Contacts of the strand formed by residues 77 - 82 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83B MSE 4.9 3.1 - - - -
84B ASP* 5.0 0.2 - - - -
54C ALA 3.4 4.0 + - - +
55C GLN* 3.6 19.2 + - - -
56C CYS* 2.9 26.9 + - - +
71C LEU* 4.2 4.5 - - - -
75C ALA 3.3 1.0 - - - -
76C ALA* 1.3 81.2 - - - +
78C ALA* 1.3 62.4 + - - +
102C ASN* 3.1 17.7 - - - -
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Residues in contact with ALA 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B MSE 4.4 3.6 - - - +
55C GLN* 4.5 1.1 - - - +
56C CYS* 3.2 19.1 - - + +
58C ASP 6.0 0.2 - - - +
67C GLY* 4.7 5.6 - - - +
70C ALA* 5.5 0.9 - - + -
71C LEU* 4.0 22.4 - - + +
77C GLY* 1.3 75.1 - - - +
79C THR* 1.3 62.1 + - - +
80C LEU* 3.9 20.9 + - + +
102C ASN 3.1 7.9 + - - -
103C ALA* 3.1 6.9 - - + +
104C ARG* 3.0 25.5 + - - +
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Residues in contact with THR 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B MSE 4.7 0.9 - - - -
130B PHE* 4.2 5.8 - - + -
55C GLN* 5.0 3.9 + - - +
56C CYS 2.9 8.6 + - - -
57C LEU* 3.5 19.2 - - + +
58C ASP 2.9 25.8 + - - -
78C ALA* 1.3 73.3 - - - +
80C LEU* 1.3 63.2 + - - +
81C ILE* 3.7 23.3 - - + -
104C ARG* 2.9 46.4 + - + +
106C VAL* 4.4 1.3 - - + -
113C PHE* 4.2 11.4 - - + -
121C HIS* 4.3 10.7 + - + -
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Residues in contact with LEU 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C ASP* 3.8 24.0 - - + +
61C ALA* 3.8 13.2 - - + -
64C GLY* 5.6 0.7 - - - -
67C GLY* 3.9 27.6 - - - -
68C LEU* 5.2 0.9 - - + -
71C LEU* 5.2 1.3 - - + -
78C ALA* 3.9 17.3 - - + +
79C THR* 1.3 77.1 - - - +
81C ILE* 1.3 59.7 + - - +
91C LEU* 3.9 34.1 - - + -
95C LEU* 4.3 21.8 - - + -
103C ALA* 4.8 4.7 - - + -
104C ARG 2.8 14.3 + - - +
105C VAL* 3.2 6.5 - - + +
106C VAL 2.8 31.9 + - - +
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Residues in contact with ILE 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C LEU* 4.1 8.5 - - + -
58C ASP 2.9 17.4 + - - +
59C CYS* 3.3 27.3 - - - +
60C PHE* 3.4 0.7 - - - -
61C ALA* 2.8 25.7 + - - +
79C THR* 3.7 17.5 - - + -
80C LEU* 1.3 70.6 - - - +
82C GLU* 1.3 61.7 + - - +
106C VAL* 3.4 19.5 - - + +
108C SER* 3.3 26.2 - - - +
109C ASN 4.3 4.3 - - - +
110C ALA* 4.4 2.2 - - - -
113C PHE* 3.4 56.1 - - + -
114C LEU* 5.9 0.4 - - + -
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Residues in contact with GLU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C CYS 5.3 0.4 - - - -
60C PHE* 3.9 5.3 - - - +
61C ALA* 3.6 13.3 + - + -
62C GLY* 2.8 35.1 + - - +
81C ILE* 1.3 76.4 - - - +
83C MSE 1.3 62.4 + - - +
84C ASP* 3.0 43.1 + - - +
87C VAL* 3.8 17.8 - - + +
88C SER* 3.9 15.8 - - - +
91C LEU* 5.1 1.6 - - + -
105C VAL* 5.0 5.4 - - + -
106C VAL 2.9 7.9 + - - +
107C ASN* 3.0 21.5 - - - +
108C SER 3.1 12.4 + - - -
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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