* 3.3 16.6 - - + +
67D GLY* 4.5 4.7 - - - +
70D ALA* 5.6 0.9 - - + -
71D LEU* 3.8 28.3 - - + +
77D GLY* 1.3 74.3 - - - +
79D THR* 1.3 62.7 + - - +
80D LEU* 3.8 20.6 - - + -
102D ASN 3.2 6.5 + - - -
103D ALA* 3.1 5.9 - - - +
104D ARG* 3.1 24.3 + - - +
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Residues in contact with THR 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D GLN* 5.0 3.9 + - - +
56D CYS 2.9 9.2 + - - -
57D LEU* 3.4 18.6 - - + +
58D ASP 2.9 25.1 + - - -
78D ALA* 1.3 72.5 - - - +
80D LEU* 1.3 63.1 + - - +
81D ILE* 3.6 23.6 - - + -
104D ARG* 3.0 46.0 + - + +
106D VAL* 4.6 2.0 - - + -
113D PHE* 4.5 9.2 - - + -
121D HIS* 4.3 11.1 + - + -
147D TRP* 6.2 0.2 - - + -
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Residues in contact with LEU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D CYS* 6.3 0.2 - - + -
58D ASP* 3.7 24.2 - - + +
61D ALA* 3.8 13.5 - - + -
64D GLY* 5.5 1.3 - - - -
67D GLY* 3.7 25.8 - - - -
68D LEU* 5.0 2.7 - - + +
71D LEU* 4.9 2.2 - - + -
78D ALA* 3.8 17.5 - - + +
79D THR* 1.3 77.4 - - - +
81D ILE* 1.3 59.1 + - - +
91D LEU* 4.1 32.5 - - + -
95D LEU* 4.3 22.9 - - + -
103D ALA* 4.9 4.3 - - + -
104D ARG 2.8 16.2 + - - +
105D VAL* 3.2 6.5 - - - +
106D VAL 2.8 32.1 + - - +
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Residues in contact with ILE 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D LEU* 3.9 10.3 - - + -
58D ASP 2.8 20.3 + - - +
59D CYS* 3.4 22.6 - - - +
60D PHE* 3.4 0.7 - - - -
61D ALA* 2.8 25.2 + - - +
79D THR* 3.6 18.4 - - + -
80D LEU* 1.3 70.8 - - - +
82D GLU* 1.3 60.9 + - - +
106D VAL* 3.5 28.3 - - + +
108D SER* 3.3 26.5 - - - +
109D ASN 4.4 3.6 - - - +
110D ALA* 4.5 2.0 - - + -
113D PHE* 3.5 48.9 - - + -
114D LEU* 5.8 0.4 - - + -
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Residues in contact with GLU 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D PHE* 4.0 5.0 - - - +
61D ALA* 3.7 8.4 + - + -
62D GLY* 2.7 34.9 + - - +
80D LEU 4.0 0.2 + - - -
81D ILE* 1.3 76.0 - - - +
83D MSE 1.3 61.9 + - - +
84D ASP* 2.9 44.7 + - - +
87D VAL* 3.7 21.2 - - + +
88D SER* 3.2 14.5 + - - +
91D LEU* 4.9 5.2 - - + -
105D VAL* 5.1 2.9 - - + -
106D VAL 2.9 8.5 + - - +
107D ASN* 3.0 14.4 - - - +
108D SER 2.9 19.2 + - - -
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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