Contacts of the strand formed by residues 121 - 127 (chain B) in PDB entry 5FHK
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 ASN 121 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A ARG* 4.3 25.9 + - - +
213A GLY 3.6 21.0 - - - +
214A ARG* 3.4 13.4 + - - -
91B GLY 2.6 15.9 + - - +
92B LYS* 3.7 24.8 - - + +
93B ILE* 2.7 30.9 + - - -
118B PRO 5.7 0.5 - - - +
119B GLU 4.1 2.4 - - - +
120B ILE* 1.3 79.3 + - - +
122B ILE* 1.3 58.4 + - - +
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Residues in contact with ILE 122 (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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213A GLY 4.9 1.0 - - - +
214A ARG 3.1 7.1 + - - -
215A PHE* 3.4 29.0 - - + -
216A GLN* 3.0 25.6 + - - +
93B ILE* 3.3 14.6 - - + +
95B ILE* 4.0 18.8 - - + -
110B LEU* 4.5 15.5 - - + -
113B PHE* 4.3 18.8 - - + -
114B MET* 4.1 26.9 - - + -
120B ILE* 3.9 4.2 + - + -
121B ASN* 1.3 80.6 - - - +
123B GLU* 1.3 70.1 + - - +
124B LEU 4.1 0.4 - - - +
281B PHE* 4.3 15.9 - - + -
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Residues in contact with GLU 123 (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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212A ARG* 5.4 8.3 - - - -
216A GLN* 3.5 27.5 + - + +
92B LYS* 3.1 36.8 + - + +
93B ILE 2.8 8.8 + - - +
94B LYS* 3.5 25.0 + - - +
95B ILE* 2.9 29.3 + - - +
121B ASN 4.2 0.2 - - - -
122B ILE* 1.3 74.9 - - - +
124B LEU* 1.3 62.4 + - - +
125B THR* 4.6 8.7 + - - -
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Residues in contact with LEU 124 (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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215A PHE* 4.0 24.5 - - + -
216A GLN 2.8 15.0 + - - +
217A ALA* 3.4 31.5 - - + -
218A ASN* 3.5 5.7 + - - +
222A VAL* 4.7 3.8 - - + -
95B ILE* 3.6 9.6 - - + -
97B THR* 3.8 21.8 - - + +
102B THR* 4.3 11.0 - - + -
107B MET* 4.4 1.8 - - - -
110B LEU* 3.5 32.5 - - + -
122B ILE* 4.0 0.8 - - + -
123B GLU* 1.3 74.8 - - - +
125B THR* 1.3 68.2 + - - +
126B THR* 3.7 30.7 - - + +
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Residues in contact with THR 125 (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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218A ASN* 3.4 24.2 - - + +
94B LYS* 5.3 0.2 - - - -
95B ILE 3.1 6.7 + - - -
96B SER* 3.4 5.9 + - - -
97B THR 3.1 20.4 + - - -
123B GLU* 4.6 9.4 + - - -
124B LEU* 1.3 78.6 + - - +
126B THR* 1.3 70.0 + - - +
127B GLU* 3.5 8.4 + - + +
138B TRP* 3.6 33.6 - - + -
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Residues in contact with THR 126 (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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99A TYR* 4.3 4.5 + - - -
218A ASN* 3.0 30.9 + - - +
219A ALA* 4.7 10.5 - - + +
222A VAL* 5.2 3.8 - - + -
97B THR* 3.5 5.2 - - - -
99B TYR* 3.5 38.1 - - + +
102B THR* 3.6 27.6 - - + +
124B LEU* 3.7 17.7 - - + -
125B THR* 1.3 76.7 - - - +
127B GLU* 1.3 58.9 + - - +
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Residues in contact with GLU 127 (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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96B SER* 3.5 20.9 - - - +
97B THR 2.9 10.5 + - - +
98B PRO* 3.8 3.5 - - - +
99B TYR* 3.1 20.9 + - - +
125B THR* 4.3 8.4 - - + +
126B THR* 1.3 75.6 - - - +
128B SER* 1.3 78.7 + - - +
129B ASN* 3.5 31.7 + - - +
130B ALA* 4.0 7.1 + - + +
132B GLN* 5.2 5.4 + - - +
133B LEU* 3.3 27.3 - - + +
138B TRP* 5.5 0.7 - - + -
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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