Contacts of the strand formed by residues 76 - 80 (chain A) in PDB entry 2FK8
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 76 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LEU* 5.4 0.4 - - - -
74A GLY 4.7 0.5 + - - -
75A MET* 1.3 73.8 - - - +
77A LEU* 1.3 63.1 + - - +
98A ASN* 3.4 29.1 + - + +
100A ILE* 3.7 35.2 - - + -
138A PRO 4.7 2.9 - - - +
139A VAL* 3.9 14.5 - - + +
140A ASP* 2.7 43.9 + - - +
141A ARG 3.3 6.6 + - - +
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 3.8 17.0 - - + -
69A LEU* 3.9 16.8 - - + -
71A LEU* 4.3 16.8 - - + -
75A MET 4.1 0.6 - - - -
76A THR* 1.3 76.5 - - - +
78A LEU* 1.3 64.1 + - - +
79A ASP* 4.8 1.8 - - + +
87A THR* 5.3 2.5 - - + +
88A MET* 5.5 2.9 - - + -
91A ALA* 3.5 30.3 - - + -
97A VAL* 4.3 3.3 - - + +
98A ASN 2.9 12.2 + - - +
99A VAL* 3.4 10.9 - - + +
100A ILE 2.9 25.1 + - - +
141A ARG* 3.6 28.0 - - + +
143A VAL* 3.9 24.7 - - + +
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A THR 4.1 0.4 + - - -
77A LEU* 1.3 75.7 - - - +
79A ASP* 1.3 59.4 + - - +
80A ILE* 3.7 30.7 - - + -
100A ILE* 3.3 30.5 - - + +
102A LEU* 3.9 18.2 - - + -
132A TRP* 6.2 0.4 - - + -
135A PHE* 3.7 37.5 - - + -
139A VAL* 4.0 13.2 - - + +
141A ARG 3.0 13.0 + - - +
142A ILE* 3.3 7.7 - - + +
143A VAL* 2.9 26.9 + - - +
166A ILE* 3.8 18.6 - - + -
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Residues in contact with ASP 79 (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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77A LEU* 4.1 2.8 + - + -
78A LEU* 1.3 73.0 - - - +
80A ILE* 1.3 71.6 + - - +
81A GLY 3.5 3.6 + - - +
82A CYS* 3.4 29.0 - - + +
87A THR* 3.6 23.7 - - + -
88A MET* 3.8 24.0 + - + +
100A ILE 2.8 10.2 + - - +
101A GLY* 3.5 0.3 - - - -
102A LEU* 3.0 27.5 + - - +
143A VAL* 3.3 26.3 - - + +
144A SER* 4.5 1.7 - - - -
145A ILE* 4.7 1.6 + - - +
302A SAM 4.7 5.1 + - - -
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Residues in contact with ILE 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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78A LEU* 3.7 27.8 - - + -
79A ASP* 1.3 69.7 - - - +
81A GLY* 1.3 62.7 - - - +
102A LEU* 4.2 8.7 - - + -
132A TRP* 4.0 16.8 - - + -
142A ILE* 3.5 24.9 - - + -
143A VAL 2.9 8.7 + - - -
144A SER* 2.9 33.2 + - - +
145A ILE 4.2 0.9 + - - -
147A ALA* 3.6 4.0 - - - +
151A PHE* 4.0 21.8 - - + -
159A PHE* 3.7 23.6 - - + -
163A CYS* 4.0 8.3 - - - -
166A ILE* 5.9 0.2 - - + -
302A SAM 3.7 21.3 - - + -
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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