Contacts of the strand formed by residues 107 - 113 (chain B) in PDB entry 3FA6
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 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B LEU* 3.8 28.0 - - + -
75B THR* 3.9 16.4 - - + +
76B VAL* 5.7 3.6 - - + -
79B ARG* 4.6 5.6 - - - +
97B GLN* 2.7 52.4 + - - +
99B LEU* 6.1 0.5 - - - +
105B PRO* 3.3 12.5 + - + +
106B LYS* 1.3 85.2 + - - +
108B SER* 1.3 65.4 + - - +
124B THR* 3.2 13.7 - - - +
125B ALA* 4.3 2.0 - - + -
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Residues in contact with SER 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B VAL* 5.6 4.7 - - - +
95B CYS 3.3 16.4 - - - -
96B GLU* 4.8 2.9 - - - -
97B GLN* 4.1 6.2 - - - +
106B LYS* 6.1 4.5 - - - -
107B THR* 1.3 78.3 - - - +
109B TRP* 1.3 69.2 + - - +
110B THR* 4.9 4.9 - - - +
123B MET* 3.5 3.6 - - - +
124B THR* 2.7 49.8 + - - +
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Residues in contact with TRP 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B PHE* 3.8 25.6 - + - -
71B PHE* 4.6 2.5 - + - -
73B GLU* 3.0 25.3 + - - -
85B VAL* 3.7 23.1 - - + -
93B MET* 3.9 19.5 - - + -
94B VAL* 4.2 0.2 - - - +
95B CYS* 2.8 50.3 + - + +
97B GLN* 3.5 21.8 - - - -
108B SER* 1.3 77.1 - - - +
110B THR* 1.3 75.9 + - - +
111B LEU* 3.8 24.9 - - + -
121B ASP* 4.5 0.4 - - - +
122B THR 3.1 11.7 - - - +
123B MET* 4.0 3.1 - - + -
138B LSR 3.5 51.3 - - + +
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Residues in contact with THR 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LYS* 4.5 14.9 - - - -
93B MET 3.3 12.8 - - - -
94B VAL* 4.0 25.4 - - + -
108B SER* 4.9 6.3 - - - +
109B TRP* 1.3 85.2 - - - +
111B LEU* 1.3 62.8 + - - +
112B GLU* 5.2 1.2 + - - +
120B ILE 3.5 1.6 + - - +
121B ASP* 3.3 9.0 - - - +
122B THR* 2.8 53.0 + - + +
124B THR* 6.1 1.6 - - + -
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B PHE* 3.7 15.5 - - + -
43B ILE* 4.3 14.4 - - + -
50B PHE* 5.8 0.7 - - + -
52B ILE* 4.2 14.6 - - + -
92B LYS* 3.3 3.8 - - - -
93B MET* 2.9 52.6 + - + +
109B TRP* 3.8 22.2 - - + -
110B THR* 1.3 81.1 - - - +
112B GLU* 1.3 60.2 + - - +
119B LEU* 4.3 16.8 - - + -
120B ILE 3.3 2.2 - - - +
121B ASP* 3.7 30.3 - - + +
138B LSR 4.1 19.3 - - + -
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B PHE* 4.1 5.4 - - - -
91B ASN* 3.2 14.0 - - + +
92B LYS* 4.0 32.8 + - + +
110B THR* 5.7 1.3 - - - +
111B LEU* 1.3 75.1 - - - +
113B LEU* 1.3 73.2 + - - +
114B THR* 3.9 6.1 + - + +
118B GLU 3.7 0.5 - - - +
119B LEU* 3.4 5.2 - - - +
120B ILE* 2.9 56.4 + - + +
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B PRO* 3.9 21.3 - - + -
2B ASN 3.6 29.2 - - - +
3B PHE* 3.8 22.0 - - + -
7B TRP* 3.7 35.9 - - + -
91B ASN* 2.8 35.9 + - - +
112B GLU* 1.3 78.0 - - - +
114B THR* 1.3 67.1 + - - +
117B GLY* 5.6 2.0 - - - -
118B GLU 3.4 7.2 - - - +
119B LEU* 4.1 8.3 - - + -
136B ARG* 4.5 4.9 - - - +
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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